Development of the Lymphoma Enterprise Architecture Database: A caBIG(tm) Silver level compliant System

PubMed Central

Huang, Taoying; Shenoy, Pareen J.; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W.; Flowers, Christopher R.

2009-01-01

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid™ (caBIG™) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system™ (LEAD™), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute’s Center for Bioinformatics to establish the LEAD™ platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD™ could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG™ can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG™ to the management of clinical and biological data. PMID:19492074

Development of the Lymphoma Enterprise Architecture Database: a caBIG Silver level compliant system.

PubMed

Huang, Taoying; Shenoy, Pareen J; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W; Flowers, Christopher R

2009-04-03

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid (caBIG) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system (LEAD), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG to the management of clinical and biological data.

Open source hardware and software platform for robotics and artificial intelligence applications

NASA Astrophysics Data System (ADS)

Liang, S. Ng; Tan, K. O.; Lai Clement, T. H.; Ng, S. K.; Mohammed, A. H. Ali; Mailah, Musa; Azhar Yussof, Wan; Hamedon, Zamzuri; Yussof, Zulkifli

2016-02-01

Recent developments in open source hardware and software platforms (Android, Arduino, Linux, OpenCV etc.) have enabled rapid development of previously expensive and sophisticated system within a lower budget and flatter learning curves for developers. Using these platform, we designed and developed a Java-based 3D robotic simulation system, with graph database, which is integrated in online and offline modes with an Android-Arduino based rubbish picking remote control car. The combination of the open source hardware and software system created a flexible and expandable platform for further developments in the future, both in the software and hardware areas, in particular in combination with graph database for artificial intelligence, as well as more sophisticated hardware, such as legged or humanoid robots.

cMapper: gene-centric connectivity mapper for EBI-RDF platform.

PubMed

Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

2017-01-15

In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at http://cmapper.ewostech.net Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapperContact:smahn@gachon.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Implementation of a Big Data Accessing and Processing Platform for Medical Records in Cloud.

PubMed

Yang, Chao-Tung; Liu, Jung-Chun; Chen, Shuo-Tsung; Lu, Hsin-Wen

2017-08-18

Big Data analysis has become a key factor of being innovative and competitive. Along with population growth worldwide and the trend aging of population in developed countries, the rate of the national medical care usage has been increasing. Due to the fact that individual medical data are usually scattered in different institutions and their data formats are varied, to integrate those data that continue increasing is challenging. In order to have scalable load capacity for these data platforms, we must build them in good platform architecture. Some issues must be considered in order to use the cloud computing to quickly integrate big medical data into database for easy analyzing, searching, and filtering big data to obtain valuable information.This work builds a cloud storage system with HBase of Hadoop for storing and analyzing big data of medical records and improves the performance of importing data into database. The data of medical records are stored in HBase database platform for big data analysis. This system performs distributed computing on medical records data processing through Hadoop MapReduce programming, and to provide functions, including keyword search, data filtering, and basic statistics for HBase database. This system uses the Put with the single-threaded method and the CompleteBulkload mechanism to import medical data. From the experimental results, we find that when the file size is less than 300MB, the Put with single-threaded method is used and when the file size is larger than 300MB, the CompleteBulkload mechanism is used to improve the performance of data import into database. This system provides a web interface that allows users to search data, filter out meaningful information through the web, and analyze and convert data in suitable forms that will be helpful for medical staff and institutions.

Lynx web services for annotations and systems analysis of multi-gene disorders.

PubMed

Sulakhe, Dinanath; Taylor, Andrew; Balasubramanian, Sandhya; Feng, Bo; Xie, Bingqing; Börnigen, Daniela; Dave, Utpal J; Foster, Ian T; Gilliam, T Conrad; Maltsev, Natalia

2014-07-01

Lynx is a web-based integrated systems biology platform that supports annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Lynx has integrated multiple classes of biomedical data (genomic, proteomic, pathways, phenotypic, toxicogenomic, contextual and others) from various public databases as well as manually curated data from our group and collaborators (LynxKB). Lynx provides tools for gene list enrichment analysis using multiple functional annotations and network-based gene prioritization. Lynx provides access to the integrated database and the analytical tools via REST based Web Services (http://lynx.ci.uchicago.edu/webservices.html). This comprises data retrieval services for specific functional annotations, services to search across the complete LynxKB (powered by Lucene), and services to access the analytical tools built within the Lynx platform. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

ENFIN--A European network for integrative systems biology.

PubMed

Kahlem, Pascal; Clegg, Andrew; Reisinger, Florian; Xenarios, Ioannis; Hermjakob, Henning; Orengo, Christine; Birney, Ewan

2009-11-01

Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

DaVIE: Database for the Visualization and Integration of Epigenetic data

PubMed Central

Fejes, Anthony P.; Jones, Meaghan J.; Kobor, Michael S.

2014-01-01

One of the challenges in the analysis of large data sets, particularly in a population-based setting, is the ability to perform comparisons across projects. This has to be done in such a way that the integrity of each individual project is maintained, while ensuring that the data are comparable across projects. These issues are beginning to be observed in human DNA methylation studies, as the Illumina 450k platform and next generation sequencing-based assays grow in popularity and decrease in price. This increase in productivity is enabling new insights into epigenetics, but also requires the development of pipelines and software capable of handling the large volumes of data. The specific problems inherent in creating a platform for the storage, comparison, integration, and visualization of DNA methylation data include data storage, algorithm efficiency and ability to interpret the results to derive biological meaning from them. Databases provide a ready-made solution to these issues, but as yet no tools exist that that leverage these advantages while providing an intuitive user interface for interpreting results in a genomic context. We have addressed this void by integrating a database to store DNA methylation data with a web interface to query and visualize the database and a set of libraries for more complex analysis. The resulting platform is called DaVIE: Database for the Visualization and Integration of Epigenetics data. DaVIE can use data culled from a variety of sources, and the web interface includes the ability to group samples by sub-type, compare multiple projects and visualize genomic features in relation to sites of interest. We have used DaVIE to identify patterns of DNA methylation in specific projects and across different projects, identify outlier samples, and cross-check differentially methylated CpG sites identified in specific projects across large numbers of samples. A demonstration server has been setup using GEO data at http://echelon.cmmt.ubc.ca/dbaccess/, with login “guest” and password “guest.” Groups may download and install their own version of the server following the instructions on the project's wiki. PMID:25278960

Geo-spatial Service and Application based on National E-government Network Platform and Cloud

NASA Astrophysics Data System (ADS)

Meng, X.; Deng, Y.; Li, H.; Yao, L.; Shi, J.

2014-04-01

With the acceleration of China's informatization process, our party and government take a substantive stride in advancing development and application of digital technology, which promotes the evolution of e-government and its informatization. Meanwhile, as a service mode based on innovative resources, cloud computing may connect huge pools together to provide a variety of IT services, and has become one relatively mature technical pattern with further studies and massive practical applications. Based on cloud computing technology and national e-government network platform, "National Natural Resources and Geospatial Database (NRGD)" project integrated and transformed natural resources and geospatial information dispersed in various sectors and regions, established logically unified and physically dispersed fundamental database and developed national integrated information database system supporting main e-government applications. Cross-sector e-government applications and services are realized to provide long-term, stable and standardized natural resources and geospatial fundamental information products and services for national egovernment and public users.

77 FR 28391 - Announcement of Requirements and Registration for “Ocular Imaging Challenge”

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-14

..., color, zoom, pan) Integrate with existing EHRs (e.g. ``single sign-on'') Where applicable, leverage and... existing office hardware platforms, and to integrate with existing EHR systems (e.g. ``single sign-on... on the acquisition devices in proprietary databases and file formats, and therefore have limited...

Get It Together: Integrating Data with XML.

ERIC Educational Resources Information Center

Miller, Ron

2003-01-01

Discusses the use of XML for data integration to move data across different platforms, including across the Internet, from a variety of sources. Topics include flexibility; standards; organizing databases; unstructured data and the use of meta tags to encode it with XML information; cost effectiveness; and eliminating client software licenses.…

IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data.

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.Graphical abstractFDA approved drug data integration for predictive modeling.

Design and Development of a Technology Platform for DNA-Encoded Library Production and Affinity Selection.

PubMed

Castañón, Jesús; Román, José Pablo; Jessop, Theodore C; de Blas, Jesús; Haro, Rubén

2018-06-01

DNA-encoded libraries (DELs) have emerged as an efficient and cost-effective drug discovery tool for the exploration and screening of very large chemical space using small-molecule collections of unprecedented size. Herein, we report an integrated automation and informatics system designed to enhance the quality, efficiency, and throughput of the production and affinity selection of these libraries. The platform is governed by software developed according to a database-centric architecture to ensure data consistency, integrity, and availability. Through its versatile protocol management functionalities, this application captures the wide diversity of experimental processes involved with DEL technology, keeps track of working protocols in the database, and uses them to command robotic liquid handlers for the synthesis of libraries. This approach provides full traceability of building-blocks and DNA tags in each split-and-pool cycle. Affinity selection experiments and high-throughput sequencing reads are also captured in the database, and the results are automatically deconvoluted and visualized in customizable representations. Researchers can compare results of different experiments and use machine learning methods to discover patterns in data. As of this writing, the platform has been validated through the generation and affinity selection of various libraries, and it has become the cornerstone of the DEL production effort at Lilly.

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data.

PubMed

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-12-12

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.

Army Communicator. Volume 36, Number 2, Summer 2011

DTIC Science & Technology

2011-06-01

Portal was utilized to provide an integrated platform for visualization of operational data derived from the CIDNE SIGACT database. Content staging...information across multiple platforms and services. Preliminary efforts during my tour were underway with SIGACT web services that allow data ...all content and data in a CM system, and the CM system itself, is fully protected against accidental deletion or corruption. Conclusion As we

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

CREDO is a unique relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and macromolecules found in experimentally determined structures from the Protein Data Bank. These interactions are integrated with further chemical and biological data. The database implements useful data structures and algorithms such as cheminformatics routines to create a comprehensive analysis platform for drug discovery. The database can be accessed through a web-based interface, downloads of data sets and web services at http://www-cryst.bioc.cam.ac.uk/credo. Database URL: http://www-cryst.bioc.cam.ac.uk/credo PMID:23868908

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data

USDA-ARS?s Scientific Manuscript database

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining data sets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data, and mol...

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.

PubMed

Chang, Suhua; Zhang, Jiajie; Liao, Xiaoyun; Zhu, Xinxing; Wang, Dahai; Zhu, Jiang; Feng, Tao; Zhu, Baoli; Gao, George F; Wang, Jian; Yang, Huanming; Yu, Jun; Wang, Jing

2007-01-01

Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have established the Influenza Virus Database (IVDB) to integrate information and create an analysis platform for genetic, genomic, and phylogenetic studies of the virus. IVDB hosts complete genome sequences of influenza A virus generated by Beijing Institute of Genomics (BIG) and curates all other published IV sequences after expert annotation. Our Q-Filter system classifies and ranks all nucleotide sequences into seven categories according to sequence content and integrity. IVDB provides a series of tools and viewers for comparative analysis of the viral genomes, genes, genetic polymorphisms and phylogenetic relationships. A search system has been developed for users to retrieve a combination of different data types by setting search options. To facilitate analysis of global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) has been developed to display the worldwide geographic distribution of chosen viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to pre-computed alignments and polymorphisms of IV genes and proteins, and presents the results as SNP distribution plots and minor allele distributions. IVDB is publicly available at http://influenza.genomics.org.cn.

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

PubMed Central

Govindaraj, Mahalingam

2015-01-01

The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away. PMID:25874133

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data

PubMed Central

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-01-01

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA’s complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform. PMID:29312567

The BioMedical Evidence Graph (BMEG) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The BMEG is a Cancer Data integration Platform that utilizes methods collected from DREAM challenges and applied to large datasets, such as the TCGA, and makes them avalible for analysis using a high performance graph database

[Exploiture and application of an internet-based Computation Platform for Integrative Pharmacology of Traditional Chinese Medicine].

PubMed

Xu, Hai-Yu; Liu, Zhen-Ming; Fu, Yan; Zhang, Yan-Qiong; Yu, Jian-Jun; Guo, Fei-Fei; Tang, Shi-Huan; Lv, Chuan-Yu; Su, Jin; Cui, Ru-Yi; Yang, Hong-Jun

2017-09-01

Recently, integrative pharmacology(IP) has become a pivotal paradigm for the modernization of traditional Chinese medicines(TCM) and combinatorial drugs discovery, which is an interdisciplinary science for establishing the in vitro and in vivo correlation between absorption, distribution, metabolism, and excretion/pharmacokinetic(ADME/PK) profiles of TCM and the molecular networks of disease by the integration of the knowledge of multi-disciplinary and multi-stages. In the present study, an internet-based Computation Platform for IP of TCM(TCM-IP, www.tcmip.cn) is established to promote the development of the emerging discipline. Among them, a big data of TCM is an important resource for TCM-IP including Chinese Medicine Formula Database, Chinese Medical Herbs Database, Chemical Database of Chinese Medicine, Target Database for Disease and Symptoms, et al. Meanwhile, some data mining and bioinformatics approaches are critical technology for TCM-IP including the identification of the TCM constituents, ADME prediction, target prediction for the TCM constituents, network construction and analysis, et al. Furthermore, network beautification and individuation design are employed to meet the consumer's requirement. We firmly believe that TCM-IP is a very useful tool for the identification of active constituents of TCM and their involving potential molecular mechanism for therapeutics, which would wildly applied in quality evaluation, clinical repositioning, scientific discovery based on original thinking, prescription compatibility and new drug of TCM, et al. Copyright© by the Chinese Pharmaceutical Association.

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

PubMed

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

A collaborative platform for consensus sessions in pathology over Internet.

PubMed

Zapletal, Eric; Le Bozec, Christel; Degoulet, Patrice; Jaulent, Marie-Christine

2003-01-01

The design of valid databases in pathology faces the problem of diagnostic disagreement between pathologists. Organizing consensus sessions between experts to reduce the variability is a difficult task. The TRIDEM platform addresses the issue to organize consensus sessions in pathology over the Internet. In this paper, we present the basis to achieve such collaborative platform. On the one hand, the platform integrates the functionalities of the IDEM consensus module that alleviates the consensus task by presenting to pathologists preliminary computed consensus through ergonomic interfaces (automatic step). On the other hand, a set of lightweight interaction tools such as vocal annotations are implemented to ease the communication between experts as they discuss a case (interactive step). The architecture of the TRIDEM platform is based on a Java-Server-Page web server that communicate with the ObjectStore PSE/PRO database used for the object storage. The HTML pages generated by the web server run Java applets to perform the different steps (automatic and interactive) of the consensus. The current limitations of the platform is to only handle a synchronous process. Moreover, improvements like re-writing the consensus workflow with a protocol such as BPML are already forecast.

wayGoo: a platform for geolocating and managing indoor and outdoor spaces

NASA Astrophysics Data System (ADS)

Thomopoulos, Stelios C. A.; Karafylli, Christina; Karafylli, Maria; Motos, Dionysis; Lampropoulos, Vassilis; Dimitros, Kostantinos; Margonis, Christos

2016-05-01

wayGoo2 is a platform for Geolocating and Managing indoor and outdoor spaces and content with multidimensional indoor and outdoor Navigation and Guidance. Its main components are a Geographic Information System, a back-end server, front-end applications and a web-based Content Management System (CMS). It constitutes a fully integrated 2D/3D space and content management system that creates a repository that consists of a database, content components and administrative data. wayGoo can connect to any third party database and event management data-source. The platform is secure as the data is only available through a Restful web service using https security protocol in conjunction with an API key used for authentication. To enhance users experience, wayGoo makes the content available by extracting components out of the repository and constructing targeted applications. The wayGoo platform supports geo-referencing of indoor and outdoor information and use of metadata. It also allows the use of existing information such as maps and databases. The platform enables planning through integration of content that is connected either spatially, temporally or contextually, and provides immediate access to all spatial data through interfaces and interactive 2D and 3D representations. wayGoo constitutes a mean to document and preserve assets through computerized techniques and provides a system that enhances the protection of your space, people and guests when combined with wayGoo notification and alert system. It constitutes a strong marketing tool providing staff and visitors with an immersive tool for navigation in indoor spaces and allowing users to organize their agenda and to discover events through wayGoo event scheduler and recommendation system. Furthermore, the wayGoo platform can be used in Security applications and event management, e.g. CBRNE incidents, man-made and natural disasters, etc., to document and geolocate information and sensor data (off line and real time) on one end, and offer navigation capabilities in indoor and outdoor spaces. Furthermore, the wayGoo platform can be used for the creation of immersive environments and experiences in conjunction with VR/AR (Virtual and Augmented Reality) technologies.

PsyGeNET: a knowledge platform on psychiatric disorders and their genes.

PubMed

Gutiérrez-Sacristán, Alba; Grosdidier, Solène; Valverde, Olga; Torrens, Marta; Bravo, Àlex; Piñero, Janet; Sanz, Ferran; Furlong, Laura I

2015-09-15

PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of a database and a web interface supporting data search, visualization, filtering and sharing. PsyGeNET integrates information from DisGeNET and data extracted from the literature by text mining, which has been curated by domain experts. It currently contains 2642 associations between 1271 genes and 37 psychiatric disease concepts. In its first release, PsyGeNET is focused on three psychiatric disorders: major depression, alcohol and cocaine use disorders. PsyGeNET represents a comprehensive, open access resource for the analysis of the molecular mechanisms underpinning psychiatric disorders and their comorbidities. The PysGeNET platform is freely available at http://www.psygenet.org/. The PsyGeNET database is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). lfurlong@imim.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

System perspectives for mobile platform design in m-Health

NASA Astrophysics Data System (ADS)

Roveda, Janet M.; Fink, Wolfgang

2016-05-01

Advances in integrated circuit technologies have led to the integration of medical sensor front ends with data processing circuits, i.e., mobile platform design for wearable sensors. We discuss design methodologies for wearable sensor nodes and their applications in m-Health. From the user perspective, flexibility, comfort, appearance, fashion, ease-of-use, and visibility are key form factors. From the technology development point of view, high accuracy, low power consumption, and high signal to noise ratio are desirable features. From the embedded software design standpoint, real time data analysis algorithms, application and database interfaces are the critical components to create successful wearable sensor-based products.

Analysis of lipid experiments (ALEX): a software framework for analysis of high-resolution shotgun lipidomics data.

PubMed

Husen, Peter; Tarasov, Kirill; Katafiasz, Maciej; Sokol, Elena; Vogt, Johannes; Baumgart, Jan; Nitsch, Robert; Ekroos, Kim; Ejsing, Christer S

2013-01-01

Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

Implementation of the CDC translational informatics platform--from genetic variants to the national Swedish Rheumatology Quality Register.

PubMed

Abugessaisa, Imad; Gomez-Cabrero, David; Snir, Omri; Lindblad, Staffan; Klareskog, Lars; Malmström, Vivianne; Tegnér, Jesper

2013-04-02

Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet. Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system. We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features. Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort.

Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register

PubMed Central

2013-01-01

Background Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet. Methods Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system. Results We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features. Conclusions Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort. PMID:23548156

Learning Asset Technology Integration Support Tool Design Document

DTIC Science & Technology

2010-05-11

language known as Hypertext Preprocessor ( PHP ) and by MySQL – a relational database management system that can also be used for content management. It...Requirements The LATIST tool will be implemented utilizing a WordPress platform with MySQL as the database. Also the LATIST system must effectively work... MySQL . When designing the LATIST system there are several considerations which must be accounted for in the working prototype. These include: • DAU

The MR-Base platform supports systematic causal inference across the human phenome

PubMed Central

Wade, Kaitlin H; Haberland, Valeriia; Baird, Denis; Laurin, Charles; Burgess, Stephen; Bowden, Jack; Langdon, Ryan; Tan, Vanessa Y; Yarmolinsky, James; Shihab, Hashem A; Timpson, Nicholas J; Evans, David M; Relton, Caroline; Martin, Richard M; Davey Smith, George

2018-01-01

Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base (http://www.mrbase.org): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies. PMID:29846171

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

NASA Astrophysics Data System (ADS)

Sushko, Iurii; Novotarskyi, Sergii; Körner, Robert; Pandey, Anil Kumar; Rupp, Matthias; Teetz, Wolfram; Brandmaier, Stefan; Abdelaziz, Ahmed; Prokopenko, Volodymyr V.; Tanchuk, Vsevolod Y.; Todeschini, Roberto; Varnek, Alexandre; Marcou, Gilles; Ertl, Peter; Potemkin, Vladimir; Grishina, Maria; Gasteiger, Johann; Schwab, Christof; Baskin, Igor I.; Palyulin, Vladimir A.; Radchenko, Eugene V.; Welsh, William J.; Kholodovych, Vladyslav; Chekmarev, Dmitriy; Cherkasov, Artem; Aires-de-Sousa, Joao; Zhang, Qing-You; Bender, Andreas; Nigsch, Florian; Patiny, Luc; Williams, Antony; Tkachenko, Valery; Tetko, Igor V.

2011-06-01

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

MIPSPlantsDB—plant database resource for integrative and comparative plant genome research

PubMed Central

Spannagl, Manuel; Noubibou, Octave; Haase, Dirk; Yang, Li; Gundlach, Heidrun; Hindemitt, Tobias; Klee, Kathrin; Haberer, Georg; Schoof, Heiko; Mayer, Klaus F. X.

2007-01-01

Genome-oriented plant research delivers rapidly increasing amount of plant genome data. Comprehensive and structured information resources are required to structure and communicate genome and associated analytical data for model organisms as well as for crops. The increase in available plant genomic data enables powerful comparative analysis and integrative approaches. PlantsDB aims to provide data and information resources for individual plant species and in addition to build a platform for integrative and comparative plant genome research. PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato. Complementary data resources for cis elements, repetive elements and extensive cross-species comparisons are implemented. The PlantsDB portal can be reached at . PMID:17202173

BioPepDB: an integrated data platform for food-derived bioactive peptides.

PubMed

Li, Qilin; Zhang, Chao; Chen, Hongjun; Xue, Jitong; Guo, Xiaolei; Liang, Ming; Chen, Ming

2018-03-12

Food-derived bioactive peptides play critical roles in regulating most biological processes and have considerable biological, medical and industrial importance. However, a large number of active peptides data, including sequence, function, source, commercial product information, references and other information are poorly integrated. BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries. Moreover, BioPepDB provides modules of prediction and hydrolysis-simulation for discovering novel peptides. It can serve as a reference database to investigate the function of different bioactive peptides. BioPepDB is available at http://bis.zju.edu.cn/biopepdbr/ . The web page utilises Apache, PHP5 and MySQL to provide the user interface for accessing the database and predict novel peptides. The database itself is operated on a specialised server.

Database of episode-integrated solar energetic proton fluences

NASA Astrophysics Data System (ADS)

Robinson, Zachary D.; Adams, James H.; Xapsos, Michael A.; Stauffer, Craig A.

2018-04-01

A new database of proton episode-integrated fluences is described. This database contains data from two different instruments on multiple satellites. The data are from instruments on the Interplanetary Monitoring Platform-8 (IMP8) and the Geostationary Operational Environmental Satellites (GOES) series. A method to normalize one set of data to one another is presented to create a seamless database spanning 1973 to 2016. A discussion of some of the characteristics that episodes exhibit is presented, including episode duration and number of peaks. As an example of what can be understood about episodes, the July 4, 2012 episode is examined in detail. The coronal mass ejections and solar flares that caused many of the fluctuations of the proton flux seen at Earth are associated with peaks in the proton flux during this episode. The reasoning for each choice is laid out to provide a reference for how CME and solar flares associations are made.

Experiences with DCE: the pro7 communication server based on OSF-DCE functionality.

PubMed

Schulte, M; Lordieck, W

1997-01-01

The pro7-communication server is a new approach to manage communication between different applications on different hardware platforms in a hospital environment. The most important features are the use of OSF/DCE for realising remote procedure calls between different platforms, the use of an SQL-92 compatible relational database and the design of a new software development tool (called protocol definition language compiler) for describing the interface of a new application, which is to integrate in a hospital environment.

Space Situational Awareness Data Processing Scalability Utilizing Google Cloud Services

NASA Astrophysics Data System (ADS)

Greenly, D.; Duncan, M.; Wysack, J.; Flores, F.

Space Situational Awareness (SSA) is a fundamental and critical component of current space operations. The term SSA encompasses the awareness, understanding and predictability of all objects in space. As the population of orbital space objects and debris increases, the number of collision avoidance maneuvers grows and prompts the need for accurate and timely process measures. The SSA mission continually evolves to near real-time assessment and analysis demanding the need for higher processing capabilities. By conventional methods, meeting these demands requires the integration of new hardware to keep pace with the growing complexity of maneuver planning algorithms. SpaceNav has implemented a highly scalable architecture that will track satellites and debris by utilizing powerful virtual machines on the Google Cloud Platform. SpaceNav algorithms for processing CDMs outpace conventional means. A robust processing environment for tracking data, collision avoidance maneuvers and various other aspects of SSA can be created and deleted on demand. Migrating SpaceNav tools and algorithms into the Google Cloud Platform will be discussed and the trials and tribulations involved. Information will be shared on how and why certain cloud products were used as well as integration techniques that were implemented. Key items to be presented are: 1.Scientific algorithms and SpaceNav tools integrated into a scalable architecture a) Maneuver Planning b) Parallel Processing c) Monte Carlo Simulations d) Optimization Algorithms e) SW Application Development/Integration into the Google Cloud Platform 2. Compute Engine Processing a) Application Engine Automated Processing b) Performance testing and Performance Scalability c) Cloud MySQL databases and Database Scalability d) Cloud Data Storage e) Redundancy and Availability

GIS Application System Design Applied to Information Monitoring

NASA Astrophysics Data System (ADS)

Qun, Zhou; Yujin, Yuan; Yuena, Kang

Natural environment information management system involves on-line instrument monitoring, data communications, database establishment, information management software development and so on. Its core lies in collecting effective and reliable environmental information, increasing utilization rate and sharing degree of environment information by advanced information technology, and maximizingly providing timely and scientific foundation for environmental monitoring and management. This thesis adopts C# plug-in application development and uses a set of complete embedded GIS component libraries and tools libraries provided by GIS Engine to finish the core of plug-in GIS application framework, namely, the design and implementation of framework host program and each functional plug-in, as well as the design and implementation of plug-in GIS application framework platform. This thesis adopts the advantages of development technique of dynamic plug-in loading configuration, quickly establishes GIS application by visualized component collaborative modeling and realizes GIS application integration. The developed platform is applicable to any application integration related to GIS application (ESRI platform) and can be as basis development platform of GIS application development.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab-based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic datasets is critically important. The high-throughput autonomous proteomic pipeline (HTAPP) described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is comprised of software that controls the acquisition of mass spectral data along with automation of post-acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user-configurable lab-based relational database. The software design of HTAPP focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples. PMID:20336676

ENFIN a network to enhance integrative systems biology.

PubMed

Kahlem, Pascal; Birney, Ewan

2007-12-01

Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing both an adapted infrastructure to connect databases and platforms to enable the generation of new bioinformatics tools as well as the experimental validation of computational predictions. We will give an overview of the projects tackled within ENFIN and discuss the challenges associated with integration for systems biology.

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

PubMed

D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

2017-01-01

Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

Spatial Data Integration Using Ontology-Based Approach

NASA Astrophysics Data System (ADS)

Hasani, S.; Sadeghi-Niaraki, A.; Jelokhani-Niaraki, M.

2015-12-01

In today's world, the necessity for spatial data for various organizations is becoming so crucial that many of these organizations have begun to produce spatial data for that purpose. In some circumstances, the need to obtain real time integrated data requires sustainable mechanism to process real-time integration. Case in point, the disater management situations that requires obtaining real time data from various sources of information. One of the problematic challenges in the mentioned situation is the high degree of heterogeneity between different organizations data. To solve this issue, we introduce an ontology-based method to provide sharing and integration capabilities for the existing databases. In addition to resolving semantic heterogeneity, better access to information is also provided by our proposed method. Our approach is consisted of three steps, the first step is identification of the object in a relational database, then the semantic relationships between them are modelled and subsequently, the ontology of each database is created. In a second step, the relative ontology will be inserted into the database and the relationship of each class of ontology will be inserted into the new created column in database tables. Last step is consisted of a platform based on service-oriented architecture, which allows integration of data. This is done by using the concept of ontology mapping. The proposed approach, in addition to being fast and low cost, makes the process of data integration easy and the data remains unchanged and thus takes advantage of the legacy application provided.

PIGD: a database for intronless genes in the Poaceae.

PubMed

Yan, Hanwei; Jiang, Cuiping; Li, Xiaoyu; Sheng, Lei; Dong, Qing; Peng, Xiaojian; Li, Qian; Zhao, Yang; Jiang, Haiyang; Cheng, Beijiu

2014-10-01

Intronless genes are a feature of prokaryotes; however, they are widespread and unequally distributed among eukaryotes and represent an important resource to study the evolution of gene architecture. Although many databases on exons and introns exist, there is currently no cohesive database that collects intronless genes in plants into a single database. In this study, we present the Poaceae Intronless Genes Database (PIGD), a user-friendly web interface to explore information on intronless genes from different plants. Five Poaceae species, Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon, are included in the current release of PIGD. Gene annotations and sequence data were collected and integrated from different databases. The primary focus of this study was to provide gene descriptions and gene product records. In addition, functional annotations, subcellular localization prediction and taxonomic distribution are reported. PIGD allows users to readily browse, search and download data. BLAST and comparative analyses are also provided through this online database, which is available at http://pigd.ahau.edu.cn/. PIGD provides a solid platform for the collection, integration and analysis of intronless genes in the Poaceae. As such, this database will be useful for subsequent bio-computational analysis in comparative genomics and evolutionary studies.

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

Metacatalog of Planetary Surface Features for Multicriteria Evaluation of Surface Evolution: the Integrated Planetary Feature Database

NASA Astrophysics Data System (ADS)

Hargitai, Henrik

2016-10-01

We have created a metacatalog, or catalog or catalogs, of surface features of Mars that also includes the actual data in the catalogs listed. The goal is to make mesoscale surface feature databases available in one place, in a GIS-ready format. The databases can be directly imported to ArcGIS or other GIS platforms, like Google Mars. Some of the catalogs in our database are also ingested into the JMARS platform.All catalogs have been previously published in a peer-reviewed journal, but they may contain updates of the published catalogs. Many of the catalogs are "integrated", i.e. they merge databases or information from various papers on the same topic, including references to each individual features listed.Where available, we have included shapefiles with polygon or linear features, however, most of the catalogs only contain point data of their center points and morphological data.One of the unexpected results of the planetary feature metacatalog is that some features have been described by several papers, using different, i.e., conflicting designations. This shows the need for the development of an identification system suitable for mesoscale (100s m to km sized) features that tracks papers and thus prevents multiple naming of the same feature.The feature database can be used for multicriteria analysis of a terrain, thus enables easy distribution pattern analysis and the correlation of the distribution of different landforms and features on Mars. Such catalog makes a scientific evaluation of potential landing sites easier and more effective during the selection process and also supports automated landing site selections.The catalog is accessible at https://planetarydatabase.wordpress.com/.

KaBOB: ontology-based semantic integration of biomedical databases.

PubMed

Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

2015-04-23

The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for formal reasoning over a wealth of integrated biomedical data.

Building an integrated neurodegenerative disease database at an academic health center.

PubMed

Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

2011-07-01

It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

An Avatar-Based Italian Sign Language Visualization System

NASA Astrophysics Data System (ADS)

Falletto, Andrea; Prinetto, Paolo; Tiotto, Gabriele

In this paper, we present an experimental system that supports the translation from Italian to Italian Sign Language (ISL) of the deaf and its visualization through a virtual character. Our objective is to develop a complete platform useful for any application and reusable on several platforms including Web, Digital Television and offline text translation. The system relies on a database that stores both a corpus of Italian words and words coded in the ISL notation system. An interface for the insertion of data is implemented, that allows future extensions and integrations.

FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer.

PubMed

Panigrahi, Priyabrata; Jere, Abhay; Anamika, Krishanpal

2018-01-01

Gene fusion is a chromosomal rearrangement event which plays a significant role in cancer due to the oncogenic potential of the chimeric protein generated through fusions. At present many databases are available in public domain which provides detailed information about known gene fusion events and their functional role. Existing gene fusion detection tools, based on analysis of transcriptomics data usually report a large number of fusion genes as potential candidates, which could be either known or novel or false positives. Manual annotation of these putative genes is indeed time-consuming. We have developed a web platform FusionHub, which acts as integrated search engine interfacing various fusion gene databases and simplifies large scale annotation of fusion genes in a seamless way. In addition, FusionHub provides three ways of visualizing fusion events: circular view, domain architecture view and network view. Design of potential siRNA molecules through ensemble method is another utility integrated in FusionHub that could aid in siRNA-based targeted therapy. FusionHub is freely available at https://fusionhub.persistent.co.in.

The Mouse Heart Attack Research Tool (mHART) 1.0 Database.

PubMed

DeLeon-Pennell, Kristine Y; Iyer, Rugmani Padmanabhan; Ma, Yonggang; Yabluchanskiy, Andriy; Zamilpa, Rogelio; Chiao, Ying Ann; Cannon, Presley; Cates, Courtney; Flynn, Elizabeth R; Halade, Ganesh V; de Castro Bras, Lisandra E; Lindsey, Merry L

2018-05-18

The generation of Big Data has enabled systems-level dissections into the mechanisms of cardiovascular pathology. Integration of genetic, proteomic, and pathophysiological variables across platforms and laboratories fosters discoveries through multidisciplinary investigations and minimizes unnecessary redundancy in research efforts. The Mouse Heart Attack Research Tool (mHART) consolidates a large dataset of over 10 years of experiments from a single laboratory for cardiovascular investigators to generate novel hypotheses and identify new predictive markers of progressive left ventricular remodeling following myocardial infarction (MI) in mice. We designed the mHART REDCap database using our own data to integrate cardiovascular community participation. We generated physiological, biochemical, cellular, and proteomic outputs from plasma and left ventricles obtained from post-MI and no MI (naïve) control groups. We included both male and female mice ranging in age from 3 to 36 months old. After variable collection, data underwent quality assessment for data curation (e.g. eliminate technical errors, check for completeness, remove duplicates, and define terms). Currently, mHART 1.0 contains >888,000 data points and includes results from >2,100 unique mice. Database performance was tested and an example provided to illustrate database utility. This report explains how the first version of the mHART database was established and provides researchers with a standard framework to aid in the integration of their data into our database or in the development of a similar database.

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

Integrated Approach to Reconstruction of Microbial Regulatory Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodionov, Dmitry A; Novichkov, Pavel S

2013-11-04

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated inmore » RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.« less

Distributed software framework and continuous integration in hydroinformatics systems

NASA Astrophysics Data System (ADS)

Zhou, Jianzhong; Zhang, Wei; Xie, Mengfei; Lu, Chengwei; Chen, Xiao

2017-08-01

When encountering multiple and complicated models, multisource structured and unstructured data, complex requirements analysis, the platform design and integration of hydroinformatics systems become a challenge. To properly solve these problems, we describe a distributed software framework and it’s continuous integration process in hydroinformatics systems. This distributed framework mainly consists of server cluster for models, distributed database, GIS (Geographic Information System) servers, master node and clients. Based on it, a GIS - based decision support system for joint regulating of water quantity and water quality of group lakes in Wuhan China is established.

A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer

PubMed Central

Gupta, Sudheer; Chaudhary, Kumardeep; Dhanda, Sandeep Kumar; Kumar, Rahul; Kumar, Shailesh; Sehgal, Manika; Nagpal, Gandharva

2016-01-01

Due to advancement in sequencing technology, genomes of thousands of cancer tissues or cell-lines have been sequenced. Identification of cancer-specific epitopes or neoepitopes from cancer genomes is one of the major challenges in the field of immunotherapy or vaccine development. This paper describes a platform Cancertope, developed for designing genome-based immunotherapy or vaccine against a cancer cell. Broadly, the integrated resources on this platform are apportioned into three precise sections. First section explains a cancer-specific database of neoepitopes generated from genome of 905 cancer cell lines. This database harbors wide range of epitopes (e.g., B-cell, CD8+ T-cell, HLA class I, HLA class II) against 60 cancer-specific vaccine antigens. Second section describes a partially personalized module developed for predicting potential neoepitopes against a user-specific cancer genome. Finally, we describe a fully personalized module developed for identification of neoepitopes from genomes of cancerous and healthy cells of a cancer-patient. In order to assist the scientific community, wide range of tools are incorporated in this platform that includes screening of epitopes against human reference proteome (http://www.imtech.res.in/raghava/cancertope/). PMID:27832200

WikiPEATia - a web based platform for assembling peatland data through ‘crowd sourcing’

NASA Astrophysics Data System (ADS)

Wisser, D.; Glidden, S.; Fieseher, C.; Treat, C. C.; Routhier, M.; Frolking, S. E.

2009-12-01

The Earth System Science community is realizing that peatlands are an important and unique terrestrial ecosystem that has not yet been well-integrated into large-scale earth system analyses. A major hurdle is the lack of accessible, geospatial data of peatland distribution, coupled with data on peatland properties (e.g., vegetation composition, peat depth, basal dates, soil chemistry, peatland class) at the global scale. This data, however, is available at the local scale. Although a comprehensive global database on peatlands probably lags similar data on more economically important ecosystems such as forests, grasslands, croplands, a large amount of field data have been collected over the past several decades. A few efforts have been made to map peatlands at large scales but existing data have not been assembled into a single geospatial database that is publicly accessible or do not depict data with a level of detail that is needed in the Earth System Science Community. A global peatland database would contribute to advances in a number of research fields such as hydrology, vegetation and ecosystem modeling, permafrost modeling, and earth system modeling. We present a Web 2.0 approach that uses state-of-the-art webserver and innovative online mapping technologies and is designed to create such a global database through ‘crowd-sourcing’. Primary functions of the online system include form-driven textual user input of peatland research metadata, spatial data input of peatland areas via a mapping interface, database editing and querying editing capabilities, as well as advanced visualization and data analysis tools. WikiPEATia provides an integrated information technology platform for assembling, integrating, and posting peatland-related geospatial datasets facilitates and encourages research community involvement. A successful effort will make existing peatland data much more useful to the research community, and will help to identify significant data gaps.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

Digital Earth system based river basin data integration

NASA Astrophysics Data System (ADS)

Zhang, Xin; Li, Wanqing; Lin, Chao

2014-12-01

Digital Earth is an integrated approach to build scientific infrastructure. The Digital Earth systems provide a three-dimensional visualization and integration platform for river basin data which include the management data, in situ observation data, remote sensing observation data and model output data. This paper studies the Digital Earth system based river basin data integration technology. Firstly, the construction of the Digital Earth based three-dimensional river basin data integration environment is discussed. Then the river basin management data integration technology is presented which is realized by general database access interface, web service and ActiveX control. Thirdly, the in situ data stored in database tables as records integration is realized with three-dimensional model of the corresponding observation apparatus display in the Digital Earth system by a same ID code. In the next two parts, the remote sensing data and the model output data integration technologies are discussed in detail. The application in the Digital Zhang River basin System of China shows that the method can effectively improve the using efficiency and visualization effect of the data.

The ESID Online Database network.

PubMed

Guzman, D; Veit, D; Knerr, V; Kindle, G; Gathmann, B; Eades-Perner, A M; Grimbacher, B

2007-03-01

Primary immunodeficiencies (PIDs) belong to the group of rare diseases. The European Society for Immunodeficiencies (ESID), is establishing an innovative European patient and research database network for continuous long-term documentation of patients, in order to improve the diagnosis, classification, prognosis and therapy of PIDs. The ESID Online Database is a web-based system aimed at data storage, data entry, reporting and the import of pre-existing data sources in an enterprise business-to-business integration (B2B). The online database is based on Java 2 Enterprise System (J2EE) with high-standard security features, which comply with data protection laws and the demands of a modern research platform. The ESID Online Database is accessible via the official website (http://www.esid.org/). Supplementary data are available at Bioinformatics online.

Toward an integrated knowledge environment to support modern oncology.

PubMed

Blake, Patrick M; Decker, David A; Glennon, Timothy M; Liang, Yong Michael; Losko, Sascha; Navin, Nicholas; Suh, K Stephen

2011-01-01

Around the world, teams of researchers continue to develop a wide range of systems to capture, store, and analyze data including treatment, patient outcomes, tumor registries, next-generation sequencing, single-nucleotide polymorphism, copy number, gene expression, drug chemistry, drug safety, and toxicity. Scientists mine, curate, and manually annotate growing mountains of data to produce high-quality databases, while clinical information is aggregated in distant systems. Databases are currently scattered, and relationships between variables coded in disparate datasets are frequently invisible. The challenge is to evolve oncology informatics from a "systems" orientation of standalone platforms and silos into an "integrated knowledge environments" that will connect "knowable" research data with patient clinical information. The aim of this article is to review progress toward an integrated knowledge environment to support modern oncology with a focus on supporting scientific discovery and improving cancer care.

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

PubMed

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web at http://spirpro.sbi.kmutt.ac.th . SpirPro is an analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro can be applied in various analyses, such as temperature stress response networking analysis in cyanobacterial models and interacting domain-domain analysis between proteins of interest.

GWFASTA: server for FASTA search in eukaryotic and microbial genomes.

PubMed

Issac, Biju; Raghava, G P S

2002-09-01

Similarity searches are a powerful method for solving important biological problems such as database scanning, evolutionary studies, gene prediction, and protein structure prediction. FASTA is a widely used sequence comparison tool for rapid database scanning. Here we describe the GWFASTA server that was developed to assist the FASTA user in similarity searches against partially and/or completely sequenced genomes. GWFASTA consists of more than 60 microbial genomes, eight eukaryote genomes, and proteomes of annotatedgenomes. Infact, it provides the maximum number of databases for similarity searching from a single platform. GWFASTA allows the submission of more than one sequence as a single query for a FASTA search. It also provides integrated post-processing of FASTA output, including compositional analysis of proteins, multiple sequences alignment, and phylogenetic analysis. Furthermore, it summarizes the search results organism-wise for prokaryotes and chromosome-wise for eukaryotes. Thus, the integration of different tools for sequence analyses makes GWFASTA a powerful toolfor biologists.

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

PubMed Central

Lee, Wonhoon; Park, Jongsun; Choi, Jaeyoung; Jung, Kyongyong; Park, Bongsoo; Kim, Donghan; Lee, Jaeyoung; Ahn, Kyohun; Song, Wonho; Kang, Seogchan; Lee, Yong-Hwan; Lee, Seunghwan

2009-01-01

Background Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data. Results The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs. Conclusion The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site . PMID:19351385

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

[Ginseng prescription rules and molecular mechanism in treating coronary heart disease based on data mining and integrative pharmacology].

PubMed

Li, Sen; Tang, Shi-Huan; Liu, Jin-Ling; Su, Jin; He, Fu-Yuan

2018-04-01

The ancient dragon Materia Medica, Compendium of Materia Medica and other works recorded that the main effect of ginseng is tonifying qi. It is reported that the main active ingredient of ginseng is ginsenoside. Modern studies have found that ginseng mono saponins are effective for cardiovascular related diseases. This paper preliminary clarified the efficacy of traditional ginseng-nourishing qi and cardiovascular disease through the traditional Chinese medicine (TCM) inheritance auxiliary platform and integration platform of association of pharmacology. With the help of TCM inheritance auxiliary platform-analysis of "Chinese medicine database", Chinese medicine treatment of modern diseases that ginseng rules, so the traditional effect associated with modern medicine and pharmacology; application integration platform enrichment analysis on the target of drug and gene function, metabolic pathway, to further explore the molecular mechanism of ginseng in the treatment of coronary heart disease, aimed at mining the molecular mechanism of ginseng in the treatment of coronary heart disease. Chinese medicine containing ginseng 307 prescriptions, 87 kinds of disease indications, western medicine disease Chinese medicine therapy for ginseng main coronary heart disease; analysis of molecular mechanism of ginseng pharmacology integration platform for the treatment of coronary heart disease. Ginsenosides（Ra₁, Ra₂, Rb₁, Rb₂, Rg₁, Ro) bind these targets, PRKAA1, PRKAA2, NDUFA4, COX5B, UQCRC1, affect chemokines, non-alcoholic fatty liver, gonadotropin, carbon metabolism, glucose metabolism and other pathways to treat coronary heart disease indirectly. The molecular mechanism of Panax ginseng's multi-component, multi-target and synergistic action is preliminarily elucidated in this paper. Copyright© by the Chinese Pharmaceutical Association.

The EPA CompTox Dashboard and Underpinning Software Architecture – a platform for data integration for environmental chemistry data (ACS Fall Meeting 7 of 12)

EPA Science Inventory

The CompTox Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for dep...

Social Networking as a Platform for Role-Playing Scientific Case Studies

ERIC Educational Resources Information Center

Geyer, Andrea M.

2014-01-01

This work discusses the design and implementation of two online case studies in a face-to-face general chemistry course. The case studies were integrated into the course to emphasize the need for science literacy in general society, to enhance critical thinking, to introduce database searching, and to improve primary literature reading skills. An…

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

yStreX: yeast stress expression database

PubMed Central

Wanichthanarak, Kwanjeera; Nookaew, Intawat; Petranovic, Dina

2014-01-01

Over the past decade genome-wide expression analyses have been often used to study how expression of genes changes in response to various environmental stresses. Many of these studies (such as effects of oxygen concentration, temperature stress, low pH stress, osmotic stress, depletion or limitation of nutrients, addition of different chemical compounds, etc.) have been conducted in the unicellular Eukaryal model, yeast Saccharomyces cerevisiae. However, the lack of a unifying or integrated, bioinformatics platform that would permit efficient and rapid use of all these existing data remain an important issue. To facilitate research by exploiting existing transcription data in the field of yeast physiology, we have developed the yStreX database. It is an online repository of analyzed gene expression data from curated data sets from different studies that capture genome-wide transcriptional changes in response to diverse environmental transitions. The first aim of this online database is to facilitate comparison of cross-platform and cross-laboratory gene expression data. Additionally, we performed different expression analyses, meta-analyses and gene set enrichment analyses; and the results are also deposited in this database. Lastly, we constructed a user-friendly Web interface with interactive visualization to provide intuitive access and to display the queried data for users with no background in bioinformatics. Database URL: http://www.ystrexdb.com PMID:25024351

AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

PubMed

Wang, Yi; Thilmony, Roger; Zhao, Yunjun; Chen, Guoping; Gu, Yong Q

2014-01-01

Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw.usda.gov/AIM Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Web-based Visualization and Query of semantically segmented multiresolution 3D Models in the Field of Cultural Heritage

NASA Astrophysics Data System (ADS)

Auer, M.; Agugiaro, G.; Billen, N.; Loos, L.; Zipf, A.

2014-05-01

Many important Cultural Heritage sites have been studied over long periods of time by different means of technical equipment, methods and intentions by different researchers. This has led to huge amounts of heterogeneous "traditional" datasets and formats. The rising popularity of 3D models in the field of Cultural Heritage in recent years has brought additional data formats and makes it even more necessary to find solutions to manage, publish and study these data in an integrated way. The MayaArch3D project aims to realize such an integrative approach by establishing a web-based research platform bringing spatial and non-spatial databases together and providing visualization and analysis tools. Especially the 3D components of the platform use hierarchical segmentation concepts to structure the data and to perform queries on semantic entities. This paper presents a database schema to organize not only segmented models but also different Levels-of-Details and other representations of the same entity. It is further implemented in a spatial database which allows the storing of georeferenced 3D data. This enables organization and queries by semantic, geometric and spatial properties. As service for the delivery of the segmented models a standardization candidate of the OpenGeospatialConsortium (OGC), the Web3DService (W3DS) has been extended to cope with the new database schema and deliver a web friendly format for WebGL rendering. Finally a generic user interface is presented which uses the segments as navigation metaphor to browse and query the semantic segmentation levels and retrieve information from an external database of the German Archaeological Institute (DAI).

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

PubMed

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

2012-05-01

MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools

PubMed Central

Postel, Alexander; Schmeiser, Stefanie; Zimmermann, Bernd; Becher, Paul

2016-01-01

Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world’s largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis. The classical swine fever (CSF) DB (CSF-DB) became a valuable tool for supporting diagnosis and epidemiological investigations of this highly contagious disease in pigs with high socio-economic impacts worldwide. The DB has been re-designed and now allows for the storage and analysis of traditionally used, well established genomic regions and of larger genomic regions including complete viral genomes. We present an application example for the analysis of highly similar viral sequences obtained in an endemic disease situation and introduce the new geographic “CSF Maps” tool. The concept of this standardized and easy-to-use DB with an integrated genetic typing module is suited to serve as a blueprint for similar platforms for other human or animal viruses. PMID:27827988

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

PubMed

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

2015-12-01

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

A web-based platform for virtual screening.

PubMed

Watson, Paul; Verdonk, Marcel; Hartshorn, Michael J

2003-09-01

A fully integrated, web-based, virtual screening platform has been developed to allow rapid virtual screening of large numbers of compounds. ORACLE is used to store information at all stages of the process. The system includes a large database of historical compounds from high throughput screenings (HTS) chemical suppliers, ATLAS, containing over 3.1 million unique compounds with their associated physiochemical properties (ClogP, MW, etc.). The database can be screened using a web-based interface to produce compound subsets for virtual screening or virtual library (VL) enumeration. In order to carry out the latter task within ORACLE a reaction data cartridge has been developed. Virtual libraries can be enumerated rapidly using the web-based interface to the cartridge. The compound subsets can be seamlessly submitted for virtual screening experiments, and the results can be viewed via another web-based interface allowing ad hoc querying of the virtual screening data stored in ORACLE.

A Patient-Held Smartcard With a Unique Identifier and an mHealth Platform to Improve the Availability of Prenatal Test Results in Rural Nigeria: Demonstration Study

PubMed Central

Eze, Chuka; Olawepo, John Olajide; Iwelunmor, Juliet; Sarpong, Daniel F; Ogidi, Amaka Grace; Patel, Dina; Oko, John Okpanachi; Onoka, Chima; Ezeanolue, Echezona Edozie

2018-01-01

Background Community-based strategies to test for HIV, hepatitis B virus (HBV), and sickle cell disease (SCD) have expanded opportunities to increase the proportion of pregnant women who are aware of their diagnosis. In order to use this information to implement evidence-based interventions, these results have to be available to skilled health providers at the point of delivery. Most electronic health platforms are dependent on the availability of reliable Internet connectivity and, thus, have limited use in many rural and resource-limited settings. Objective Here we describe our work on the development and deployment of an integrated mHealth platform that is able to capture medical information, including test results, and encrypt it into a patient-held smartcard that can be read at the point of delivery without the need for an Internet connection. Methods We engaged a team of implementation scientists, public health experts, and information technology specialists in a requirement-gathering process to inform the design of a prototype for a platform that uses smartcard technology, database deployment, and mobile phone app development. Key design decisions focused on usability, scalability, and security. Results We successfully designed an integrated mHealth platform and deployed it in 4 health facilities across Benue State, Nigeria. We developed the Vitira Health platform to store test results of HIV, HBV, and SCD in a database, and securely encrypt the results on a Quick Response code embedded on a smartcard. We used a mobile app to read the contents on the smartcard without the need for Internet connectivity. Conclusions Our findings indicate that it is possible to develop a patient-held smartcard and an mHealth platform that contains vital health information that can be read at the point of delivery using a mobile phone-based app without an Internet connection. Trial Registration ClinicalTrials.gov NCT03027258; https://clinicaltrials.gov/ct2/show/NCT03027258 (Archived by WebCite at http://www.webcitation.org/6owR2D0kE) PMID:29335234

Functional Interaction Network Construction and Analysis for Disease Discovery.

PubMed

Wu, Guanming; Haw, Robin

2017-01-01

Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform. In this chapter, we describe the detailed procedures on how this functional interaction network is constructed by integrating multiple external data sources, extracting functional interactions from human curated pathway databases, building a machine learning classifier called a Naïve Bayesian Classifier, predicting interactions based on the trained Naïve Bayesian Classifier, and finally constructing the functional interaction database. We also provide an example on how to use ReactomeFIViz for performing network-based data analysis for a list of genes.

KDE Bioscience: platform for bioinformatics analysis workflows.

PubMed

Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

2006-08-01

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

BRISK--research-oriented storage kit for biology-related data.

PubMed

Tan, Alan; Tripp, Ben; Daley, Denise

2011-09-01

In genetic science, large-scale international research collaborations represent a growing trend. These collaborations have demanding and challenging database, storage, retrieval and communication needs. These studies typically involve demographic and clinical data, in addition to the results from numerous genomic studies (omics studies) such as gene expression, eQTL, genome-wide association and methylation studies, which present numerous challenges, thus the need for data integration platforms that can handle these complex data structures. Inefficient methods of data transfer and access control still plague research collaboration. As science becomes more and more collaborative in nature, the need for a system that adequately manages data sharing becomes paramount. Biology-Related Information Storage Kit (BRISK) is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists. The software, documentation, Java source code and demo are available at http://genapha.icapture.ubc.ca/brisk/index.jsp. BRISK was developed in Java, and tested on an Apache Tomcat 6 server with a MySQL database. denise.daley@hli.ubc.ca.

Analysis of outcomes in radiation oncology: An integrated computational platform

PubMed Central

Liu, Dezhi; Ajlouni, Munther; Jin, Jian-Yue; Ryu, Samuel; Siddiqui, Farzan; Patel, Anushka; Movsas, Benjamin; Chetty, Indrin J.

2009-01-01

Radiotherapy research and outcome analyses are essential for evaluating new methods of radiation delivery and for assessing the benefits of a given technology on locoregional control and overall survival. In this article, a computational platform is presented to facilitate radiotherapy research and outcome studies in radiation oncology. This computational platform consists of (1) an infrastructural database that stores patient diagnosis, IMRT treatment details, and follow-up information, (2) an interface tool that is used to import and export IMRT plans in DICOM RT and AAPM/RTOG formats from a wide range of planning systems to facilitate reproducible research, (3) a graphical data analysis and programming tool that visualizes all aspects of an IMRT plan including dose, contour, and image data to aid the analysis of treatment plans, and (4) a software package that calculates radiobiological models to evaluate IMRT treatment plans. Given the limited number of general-purpose computational environments for radiotherapy research and outcome studies, this computational platform represents a powerful and convenient tool that is well suited for analyzing dose distributions biologically and correlating them with the delivered radiation dose distributions and other patient-related clinical factors. In addition the database is web-based and accessible by multiple users, facilitating its convenient application and use. PMID:19544785

Geospatial Data Management Platform for Urban Groundwater

NASA Astrophysics Data System (ADS)

Gaitanaru, D.; Priceputu, A.; Gogu, C. R.

2012-04-01

Due to the large amount of civil work projects and research studies, large quantities of geo-data are produced for the urban environments. These data are usually redundant as well as they are spread in different institutions or private companies. Time consuming operations like data processing and information harmonisation represents the main reason to systematically avoid the re-use of data. The urban groundwater data shows the same complex situation. The underground structures (subway lines, deep foundations, underground parkings, and others), the urban facility networks (sewer systems, water supply networks, heating conduits, etc), the drainage systems, the surface water works and many others modify continuously. As consequence, their influence on groundwater changes systematically. However, these activities provide a large quantity of data, aquifers modelling and then behaviour prediction can be done using monitored quantitative and qualitative parameters. Due to the rapid evolution of technology in the past few years, transferring large amounts of information through internet has now become a feasible solution for sharing geoscience data. Furthermore, standard platform-independent means to do this have been developed (specific mark-up languages like: GML, GeoSciML, WaterML, GWML, CityML). They allow easily large geospatial databases updating and sharing through internet, even between different companies or between research centres that do not necessarily use the same database structures. For Bucharest City (Romania) an integrated platform for groundwater geospatial data management is developed under the framework of a national research project - "Sedimentary media modeling platform for groundwater management in urban areas" (SIMPA) financed by the National Authority for Scientific Research of Romania. The platform architecture is based on three components: a geospatial database, a desktop application (a complex set of hydrogeological and geological analysis tools) and a front-end geoportal service. The SIMPA platform makes use of mark-up transfer standards to provide a user-friendly application that can be accessed through internet to query, analyse, and visualise geospatial data related to urban groundwater. The platform holds the information within the local groundwater geospatial databases and the user is able to access this data through a geoportal service. The database architecture allows storing accurate and very detailed geological, hydrogeological, and infrastructure information that can be straightforwardly generalized and further upscaled. The geoportal service offers the possibility of querying a dataset from the spatial database. The query is coded in a standard mark-up language, and sent to the server through a standard Hyper Text Transfer Protocol (http) to be processed by the local application. After the validation of the query, the results are sent back to the user to be displayed by the geoportal application. The main advantage of the SIMPA platform is that it offers to the user the possibility to make a primary multi-criteria query, which results in a smaller set of data to be analysed afterwards. This improves both the transfer process parameters and the user's means of creating the desired query.

NoSQL data model for semi-automatic integration of ethnomedicinal plant data from multiple sources.

PubMed

Ningthoujam, Sanjoy Singh; Choudhury, Manabendra Dutta; Potsangbam, Kumar Singh; Chetia, Pankaj; Nahar, Lutfun; Sarker, Satyajit D; Basar, Norazah; Das Talukdar, Anupam

2014-01-01

Sharing traditional knowledge with the scientific community could refine scientific approaches to phytochemical investigation and conservation of ethnomedicinal plants. As such, integration of traditional knowledge with scientific data using a single platform for sharing is greatly needed. However, ethnomedicinal data are available in heterogeneous formats, which depend on cultural aspects, survey methodology and focus of the study. Phytochemical and bioassay data are also available from many open sources in various standards and customised formats. To design a flexible data model that could integrate both primary and curated ethnomedicinal plant data from multiple sources. The current model is based on MongoDB, one of the Not only Structured Query Language (NoSQL) databases. Although it does not contain schema, modifications were made so that the model could incorporate both standard and customised ethnomedicinal plant data format from different sources. The model presented can integrate both primary and secondary data related to ethnomedicinal plants. Accommodation of disparate data was accomplished by a feature of this database that supported a different set of fields for each document. It also allowed storage of similar data having different properties. The model presented is scalable to a highly complex level with continuing maturation of the database, and is applicable for storing, retrieving and sharing ethnomedicinal plant data. It can also serve as a flexible alternative to a relational and normalised database. Copyright © 2014 John Wiley & Sons, Ltd.

JBioWH: an open-source Java framework for bioinformatics data integration

PubMed Central

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

JBioWH: an open-source Java framework for bioinformatics data integration.

PubMed

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

Transparent Global Seismic Hazard and Risk Assessment

NASA Astrophysics Data System (ADS)

Smolka, Anselm; Schneider, John; Pinho, Rui; Crowley, Helen

2013-04-01

Vulnerability to earthquakes is increasing, yet advanced reliable risk assessment tools and data are inaccessible to most, despite being a critical basis for managing risk. Also, there are few, if any, global standards that allow us to compare risk between various locations. The Global Earthquake Model (GEM) is a unique collaborative effort that aims to provide organizations and individuals with tools and resources for transparent assessment of earthquake risk anywhere in the world. By pooling data, knowledge and people, GEM acts as an international forum for collaboration and exchange, and leverages the knowledge of leading experts for the benefit of society. Sharing of data and risk information, best practices, and approaches across the globe is key to assessing risk more effectively. Through global projects, open-source IT development and collaborations with more than 10 regions, leading experts are collaboratively developing unique global datasets, best practice, open tools and models for seismic hazard and risk assessment. Guided by the needs and experiences of governments, companies and citizens at large, they work in continuous interaction with the wider community. A continuously expanding public-private partnership constitutes the GEM Foundation, which drives the collaborative GEM effort. An integrated and holistic approach to risk is key to GEM's risk assessment platform, OpenQuake, that integrates all above-mentioned contributions and will become available towards the end of 2014. Stakeholders worldwide will be able to calculate, visualise and investigate earthquake risk, capture new data and to share their findings for joint learning. Homogenized information on hazard can be combined with data on exposure (buildings, population) and data on their vulnerability, for loss assessment around the globe. Furthermore, for a true integrated view of seismic risk, users can add social vulnerability and resilience indices to maps and estimate the costs and benefits of different risk management measures. The following global data, models and methodologies will be available in the platform. Some of these will be released to the public already before, such as the ISC-GEM global instrumental catalogue (released January 2013). Datasets: • Global Earthquake History Catalogue [1000-1903] • Global Instrumental Catalogue [1900-2009] • Global Geodetic Strain Rate Model • Global Active Fault Database • Tectonic Regionalisation • Buildings and Population Database • Earthquake Consequences Database • Physical Vulnerability Database • Socio-Economic Vulnerability and Resilience Indicators Models: • Seismic Source Models • Ground Motion (Attenuation) Models • Physical Exposure Models • Physical Vulnerability Models • Composite Index Models (social vulnerability, resilience, indirect loss) The aforementioned models developed under the GEM framework will be combined to produce estimates of hazard and risk at a global scale. Furthermore, building on many ongoing efforts and knowledge of scientists worldwide, GEM will integrate state-of-the-art data, models, results and open-source tools into a single platform that is to serve as a "clearinghouse" on seismic risk. The platform will continue to increase in value, in particular for use in local contexts, through contributions and collaborations with scientists and organisations worldwide.

Clinical results of HIS, RIS, PACS integration using data integration CASE tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Chan, Hing-Ming; Breant, Claudine M.; Huang, Lu J.; Valentino, Daniel J.

1995-05-01

Current infrastructure research in PACS is dominated by the development of communication networks (local area networks, teleradiology, ATM networks, etc.), multimedia display workstations, and hierarchical image storage architectures. However, limited work has been performed on developing flexible, expansible, and intelligent information processing architectures for the vast decentralized image and text data repositories prevalent in healthcare environments. Patient information is often distributed among multiple data management systems. Current large-scale efforts to integrate medical information and knowledge sources have been costly with limited retrieval functionality. Software integration strategies to unify distributed data and knowledge sources is still lacking commercially. Systems heterogeneity (i.e., differences in hardware platforms, communication protocols, database management software, nomenclature, etc.) is at the heart of the problem and is unlikely to be standardized in the near future. In this paper, we demonstrate the use of newly available CASE (computer- aided software engineering) tools to rapidly integrate HIS, RIS, and PACS information systems. The advantages of these tools include fast development time (low-level code is generated from graphical specifications), and easy system maintenance (excellent documentation, easy to perform changes, and centralized code repository in an object-oriented database). The CASE tools are used to develop and manage the `middle-ware' in our client- mediator-serve architecture for systems integration. Our architecture is scalable and can accommodate heterogeneous database and communication protocols.

Improving healthcare services using web based platform for management of medical case studies.

PubMed

Ogescu, Cristina; Plaisanu, Claudiu; Udrescu, Florian; Dumitru, Silviu

2008-01-01

The paper presents a web based platform for management of medical cases, support for healthcare specialists in taking the best clinical decision. Research has been oriented mostly on multimedia data management, classification algorithms for querying, retrieving and processing different medical data types (text and images). The medical case studies can be accessed by healthcare specialists and by students as anonymous case studies providing trust and confidentiality in Internet virtual environment. The MIDAS platform develops an intelligent framework to manage sets of medical data (text, static or dynamic images), in order to optimize the diagnosis and the decision process, which will reduce the medical errors and will increase the quality of medical act. MIDAS is an integrated project working on medical information retrieval from heterogeneous, distributed medical multimedia database.

Development of Climate Change Adaptation Platform using Spatial Information

NASA Astrophysics Data System (ADS)

Lee, J.; Oh, K. Y.; Lee, M. J.; Han, W. J.

2014-12-01

Climate change adaptation has attracted growing attention with the recent extreme weather conditions that affect people around the world. More and more countries, including the Republic of Korea, have begun to hatch adaptation plan to resolve these matters of great concern. They all, meanwhile, have mentioned that it should come first to integrate climate information in all analysed areas. That's because climate information is not independently made through one source; that is to say, the climate information is connected one another in a complicated way. That is the reason why we have to promote integrated climate change adaptation platform before setting up climate change adaptation plan. Therefore, the large-scaled project has been actively launched and worked on. To date, we researched 620 literatures and interviewed 51 government organizations. Based on the results of the researches and interviews, we obtained 2,725 impacts about vulnerability assessment information such as Monitoring and Forecasting, Health, Disaster, Agriculture, Forest, Water Management, Ecosystem, Ocean/Fisheries, Industry/Energy. Among 2,725 impacts, 995 impacts are made into a database until now. This database is made up 3 sub categories like Climate-Exposure, Sensitivity, Adaptive capacity, presented by IPCC. Based on the constructed database, vulnerability assessments were carried out in order to evaluate climate change capacity of local governments all over the country. These assessments were conducted by using web-based vulnerability assessment tool which was newly developed through this project. These results have shown that, metropolitan areas like Seoul, Pusan, Inchon, and so on have high risks more than twice than rural areas. Acknowledgements: The authors appreciate the support that this study has received from "Development of integrated model for climate change impact and vulnerability assessment and strengthening the framework for model implementation ", an initiative of the Korea Environmental & Industry Technology Institute .

Integration and management of massive remote-sensing data based on GeoSOT subdivision model

NASA Astrophysics Data System (ADS)

Li, Shuang; Cheng, Chengqi; Chen, Bo; Meng, Li

2016-07-01

Owing to the rapid development of earth observation technology, the volume of spatial information is growing rapidly; therefore, improving query retrieval speed from large, rich data sources for remote-sensing data management systems is quite urgent. A global subdivision model, geographic coordinate subdivision grid with one-dimension integer coding on 2n-tree, which we propose as a solution, has been used in data management organizations. However, because a spatial object may cover several grids, ample data redundancy will occur when data are stored in relational databases. To solve this redundancy problem, we first combined the subdivision model with the spatial array database containing the inverted index. We proposed an improved approach for integrating and managing massive remote-sensing data. By adding a spatial code column in an array format in a database, spatial information in remote-sensing metadata can be stored and logically subdivided. We implemented our method in a Kingbase Enterprise Server database system and compared the results with the Oracle platform by simulating worldwide image data. Experimental results showed that our approach performed better than Oracle in terms of data integration and time and space efficiency. Our approach also offers an efficient storage management system for existing storage centers and management systems.

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

PubMed

Williams, Eleanor; Moore, Josh; Li, Simon W; Rustici, Gabriella; Tarkowska, Aleksandra; Chessel, Anatole; Leo, Simone; Antal, Bálint; Ferguson, Richard K; Sarkans, Ugis; Brazma, Alvis; Salas, Rafael E Carazo; Swedlow, Jason R

2017-08-01

Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links data from several imaging modalities, including high-content screening, super-resolution and time-lapse microscopy, digital pathology, public genetic or chemical databases, and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.

dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.

PubMed

Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

2016-01-01

Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf.

dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock

PubMed Central

Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

2016-01-01

Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf. PMID:26727469

Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

1999-07-01

The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

[Analysis on composition and medication regularities of prescriptions treating hypochondriac pain based on traditional Chinese medicine inheritance support system inheritance support platform].

PubMed

Zhao, Yan-qing; Teng, Jing

2015-03-01

To analyze the composition and medication regularities of prescriptions treating hypochondriac pain in Chinese journal full-text database (CNKI) based on the traditional Chinese medicine inheritance support system, in order to provide a reference for further research and development for new traditional Chinese medicines treating hypochondriac pain. The traditional Chinese medicine inheritance support platform software V2. 0 was used to build a prescription database of Chinese medicines treating hypochondriac pain. The software integration data mining method was used to distribute prescriptions according to "four odors", "five flavors" and "meridians" in the database and achieve frequency statistics, syndrome distribution, prescription regularity and new prescription analysis. An analysis were made for 192 prescriptions treating hypochondriac pain to determine the frequencies of medicines in prescriptions, commonly used medicine pairs and combinations and summarize 15 new prescriptions. This study indicated that the prescriptions treating hypochondriac pain in Chinese journal full-text database are mostly those for soothing liver-qi stagnation, promoting qi and activating blood, clearing heat and promoting dampness, and invigorating spleen and removing phlem, with a cold property and bitter taste, and reflect the principles of "distinguish deficiency and excess and relieving pain by smoothening meridians" in treating hypochondriac pain.

PlantRGDB: A Database of Plant Retrocopied Genes.

PubMed

Wang, Yi

2017-01-01

RNA-based gene duplication, known as retrocopy, plays important roles in gene origination and genome evolution. The genomes of many plants have been sequenced, offering an opportunity to annotate and mine the retrocopies in plant genomes. However, comprehensive and unified annotation of retrocopies in these plants is still lacking. In this study I constructed the PlantRGDB (Plant Retrocopied Gene DataBase), the first database of plant retrocopies, to provide a putatively complete centralized list of retrocopies in plant genomes. The database is freely accessible at http://probes.pw.usda.gov/plantrgdb or http://aegilops.wheat.ucdavis.edu/plantrgdb. It currently integrates 49 plant species and 38,997 retrocopies along with characterization information. PlantRGDB provides a user-friendly web interface for searching, browsing and downloading the retrocopies in the database. PlantRGDB also offers graphical viewer-integrated sequence information for displaying the structure of each retrocopy. The attributes of the retrocopies of each species are reported using a browse function. In addition, useful tools, such as an advanced search and BLAST, are available to search the database more conveniently. In conclusion, the database will provide a web platform for obtaining valuable insight into the generation of retrocopies and will supplement research on gene duplication and genome evolution in plants. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi.

PubMed

Parikh, Priti P; Minning, Todd A; Nguyen, Vinh; Lalithsena, Sarasi; Asiaee, Amir H; Sahoo, Satya S; Doshi, Prashant; Tarleton, Rick; Sheth, Amit P

2012-01-01

Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge. We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results. The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.

A service-based framework for pharmacogenomics data integration

NASA Astrophysics Data System (ADS)

Wang, Kun; Bai, Xiaoying; Li, Jing; Ding, Cong

2010-08-01

Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

Simple re-instantiation of small databases using cloud computing.

PubMed

Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M

2013-01-01

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. PMID:24564380

A collection of open source applications for mass spectrometry data mining.

PubMed

Gallardo, Óscar; Ovelleiro, David; Gay, Marina; Carrascal, Montserrat; Abian, Joaquin

2014-10-01

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Remote monitoring of patients with implanted devices: data exchange and integration.

PubMed

Van der Velde, Enno T; Atsma, Douwe E; Foeken, Hylke; Witteman, Tom A; Hoekstra, Wybo H G J

2013-06-01

Remote follow-up of implanted implantable cardioverter defibrillators (ICDs) may offer a solution to the problem of overcrowded outpatient clinics, and may also be effective in detecting clinical events early. Data obtained from remote follow up systems, as developed by all major device companies, are stored in a central database system, operated and owned by the device company. A problem now arises that the patient's clinical information is partly stored in the local electronic health record (EHR) system in the hospital, and partly in the remote monitoring database, which may potentially result in patient safety issues. To address the requirement of integrating remote monitoring data in the local EHR, the Integrating the Healthcare Enterprise (IHE) Implantable Device Cardiac Observation (IDCO) profile has been developed. This IHE IDCO profile has been adapted by all major device companies. In our hospital, we have implemented the IHE IDCO profile to import data from the remote databases from two device vendors into the departmental Cardiology Information System (EPD-Vision). Data is exchanged via a HL7/XML communication protocol, as defined in the IHE IDCO profile. By implementing the IHE IDCO profile, we have been able to integrate the data from the remote monitoring databases in our local EHRs. It can be expected that remote monitoring systems will develop into dedicated monitoring and therapy platforms. Data retrieved from these systems should form an integral part of the electronic patient record as more and more out-patient clinic care will shift to personalized care provided at a distance, in other words at the patient's home.

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

PubMed Central

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H.; Lau, Ching C.; Behl, Sanjiv; Man, Tsz-Kwong

2007-01-01

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License. PMID:19936083

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

PubMed

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

2007-10-06

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

PRGdb: a bioinformatics platform for plant resistance gene analysis

PubMed Central

Sanseverino, Walter; Roma, Guglielmo; De Simone, Marco; Faino, Luigi; Melito, Sara; Stupka, Elia; Frusciante, Luigi; Ercolano, Maria Raffaella

2010-01-01

PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16 000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations. PMID:19906694

Blue guardian: an open architecture for rapid ISR demonstration

NASA Astrophysics Data System (ADS)

Barrett, Donald A.; Borntrager, Luke A.; Green, David M.

2016-05-01

Throughout the Department of Defense (DoD), acquisition, platform integration, and life cycle costs for weapons systems have continued to rise. Although Open Architecture (OA) interface standards are one of the primary methods being used to reduce these costs, the Air Force Rapid Capabilities Office (AFRCO) has extended the OA concept and chartered the Open Mission System (OMS) initiative with industry to develop and demonstrate a consensus-based, non-proprietary, OA standard for integrating subsystems and services into airborne platforms. The new OMS standard provides the capability to decouple vendor-specific sensors, payloads, and service implementations from platform-specific architectures and is still in the early stages of maturation and demonstration. The Air Force Research Laboratory (AFRL) - Sensors Directorate has developed the Blue Guardian program to demonstrate advanced sensing technology utilizing open architectures in operationally relevant environments. Over the past year, Blue Guardian has developed a platform architecture using the Air Force's OMS reference architecture and conducted a ground and flight test program of multiple payload combinations. Systems tested included a vendor-unique variety of Full Motion Video (FMV) systems, a Wide Area Motion Imagery (WAMI) system, a multi-mode radar system, processing and database functions, multiple decompression algorithms, multiple communications systems, and a suite of software tools. Initial results of the Blue Guardian program show the promise of OA to DoD acquisitions, especially for Intelligence, Surveillance and Reconnaissance (ISR) payload applications. Specifically, the OMS reference architecture was extremely useful in reducing the cost and time required for integrating new systems.

An Imaging Sensor-Aided Vision Navigation Approach that Uses a Geo-Referenced Image Database.

PubMed

Li, Yan; Hu, Qingwu; Wu, Meng; Gao, Yang

2016-01-28

In determining position and attitude, vision navigation via real-time image processing of data collected from imaging sensors is advanced without a high-performance global positioning system (GPS) and an inertial measurement unit (IMU). Vision navigation is widely used in indoor navigation, far space navigation, and multiple sensor-integrated mobile mapping. This paper proposes a novel vision navigation approach aided by imaging sensors and that uses a high-accuracy geo-referenced image database (GRID) for high-precision navigation of multiple sensor platforms in environments with poor GPS. First, the framework of GRID-aided vision navigation is developed with sequence images from land-based mobile mapping systems that integrate multiple sensors. Second, a highly efficient GRID storage management model is established based on the linear index of a road segment for fast image searches and retrieval. Third, a robust image matching algorithm is presented to search and match a real-time image with the GRID. Subsequently, the image matched with the real-time scene is considered to calculate the 3D navigation parameter of multiple sensor platforms. Experimental results show that the proposed approach retrieves images efficiently and has navigation accuracies of 1.2 m in a plane and 1.8 m in height under GPS loss in 5 min and within 1500 m.

An Imaging Sensor-Aided Vision Navigation Approach that Uses a Geo-Referenced Image Database

PubMed Central

Li, Yan; Hu, Qingwu; Wu, Meng; Gao, Yang

2016-01-01

In determining position and attitude, vision navigation via real-time image processing of data collected from imaging sensors is advanced without a high-performance global positioning system (GPS) and an inertial measurement unit (IMU). Vision navigation is widely used in indoor navigation, far space navigation, and multiple sensor-integrated mobile mapping. This paper proposes a novel vision navigation approach aided by imaging sensors and that uses a high-accuracy geo-referenced image database (GRID) for high-precision navigation of multiple sensor platforms in environments with poor GPS. First, the framework of GRID-aided vision navigation is developed with sequence images from land-based mobile mapping systems that integrate multiple sensors. Second, a highly efficient GRID storage management model is established based on the linear index of a road segment for fast image searches and retrieval. Third, a robust image matching algorithm is presented to search and match a real-time image with the GRID. Subsequently, the image matched with the real-time scene is considered to calculate the 3D navigation parameter of multiple sensor platforms. Experimental results show that the proposed approach retrieves images efficiently and has navigation accuracies of 1.2 m in a plane and 1.8 m in height under GPS loss in 5 min and within 1500 m. PMID:26828496

Semantic Web repositories for genomics data using the eXframe platform.

PubMed

Merrill, Emily; Corlosquet, Stéphane; Ciccarese, Paolo; Clark, Tim; Das, Sudeshna

2014-01-01

With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge.

Deployment of Directory Service for IEEE N Bus Test System Information

NASA Astrophysics Data System (ADS)

Barman, Amal; Sil, Jaya

2008-10-01

Exchanging information over Internet and Intranet becomes a defacto standard in computer applications, among various users and organizations. Distributed system study, e-governance etc require transparent information exchange between applications, constituencies, manufacturers, and vendors. To serve these purposes database system is needed for storing system data and other relevant information. Directory service, which is a specialized database along with access protocol, could be the single solution since it runs over TCP/IP, supported by all POSIX compliance platforms and is based on open standard. This paper describes a way to deploy directory service, to store IEEE n bus test system data and integrating load flow program with it.

A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

PubMed

Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

2014-10-12

BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

Performance assessment of EMR systems based on post-relational database.

PubMed

Yu, Hai-Yan; Li, Jing-Song; Zhang, Xiao-Guang; Tian, Yu; Suzuki, Muneou; Araki, Kenji

2012-08-01

Post-relational databases provide high performance and are currently widely used in American hospitals. As few hospital information systems (HIS) in either China or Japan are based on post-relational databases, here we introduce a new-generation electronic medical records (EMR) system called Hygeia, which was developed with the post-relational database Caché and the latest platform Ensemble. Utilizing the benefits of a post-relational database, Hygeia is equipped with an "integration" feature that allows all the system users to access data-with a fast response time-anywhere and at anytime. Performance tests of databases in EMR systems were implemented in both China and Japan. First, a comparison test was conducted between a post-relational database, Caché, and a relational database, Oracle, embedded in the EMR systems of a medium-sized first-class hospital in China. Second, a user terminal test was done on the EMR system Izanami, which is based on the identical database Caché and operates efficiently at the Miyazaki University Hospital in Japan. The results proved that the post-relational database Caché works faster than the relational database Oracle and showed perfect performance in the real-time EMR system.

A Patient-Held Smartcard With a Unique Identifier and an mHealth Platform to Improve the Availability of Prenatal Test Results in Rural Nigeria: Demonstration Study.

PubMed

Gbadamosi, Semiu Olatunde; Eze, Chuka; Olawepo, John Olajide; Iwelunmor, Juliet; Sarpong, Daniel F; Ogidi, Amaka Grace; Patel, Dina; Oko, John Okpanachi; Onoka, Chima; Ezeanolue, Echezona Edozie

2018-01-15

Community-based strategies to test for HIV, hepatitis B virus (HBV), and sickle cell disease (SCD) have expanded opportunities to increase the proportion of pregnant women who are aware of their diagnosis. In order to use this information to implement evidence-based interventions, these results have to be available to skilled health providers at the point of delivery. Most electronic health platforms are dependent on the availability of reliable Internet connectivity and, thus, have limited use in many rural and resource-limited settings. Here we describe our work on the development and deployment of an integrated mHealth platform that is able to capture medical information, including test results, and encrypt it into a patient-held smartcard that can be read at the point of delivery without the need for an Internet connection. We engaged a team of implementation scientists, public health experts, and information technology specialists in a requirement-gathering process to inform the design of a prototype for a platform that uses smartcard technology, database deployment, and mobile phone app development. Key design decisions focused on usability, scalability, and security. We successfully designed an integrated mHealth platform and deployed it in 4 health facilities across Benue State, Nigeria. We developed the Vitira Health platform to store test results of HIV, HBV, and SCD in a database, and securely encrypt the results on a Quick Response code embedded on a smartcard. We used a mobile app to read the contents on the smartcard without the need for Internet connectivity. Our findings indicate that it is possible to develop a patient-held smartcard and an mHealth platform that contains vital health information that can be read at the point of delivery using a mobile phone-based app without an Internet connection. ClinicalTrials.gov NCT03027258; https://clinicaltrials.gov/ct2/show/NCT03027258 (Archived by WebCite at http://www.webcitation.org/6owR2D0kE). ©Semiu Olatunde Gbadamosi, Chuka Eze, John Olajide Olawepo, Juliet Iwelunmor, Daniel F Sarpong, Amaka Grace Ogidi, Dina Patel, John Okpanachi Oko, Chima Onoka, Echezona Edozie Ezeanolue. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 15.01.2018.

BμG@Sbase—a microbial gene expression and comparative genomic database

PubMed Central

Witney, Adam A.; Waldron, Denise E.; Brooks, Lucy A.; Tyler, Richard H.; Withers, Michael; Stoker, Neil G.; Wren, Brendan W.; Butcher, Philip D.; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future. PMID:21948792

BμG@Sbase--a microbial gene expression and comparative genomic database.

PubMed

Witney, Adam A; Waldron, Denise E; Brooks, Lucy A; Tyler, Richard H; Withers, Michael; Stoker, Neil G; Wren, Brendan W; Butcher, Philip D; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future.

Integrating In Silico Resources to Map a Signaling Network

PubMed Central

Liu, Hanqing; Beck, Tim N.; Golemis, Erica A.; Serebriiskii, Ilya G.

2013-01-01

The abundance of publicly available life science databases offer a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol to building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.

PubMed

Kim, Woo-Yeon; Kang, Sungsoo; Kim, Byoung-Chul; Oh, Jeehyun; Cho, Seongwoong; Bhak, Jong; Choi, Jong-Soon

2008-01-01

Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date. We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category. SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.

Technologies and standards in the information systems of the soil-geographic database of Russia

NASA Astrophysics Data System (ADS)

Golozubov, O. M.; Rozhkov, V. A.; Alyabina, I. O.; Ivanov, A. V.; Kolesnikova, V. M.; Shoba, S. A.

2015-01-01

The achievements, problems, and challenges of the modern stage of the development of the Soil-Geographic Database of Russia (SGDBR) and the history of this project are outlined. The structure of the information system of the SGDBR as an internet-based resource to collect data on soil profiles and to integrate the geographic and attribute databases on the same platform is described. The pilot project in Rostov oblast illustrates the inclusion of regional information in the SGDBR and its application for solving practical problems. For the first time in Russia, the GeoRSS standard based on the structured hypertext representation of the geographic and attribute information has been applied in the state system for the agromonitoring of agricultural lands in Rostov oblast and information exchange through the internet.

Human Connectome Project Informatics: quality control, database services, and data visualization

PubMed Central

Marcus, Daniel S.; Harms, Michael P.; Snyder, Abraham Z.; Jenkinson, Mark; Wilson, J Anthony; Glasser, Matthew F.; Barch, Deanna M.; Archie, Kevin A.; Burgess, Gregory C.; Ramaratnam, Mohana; Hodge, Michael; Horton, William; Herrick, Rick; Olsen, Timothy; McKay, Michael; House, Matthew; Hileman, Michael; Reid, Erin; Harwell, John; Coalson, Timothy; Schindler, Jon; Elam, Jennifer S.; Curtiss, Sandra W.; Van Essen, David C.

2013-01-01

The Human Connectome Project (HCP) has developed protocols, standard operating and quality control procedures, and a suite of informatics tools to enable high throughput data collection, data sharing, automated data processing and analysis, and data mining and visualization. Quality control procedures include methods to maintain data collection consistency over time, to measure head motion, and to establish quantitative modality-specific overall quality assessments. Database services developed as customizations of the XNAT imaging informatics platform support both internal daily operations and open access data sharing. The Connectome Workbench visualization environment enables user interaction with HCP data and is increasingly integrated with the HCP's database services. Here we describe the current state of these procedures and tools and their application in the ongoing HCP study. PMID:23707591

Tempest: Accelerated MS/MS database search software for heterogeneous computing platforms

PubMed Central

Adamo, Mark E.; Gerber, Scott A.

2017-01-01

MS/MS database search algorithms derive a set of candidate peptide sequences from in-silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU generates peptide candidates that are asynchronously sent to a discrete GPU to be scored against experimental spectra in parallel (Milloy et al., 2012). The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. PMID:27603022

Flexible workflow sharing and execution services for e-scientists

NASA Astrophysics Data System (ADS)

Kacsuk, Péter; Terstyanszky, Gábor; Kiss, Tamas; Sipos, Gergely

2013-04-01

The sequence of computational and data manipulation steps required to perform a specific scientific analysis is called a workflow. Workflows that orchestrate data and/or compute intensive applications on Distributed Computing Infrastructures (DCIs) recently became standard tools in e-science. At the same time the broad and fragmented landscape of workflows and DCIs slows down the uptake of workflow-based work. The development, sharing, integration and execution of workflows is still a challenge for many scientists. The FP7 "Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs" (SHIWA) project significantly improved the situation, with a simulation platform that connects different workflow systems, different workflow languages, different DCIs and workflows into a single, interoperable unit. The SHIWA Simulation Platform is a service package, already used by various scientific communities, and used as a tool by the recently started ER-flow FP7 project to expand the use of workflows among European scientists. The presentation will introduce the SHIWA Simulation Platform and the services that ER-flow provides based on the platform to space and earth science researchers. The SHIWA Simulation Platform includes: 1. SHIWA Repository: A database where workflows and meta-data about workflows can be stored. The database is a central repository to discover and share workflows within and among communities . 2. SHIWA Portal: A web portal that is integrated with the SHIWA Repository and includes a workflow executor engine that can orchestrate various types of workflows on various grid and cloud platforms. 3. SHIWA Desktop: A desktop environment that provides similar access capabilities than the SHIWA Portal, however it runs on the users' desktops/laptops instead of a portal server. 4. Workflow engines: the ASKALON, Galaxy, GWES, Kepler, LONI Pipeline, MOTEUR, Pegasus, P-GRADE, ProActive, Triana, Taverna and WS-PGRADE workflow engines are already integrated with the execution engine of the SHIWA Portal. Other engines can be added when required. Through the SHIWA Portal one can define and run simulations on the SHIWA Virtual Organisation, an e-infrastructure that gathers computing and data resources from various DCIs, including the European Grid Infrastructure. The Portal via third party workflow engines provides support for the most widely used academic workflow engines and it can be extended with other engines on demand. Such extensions translate between workflow languages and facilitate the nesting of workflows into larger workflows even when those are written in different languages and require different interpreters for execution. Through the workflow repository and the portal lonely scientists and scientific collaborations can share and offer workflows for reuse and execution. Given the integrated nature of the SHIWA Simulation Platform the shared workflows can be executed online, without installing any special client environment and downloading workflows. The FP7 "Building a European Research Community through Interoperable Workflows and Data" (ER-flow) project disseminates the achievements of the SHIWA project and use these achievements to build workflow user communities across Europe. ER-flow provides application supports to research communities within and beyond the project consortium to develop, share and run workflows with the SHIWA Simulation Platform.

Tile-in-ONE: A web platform which integrates Tile Calorimeter data quality and calibration assessment

NASA Astrophysics Data System (ADS)

Sivolella, A.; Ferreira, F.; Maidantchik, C.; Solans, C.; Solodkov, A.; Burghgrave, B.; Smirnov, Y.

2015-12-01

The ATLAS Tile Calorimeter collaboration assesses the quality of calibration data in order to ensure its proper operation. A number of tasks is then performed by executing several tools and accessing web systems, which were independently developed to meet distinct collaboration's requirements and do not necessarily are connected with each other. Thus, to attend the collaboration needs, several programs are usually implemented without a global perspective of the detector, requiring basic software features. In addition, functionalities may overlap in their objectives and frequently replicate resources retrieval mechanisms. Tile-in-ONE is a designed and implemented platform that assembles various web systems used by the calorimeter community through a single framework and a standard technology. It provides an infrastructure to support the code implementation, avoiding duplication of work while integrating with an overall view of the detector status. Database connectors smooth the process of information access since developers do not need to be aware of where records are placed and how to extract them. Within the environment, a dashboard stands for a particular Tile operation aspect and gets together plug-ins, i.e. software components that add specific features to an existing application. A server contains the platform core, which represents the basic environment to deal with the configuration, manage user settings and load plug-ins at runtime. A web middleware assists users to develop their own plug-ins, perform tests and integrate them into the platform as a whole. Backends are employed to allow that any type of application is interpreted and displayed in a uniform way. This paper describes Tile-in-ONE web platform.

Computing health quality measures using Informatics for Integrating Biology and the Bedside.

PubMed

Klann, Jeffrey G; Murphy, Shawn N

2013-04-19

The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)'s Query Health platform to move toward this goal. Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow complexity that is intractable for current database systems (both in terms of implementation and computation). Our translator, which supports the subset of HQMF currently expressible in i2b2-XML, may represent the beginnings of a practical compromise. It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers.

Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside

PubMed Central

Murphy, Shawn N

2013-01-01

Background The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)’s Query Health platform to move toward this goal. Objective Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. Methods We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. Results The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. Conclusions HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow complexity that is intractable for current database systems (both in terms of implementation and computation). Our translator, which supports the subset of HQMF currently expressible in i2b2-XML, may represent the beginnings of a practical compromise. It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers. PMID:23603227

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

PubMed Central

Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

2015-01-01

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

PDTCM: a systems pharmacology platform of traditional Chinese medicine for psoriasis.

PubMed

Wang, Dongmei; Gu, Jiangyong; Zhu, Wei; Luo, Fang; Chen, Lirong; Xu, Xiaojie; Lu, Chuanjian

2017-12-01

Psoriasis is a refractory skin disorder, and usually requires a lifetime control. Traditional Chinese medicine (TCM) is effective and safe for this disease. However, the cellular and molecular mechanisms of TCM remedies for psoriasis are still not fully understood. TCM contains numerous natural products. Natural products have historically been invaluable as a resource of therapeutic agents. Yet, there is no integrated information about active compounds of TCM for psoriasis. We use systems pharmacology methods to develop the Psoriasis Database of Traditional Chinese Medicine (PDTCM). The database covered a number of psoriasis-related information (formulas, TCM, compounds, target proteins, diseases and biomarkers). With these data information, an online platform was constructed Results: PDTCM comprises 38 empirical therapeutic formulas, 34373 compounds from 1424 medicinal plants, 44 psoriasis-related proteins and 76 biomarkers from 111 related diseases. On this platform, users can screen active compounds for a psoriasis-related target and explore molecular mechanisms of TCM. Accordingly, users can also download the retrieved structures and data information with a defined value set. In addition, it helps to get a better understanding of Chinese prescriptions in disease treatment. With the systems pharmacology-based data, PDTCM would become a valuable resource for TCM in psoriasis-related research. Key messages PDTCM platform comprises a great deal of data on TCM and psoriasis. On this platform, users can retrieve and get needed information with systems pharmacology methods, such as active compounds screening, target prediction and molecular mechanisms exploration. It is a tool for psoriasis-related research on natural drugs systematically.

Researcher and Author Profiles: Opportunities, Advantages, and Limitations

PubMed Central

2017-01-01

Currently available online profiling platforms offer various services for researchers and authors. Opening an individual account and filling it with scholarly contents increase visibility of research output and boost its impact. This article overviews some of the widely used and emerging profiling platforms, highlighting their tools for sharing scholarly items, crediting individuals, and facilitating networking. Global bibliographic databases and search platforms, such as Scopus, Web of Science, PubMed, and Google Scholar, are widely used for profiling authors with indexed publications. Scholarly networking websites, such as ResearchGate and Academia.edu, provide indispensable services for researchers poorly visible elsewhere on the Internet. Several specialized platforms are designed to offer profiling along with their main functionalities, such as reference management and archiving. The Open Researcher and Contributor Identification (ORCID) project has offered a solution to the author name disambiguation. It has been integrated with numerous bibliographic databases, platforms, and manuscript submission systems to help research managers and journal editors select and credit the best reviewers, and other scholarly contributors. Individuals with verifiable reviewer and editorial accomplishments are also covered by Publons, which is an increasingly recognized service for publicizing and awarding reviewer comments. Currently available profiling formats have numerous advantages and some limitations. The advantages are related to their openness and chances of boosting the researcher impact. Some of the profiling websites are complementary to each other. The underutilization of various profiling websites and their inappropriate uses for promotion of ‘predatory’ journals are among reported limitations. A combined approach to the profiling systems is advocated in this article. PMID:28960025

Macrostrat: A Platform for Geological Data Integration and Deep-Time Earth Crust Research

NASA Astrophysics Data System (ADS)

Peters, Shanan E.; Husson, Jon M.; Czaplewski, John

2018-04-01

Characterizing the lithology, age, and physical-chemical properties of rocks and sediments in the Earth's upper crust is necessary to fully assess energy, water, and mineral resources and to address many fundamental questions. Although a large number of geological maps, regional geological syntheses, and sample-based measurements have been produced, there is no openly available database that integrates rock record-derived data, while also facilitating large-scale, quantitative characterization of the volume, age, and material properties of the upper crust. Here we describe Macrostrat, a relational geospatial database and supporting cyberinfrastructure that is designed to enable quantitative spatial and geochronological analyses of the entire assemblage of surface and subsurface sedimentary, igneous, and metamorphic rocks. Macrostrat contains general, comprehensive summaries of the age and properties of 33,903 lithologically and chronologically defined geological units distributed across 1,474 regions in North and South America, the Caribbean, New Zealand, and the deep sea. Sample-derived data, including fossil occurrences in the Paleobiology Database, more than 180,000 geochemical and outcrop-derived measurements, and more than 2.3 million bedrock geologic map units from over 200 map sources, are linked to specific Macrostrat units and/or lithologies. Macrostrat has generated numerous quantitative results and its infrastructure is used as a data platform in several independently developed mobile applications. It is necessary to expand geographic coverage and to refine age models and material properties to arrive at a more precise characterization of the upper crust globally and test fundamental hypotheses about the long-term evolution of Earth systems.

EcoliWiki: a wiki-based community resource for Escherichia coli

PubMed Central

McIntosh, Brenley K.; Renfro, Daniel P.; Knapp, Gwendowlyn S.; Lairikyengbam, Chanchala R.; Liles, Nathan M.; Niu, Lili; Supak, Amanda M.; Venkatraman, Anand; Zweifel, Adrienne E.; Siegele, Deborah A.; Hu, James C.

2012-01-01

EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates information on laboratory strains of Escherichia coli, its phages, plasmids and mobile genetic elements. As one of the early adopters of the wiki approach to model organism databases, EcoliWiki was designed to not only facilitate community-driven sharing of biological knowledge about E. coli as a model organism, but also to be interoperable with other data resources. EcoliWiki content currently covers genes from five laboratory E. coli strains, 21 bacteriophage genomes, F plasmid and eight transposons. EcoliWiki integrates the Mediawiki wiki platform with other open-source software tools and in-house software development to extend how wikis can be used for model organism databases. EcoliWiki can be accessed online at http://ecoliwiki.net. PMID:22064863

[Research and development of medical case database: a novel medical case information system integrating with biospecimen management].

PubMed

Pan, Shiyang; Mu, Yuan; Wang, Hong; Wang, Tong; Huang, Peijun; Ma, Jianfeng; Jiang, Li; Zhang, Jie; Gu, Bing; Yi, Lujiang

2010-04-01

To meet the needs of management of medical case information and biospecimen simultaneously, we developed a novel medical case information system integrating with biospecimen management. The database established by MS SQL Server 2000 covered, basic information, clinical diagnosis, imaging diagnosis, pathological diagnosis and clinical treatment of patient; physicochemical property, inventory management and laboratory analysis of biospecimen; users log and data maintenance. The client application developed by Visual C++ 6.0 was used to implement medical case and biospecimen management, which was based on Client/Server model. This system can perform input, browse, inquest, summary of case and related biospecimen information, and can automatically synthesize case-records based on the database. Management of not only a long-term follow-up on individual, but also of grouped cases organized according to the aim of research can be achieved by the system. This system can improve the efficiency and quality of clinical researches while biospecimens are used coordinately. It realizes synthesized and dynamic management of medical case and biospecimen, which may be considered as a new management platform.

Multifunctional millimeter-wave radar system for helicopter safety

NASA Astrophysics Data System (ADS)

Goshi, Darren S.; Case, Timothy J.; McKitterick, John B.; Bui, Long Q.

2012-06-01

A multi-featured sensor solution has been developed that enhances the operational safety and functionality of small airborne platforms, representing an invaluable stride toward enabling higher-risk, tactical missions. This paper demonstrates results from a recently developed multi-functional sensor system that integrates a high performance millimeter-wave radar front end, an evidence grid-based integration processing scheme, and the incorporation into a 3D Synthetic Vision System (SVS) display. The front end architecture consists of a w-band real-beam scanning radar that generates a high resolution real-time radar map and operates with an adaptable antenna architecture currently configured with an interferometric capability for target height estimation. The raw sensor data is further processed within an evidence grid-based integration functionality that results in high-resolution maps in the region surrounding the platform. Lastly, the accumulated radar results are displayed in a fully rendered 3D SVS environment integrated with local database information to provide the best representation of the surrounding environment. The integrated system concept will be discussed and initial results from an experimental flight test of this developmental system will be presented. Specifically, the forward-looking operation of the system demonstrates the system's ability to produce high precision terrain mapping with obstacle detection and avoidance capability, showcasing the system's versatility in a true operational environment.

Airport databases for 3D synthetic-vision flight-guidance displays: database design, quality assessment, and data generation

NASA Astrophysics Data System (ADS)

Friedrich, Axel; Raabe, Helmut; Schiefele, Jens; Doerr, Kai Uwe

1999-07-01

In future aircraft cockpit designs SVS (Synthetic Vision System) databases will be used to display 3D physical and virtual information to pilots. In contrast to pure warning systems (TAWS, MSAW, EGPWS) SVS serve to enhance pilot spatial awareness by 3-dimensional perspective views of the objects in the environment. Therefore all kind of aeronautical relevant data has to be integrated into the SVS-database: Navigation- data, terrain-data, obstacles and airport-Data. For the integration of all these data the concept of a GIS (Geographical Information System) based HQDB (High-Quality- Database) has been created at the TUD (Technical University Darmstadt). To enable database certification, quality- assessment procedures according to ICAO Annex 4, 11, 14 and 15 and RTCA DO-200A/EUROCAE ED76 were established in the concept. They can be differentiated in object-related quality- assessment-methods following the keywords accuracy, resolution, timeliness, traceability, assurance-level, completeness, format and GIS-related quality assessment methods with the keywords system-tolerances, logical consistence and visual quality assessment. An airport database is integrated in the concept as part of the High-Quality- Database. The contents of the HQDB are chosen so that they support both Flight-Guidance-SVS and other aeronautical applications like SMGCS (Surface Movement and Guidance Systems) and flight simulation as well. Most airport data are not available. Even though data for runways, threshold, taxilines and parking positions were to be generated by the end of 1997 (ICAO Annex 11 and 15) only a few countries fulfilled these requirements. For that reason methods of creating and certifying airport data have to be found. Remote sensing and digital photogrammetry serve as means to acquire large amounts of airport objects with high spatial resolution and accuracy in much shorter time than with classical surveying methods. Remotely sensed images can be acquired from satellite-platforms or aircraft-platforms. To achieve the highest horizontal accuracy requirements stated in ICAO Annex 14 for runway centerlines (0.50 meters), at the present moment only images acquired from aircraft based sensors can be used as source data. Still, ground reference by GCP (Ground Control-points) is obligatory. A DEM (Digital Elevation Model) can be created automatically in the photogrammetric process. It can be used as highly accurate elevation model for the airport area. The final verification of airport data is accomplished by independent surveyed runway- and taxiway- control-points. The concept of generation airport-data by means of remote sensing and photogrammetry was tested with the Stuttgart/Germany airport. The results proved that the final accuracy was within the accuracy specification defined by ICAO Annex 14.

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

PubMed Central

Baumbach, Jan

2007-01-01

Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at . PMID:17986320

Database integration in a multimedia-modeling environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dorow, Kevin E.

2002-09-02

Integration of data from disparate remote sources has direct applicability to modeling, which can support Brownfield assessments. To accomplish this task, a data integration framework needs to be established. A key element in this framework is the metadata that creates the relationship between the pieces of information that are important in the multimedia modeling environment and the information that is stored in the remote data source. The design philosophy is to allow modelers and database owners to collaborate by defining this metadata in such a way that allows interaction between their components. The main parts of this framework include toolsmore » to facilitate metadata definition, database extraction plan creation, automated extraction plan execution / data retrieval, and a central clearing house for metadata and modeling / database resources. Cross-platform compatibility (using Java) and standard communications protocols (http / https) allow these parts to run in a wide variety of computing environments (Local Area Networks, Internet, etc.), and, therefore, this framework provides many benefits. Because of the specific data relationships described in the metadata, the amount of data that have to be transferred is kept to a minimum (only the data that fulfill a specific request are provided as opposed to transferring the complete contents of a data source). This allows for real-time data extraction from the actual source. Also, the framework sets up collaborative responsibilities such that the different types of participants have control over the areas in which they have domain knowledge-the modelers are responsible for defining the data relevant to their models, while the database owners are responsible for mapping the contents of the database using the metadata definitions. Finally, the data extraction mechanism allows for the ability to control access to the data and what data are made available.« less

Cloud storage based mobile assessment facility for patients with post-traumatic stress disorder using integrated signal processing algorithm

NASA Astrophysics Data System (ADS)

Balbin, Jessie R.; Pinugu, Jasmine Nadja J.; Basco, Abigail Joy S.; Cabanada, Myla B.; Gonzales, Patrisha Melrose V.; Marasigan, Juan Carlos C.

2017-06-01

The research aims to build a tool in assessing patients for post-traumatic stress disorder or PTSD. The parameters used are heart rate, skin conductivity, and facial gestures. Facial gestures are recorded using OpenFace, an open-source face recognition program that uses facial action units in to track facial movements. Heart rate and skin conductivity is measured through sensors operated using Raspberry Pi. Results are stored in a database for easy and quick access. Databases to be used are uploaded to a cloud platform so that doctors have direct access to the data. This research aims to analyze these parameters and give accurate assessment of the patient.

The Research of Spatial-Temporal Analysis and Decision-Making Assistant System for Disabled Person Affairs Based on Mapworld

NASA Astrophysics Data System (ADS)

Zhang, J. H.; Yang, J.; Sun, Y. S.

2015-06-01

This system combines the Mapworld platform and informationization of disabled person affairs, uses the basic information of disabled person as center frame. Based on the disabled person population database, the affairs management system and the statistical account system, the data were effectively integrated and the united information resource database was built. Though the data analysis and mining, the system provides powerful data support to the decision making, the affairs managing and the public serving. It finally realizes the rationalization, normalization and scientization of disabled person affairs management. It also makes significant contributions to the great-leap-forward development of the informationization of China Disabled Person's Federation.

NUREBASE: database of nuclear hormone receptors.

PubMed

Duarte, Jorge; Perrière, Guy; Laudet, Vincent; Robinson-Rechavi, Marc

2002-01-01

Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature of nuclear receptors, we have developed NUREBASE, a database containing protein and DNA sequences, reviewed protein alignments and phylogenies, taxonomy and annotations for all nuclear receptors. The reviewed NUREBASE is completed by NUREBASE_DAILY, automatically updated every 24 h. Both databases are organized under a client/server architecture, with a client written in Java which runs on any platform. This client, named FamFetch, integrates a graphical interface allowing selection of families, and manipulation of phylogenies and alignments. NUREBASE sequence data is also accessible through a World Wide Web server, allowing complex queries. All information on accessing and installing NUREBASE may be found at http://www.ens-lyon.fr/LBMC/laudet/nurebase.html.

HRGFish: A database of hypoxia responsive genes in fishes

NASA Astrophysics Data System (ADS)

Rashid, Iliyas; Nagpure, Naresh Sahebrao; Srivastava, Prachi; Kumar, Ravindra; Pathak, Ajey Kumar; Singh, Mahender; Kushwaha, Basdeo

2017-02-01

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

The European general thoracic surgery database project.

PubMed

Falcoz, Pierre Emmanuel; Brunelli, Alessandro

2014-05-01

The European Society of Thoracic Surgeons (ESTS) Database is a free registry created by ESTS in 2001. The current online version was launched in 2007. It runs currently on a Dendrite platform with extensive data security and frequent backups. The main features are a specialty-specific, procedure-specific, prospectively maintained, periodically audited and web-based electronic database, designed for quality control and performance monitoring, which allows for the collection of all general thoracic procedures. Data collection is the "backbone" of the ESTS database. It includes many risk factors, processes of care and outcomes, which are specially designed for quality control and performance audit. The user can download and export their own data and use them for internal analyses and quality control audits. The ESTS database represents the gold standard of clinical data collection for European General Thoracic Surgery. Over the past years, the ESTS database has achieved many accomplishments. In particular, the database hit two major milestones: it now includes more than 235 participating centers and 70,000 surgical procedures. The ESTS database is a snapshot of surgical practice that aims at improving patient care. In other words, data capture should become integral to routine patient care, with the final objective of improving quality of care within Europe.

A proof of concept for epidemiological research using structured reporting with pulmonary embolism as a use case.

PubMed

Daniel, Pinto Dos Santos; Sonja, Scheibl; Gordon, Arnhold; Aline, Maehringer-Kunz; Christoph, Düber; Peter, Mildenberger; Roman, Kloeckner

2018-05-10

This paper studies the possibilities of an integrated IT-based workflow for epidemiological research in pulmonary embolism using freely available tools and structured reporting. We included a total of 521 consecutive cases which had been referred to the radiology department for computed tomography pulmonary angiography (CTPA) with suspected pulmonary embolism (PE). Free-text reports were transformed into structured reports using a freely available IHE-MRRT-compliant reporting platform. D-dimer values were retrieved from the hospitals laboratory results system. All information was stored in the platform's database and visualized using freely available tools. For further analysis, we directly accessed the platform's database with an advanced analytics tool (RapidMiner). We were able developed an integrated workflow for epidemiological statistics from reports obtained in clinical routine. The report data allowed for automated calculation of epidemiological parameters. Prevalence of pulmonary embolism was 27.6%. The mean age in patients with and without pulmonary embolism did not differ (62.8 years and 62.0 years, respectively, p=0.987). As expected, there was a significant difference in mean D-dimer values (10.13 mg/L FEU and 3.12 mg/L FEU, respectively, p<0.001). Structured reporting can make data obtained from clinical routine more accessible. Designing practical workflows is feasible using freely available tools and allows for the calculation of epidemiological statistics on a near real-time basis. Therefore, radiologists should push for the implementation of structured reporting in clinical routine. Advances in knowledge: Theoretical benefits of structured reporting have long been discussed, but practical implementation demonstrating those benefits has been lacking. Here we present a first experience providing proof that structured reporting will make data from clinical routine more accessible.

Techniques for integrating ‐omics data

PubMed Central

Akula, Siva Prasad; Miriyala, Raghava Naidu; Thota, Hanuman; Rao, Allam Appa; Gedela, Srinubabu

2009-01-01

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present ‐omics community, because ‐omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data. PMID:19255651

Techniques for integrating -omics data.

PubMed

Akula, Siva Prasad; Miriyala, Raghava Naidu; Thota, Hanuman; Rao, Allam Appa; Gedela, Srinubabu

2009-01-01

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.

Integration of Evidence Base into a Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

Saile, Lyn; Lopez, Vilma; Bickham, Grandin; Kerstman, Eric; FreiredeCarvalho, Mary; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

INTRODUCTION: A probabilistic decision support model such as the Integrated Medical Model (IMM) utilizes an immense amount of input data that necessitates a systematic, integrated approach for data collection, and management. As a result of this approach, IMM is able to forecasts medical events, resource utilization and crew health during space flight. METHODS: Inflight data is the most desirable input for the Integrated Medical Model. Non-attributable inflight data is collected from the Lifetime Surveillance for Astronaut Health study as well as the engineers, flight surgeons, and astronauts themselves. When inflight data is unavailable cohort studies, other models and Bayesian analyses are used, in addition to subject matters experts input on occasion. To determine the quality of evidence of a medical condition, the data source is categorized and assigned a level of evidence from 1-5; the highest level is one. The collected data reside and are managed in a relational SQL database with a web-based interface for data entry and review. The database is also capable of interfacing with outside applications which expands capabilities within the database itself. Via the public interface, customers can access a formatted Clinical Findings Form (CLiFF) that outlines the model input and evidence base for each medical condition. Changes to the database are tracked using a documented Configuration Management process. DISSCUSSION: This strategic approach provides a comprehensive data management plan for IMM. The IMM Database s structure and architecture has proven to support additional usages. As seen by the resources utilization across medical conditions analysis. In addition, the IMM Database s web-based interface provides a user-friendly format for customers to browse and download the clinical information for medical conditions. It is this type of functionality that will provide Exploratory Medicine Capabilities the evidence base for their medical condition list. CONCLUSION: The IMM Database in junction with the IMM is helping NASA aerospace program improve the health care and reduce risk for the astronauts crew. Both the database and model will continue to expand to meet customer needs through its multi-disciplinary evidence based approach to managing data. Future expansion could serve as a platform for a Space Medicine Wiki of medical conditions.

Route Sanitizer: Connected Vehicle Trajectory De-Identification Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, Jason M; Ferber, Aaron E

Route Sanitizer is ORNL's connected vehicle moving object database de-identification tool and a graphical user interface to ORNL's connected vehicle de-identification algorithm. It uses the Google Chrome (soon to be Electron) platform so it will run on different computing platforms. The basic de-identification strategy is record redaction: portions of a vehicle trajectory (e.g. sequences of precise temporal spatial records) are removed. It does not alter retained records. The algorithm uses custom techniques to find areas within trajectories that may be considered private, then it suppresses those in addition to enough of the trajectory surrounding those locations to protect against "inferencemore » attacks" in a mathematically sound way. Map data is integrated into the process to make this possible.« less

BioAcoustica: a free and open repository and analysis platform for bioacoustics

PubMed Central

Baker, Edward; Price, Ben W.; Rycroft, S. D.; Smith, Vincent S.

2015-01-01

We describe an online open repository and analysis platform, BioAcoustica (http://bio.acousti.ca), for recordings of wildlife sounds. Recordings can be annotated using a crowdsourced approach, allowing voice introductions and sections with extraneous noise to be removed from analyses. This system is based on the Scratchpads virtual research environment, the BioVeL portal and the Taverna workflow management tool, which allows for analysis of recordings using a grid computing service. At present the analyses include spectrograms, oscillograms and dominant frequency analysis. Further analyses can be integrated to meet the needs of specific researchers or projects. Researchers can upload and annotate their recordings to supplement traditional publication. Database URL: http://bio.acousti.ca PMID:26055102

Radiology and Enterprise Medical Imaging Extensions (REMIX).

PubMed

Erdal, Barbaros S; Prevedello, Luciano M; Qian, Songyue; Demirer, Mutlu; Little, Kevin; Ryu, John; O'Donnell, Thomas; White, Richard D

2018-02-01

Radiology and Enterprise Medical Imaging Extensions (REMIX) is a platform originally designed to both support the medical imaging-driven clinical and clinical research operational needs of Department of Radiology of The Ohio State University Wexner Medical Center. REMIX accommodates the storage and handling of "big imaging data," as needed for large multi-disciplinary cancer-focused programs. The evolving REMIX platform contains an array of integrated tools/software packages for the following: (1) server and storage management; (2) image reconstruction; (3) digital pathology; (4) de-identification; (5) business intelligence; (6) texture analysis; and (7) artificial intelligence. These capabilities, along with documentation and guidance, explaining how to interact with a commercial system (e.g., PACS, EHR, commercial database) that currently exists in clinical environments, are to be made freely available.

Semantic Web repositories for genomics data using the eXframe platform

PubMed Central

2014-01-01

Background With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge. PMID:25093072

Coordinating complex decision support activities across distributed applications

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1994-01-01

Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

A Novel Concept for the Search and Retrieval of the Derwent Markush Resource Database.

PubMed

Barth, Andreas; Stengel, Thomas; Litterst, Edwin; Kraut, Hans; Matuszczyk, Henry; Ailer, Franz; Hajkowski, Steve

2016-05-23

The representation of and search for generic chemical structures (Markush) remains a continuing challenge. Several research groups have addressed this problem, and over time a limited number of practical solutions have been proposed. Today there are two large commercial providers of Markush databases: Chemical Abstracts Service (CAS) and Thomson Reuters. The Thomson Reuters "Derwent" Markush database is currently offered via the online services Questel and STN and as a data feed for in-house use. The aim of this paper is to briefly review the existing Markush systems (databases plus search engines) and to describe our new approach for the implementation of the Derwent Markush Resource on STN. Our new approach demonstrates the integration of the Derwent Markush Resource database into the existing chemistry-focused STN platform without loss of detail. This provides compatibility with other structure and Markush databases on STN and at the same time makes it possible to deploy the specific features and functions of the Derwent approach. It is shown that the different Markush languages developed by CAS and Derwent can be combined into a single general Markush description. In this concept the generic nodes are grouped together in a unique hierarchy where all chemical elements and fragments can be integrated. As a consequence, both systems are searchable using a single structure query. Moreover, the presented concept could serve as a promising starting point for a common generalized description of Markush structures.

U.S. Army Research Laboratory (ARL) multimodal signatures database

NASA Astrophysics Data System (ADS)

Bennett, Kelly

2008-04-01

The U.S. Army Research Laboratory (ARL) Multimodal Signatures Database (MMSDB) is a centralized collection of sensor data of various modalities that are co-located and co-registered. The signatures include ground and air vehicles, personnel, mortar, artillery, small arms gunfire from potential sniper weapons, explosives, and many other high value targets. This data is made available to Department of Defense (DoD) and DoD contractors, Intel agencies, other government agencies (OGA), and academia for use in developing target detection, tracking, and classification algorithms and systems to protect our Soldiers. A platform independent Web interface disseminates the signatures to researchers and engineers within the scientific community. Hierarchical Data Format 5 (HDF5) signature models provide an excellent solution for the sharing of complex multimodal signature data for algorithmic development and database requirements. Many open source tools for viewing and plotting HDF5 signatures are available over the Web. Seamless integration of HDF5 signatures is possible in both proprietary computational environments, such as MATLAB, and Free and Open Source Software (FOSS) computational environments, such as Octave and Python, for performing signal processing, analysis, and algorithm development. Future developments include extending the Web interface into a portal system for accessing ARL algorithms and signatures, High Performance Computing (HPC) resources, and integrating existing database and signature architectures into sensor networking environments.

Development of the updated system of city underground pipelines based on Visual Studio

NASA Astrophysics Data System (ADS)

Zhang, Jianxiong; Zhu, Yun; Li, Xiangdong

2009-10-01

Our city has owned the integrated pipeline network management system with ArcGIS Engine 9.1 as the bottom development platform and with Oracle9i as basic database for storaging data. In this system, ArcGIS SDE9.1 is applied as the spatial data engine, and the system was a synthetic management software developed with Visual Studio visualization procedures development tools. As the pipeline update function of the system has the phenomenon of slower update and even sometimes the data lost, to ensure the underground pipeline data can real-time be updated conveniently and frequently, and the actuality and integrity of the underground pipeline data, we have increased a new update module in the system developed and researched by ourselves. The module has the powerful data update function, and can realize the function of inputting and outputting and rapid update volume of data. The new developed module adopts Visual Studio visualization procedures development tools, and uses access as the basic database to storage data. We can edit the graphics in AutoCAD software, and realize the database update using link between the graphics and the system. Practice shows that the update module has good compatibility with the original system, reliable and high update efficient of the database.

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

compendiumdb: an R package for retrieval and storage of functional genomics data.

PubMed

Nandal, Umesh K; van Kampen, Antoine H C; Moerland, Perry D

2016-09-15

Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving and storing a large number of expression profiles from a wide range of different studies and platforms. The compendiumdb R package provides an environment for downloading functional genomics data from GEO, parsing the information into a local or remote database and interacting with the database using dedicated R functions, thus enabling seamless integration with other tools available in R/Bioconductor. The compendiumdb package is written in R, MySQL and Perl. Source code and binaries are available from CRAN (http://cran.r-project.org/web/packages/compendiumdb/) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license. p.d.moerland@amc.uva.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

Moving BASISplus and TECHLIBplus from VAX/VMS to UNIX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dominiak, R.

1993-12-31

BASISplus is used at the Laboratory by the Technical Information Services (TIS) Department which is part of the Information and Publishing Division at ARGONNE. TIS operates the Argonne Information Management System (AIM). The AIM System consists of the ANL Libraries On-Line Database (a TECHLIBplus database), the Current Journals Database (IDI`s current contents search), the ANL Publications Tracking Database (a TECHLIBplus database), the Powder Diffraction File Database, and several CD-ROM databases available through a Novell network. The AIM System is available from the desktop of ANL staff through modem and network connections, as well as from the 10 science libraries atmore » ARGONNE. TIS has been a BASISplus and TECHLIBplus site from the start, and never migrated from BASIS K. The decision to migrate from the VAX/VMS platform to a UNIX platform. Migrating a product from one platform to another involves many decisions and considerations. These justifications, decisions, and considerations are explored in this report.« less

Brain-CODE: A Secure Neuroinformatics Platform for Management, Federation, Sharing and Analysis of Multi-Dimensional Neuroscience Data.

PubMed

Vaccarino, Anthony L; Dharsee, Moyez; Strother, Stephen; Aldridge, Don; Arnott, Stephen R; Behan, Brendan; Dafnas, Costas; Dong, Fan; Edgecombe, Kenneth; El-Badrawi, Rachad; El-Emam, Khaled; Gee, Tom; Evans, Susan G; Javadi, Mojib; Jeanson, Francis; Lefaivre, Shannon; Lutz, Kristen; MacPhee, F Chris; Mikkelsen, Jordan; Mikkelsen, Tom; Mirotchnick, Nicholas; Schmah, Tanya; Studzinski, Christa M; Stuss, Donald T; Theriault, Elizabeth; Evans, Kenneth R

2018-01-01

Historically, research databases have existed in isolation with no practical avenue for sharing or pooling medical data into high dimensional datasets that can be efficiently compared across databases. To address this challenge, the Ontario Brain Institute's "Brain-CODE" is a large-scale neuroinformatics platform designed to support the collection, storage, federation, sharing and analysis of different data types across several brain disorders, as a means to understand common underlying causes of brain dysfunction and develop novel approaches to treatment. By providing researchers access to aggregated datasets that they otherwise could not obtain independently, Brain-CODE incentivizes data sharing and collaboration and facilitates analyses both within and across disorders and across a wide array of data types, including clinical, neuroimaging and molecular. The Brain-CODE system architecture provides the technical capabilities to support (1) consolidated data management to securely capture, monitor and curate data, (2) privacy and security best-practices, and (3) interoperable and extensible systems that support harmonization, integration, and query across diverse data modalities and linkages to external data sources. Brain-CODE currently supports collaborative research networks focused on various brain conditions, including neurodevelopmental disorders, cerebral palsy, neurodegenerative diseases, epilepsy and mood disorders. These programs are generating large volumes of data that are integrated within Brain-CODE to support scientific inquiry and analytics across multiple brain disorders and modalities. By providing access to very large datasets on patients with different brain disorders and enabling linkages to provincial, national and international databases, Brain-CODE will help to generate new hypotheses about the biological bases of brain disorders, and ultimately promote new discoveries to improve patient care.

Brain-CODE: A Secure Neuroinformatics Platform for Management, Federation, Sharing and Analysis of Multi-Dimensional Neuroscience Data

PubMed Central

Vaccarino, Anthony L.; Dharsee, Moyez; Strother, Stephen; Aldridge, Don; Arnott, Stephen R.; Behan, Brendan; Dafnas, Costas; Dong, Fan; Edgecombe, Kenneth; El-Badrawi, Rachad; El-Emam, Khaled; Gee, Tom; Evans, Susan G.; Javadi, Mojib; Jeanson, Francis; Lefaivre, Shannon; Lutz, Kristen; MacPhee, F. Chris; Mikkelsen, Jordan; Mikkelsen, Tom; Mirotchnick, Nicholas; Schmah, Tanya; Studzinski, Christa M.; Stuss, Donald T.; Theriault, Elizabeth; Evans, Kenneth R.

2018-01-01

Historically, research databases have existed in isolation with no practical avenue for sharing or pooling medical data into high dimensional datasets that can be efficiently compared across databases. To address this challenge, the Ontario Brain Institute’s “Brain-CODE” is a large-scale neuroinformatics platform designed to support the collection, storage, federation, sharing and analysis of different data types across several brain disorders, as a means to understand common underlying causes of brain dysfunction and develop novel approaches to treatment. By providing researchers access to aggregated datasets that they otherwise could not obtain independently, Brain-CODE incentivizes data sharing and collaboration and facilitates analyses both within and across disorders and across a wide array of data types, including clinical, neuroimaging and molecular. The Brain-CODE system architecture provides the technical capabilities to support (1) consolidated data management to securely capture, monitor and curate data, (2) privacy and security best-practices, and (3) interoperable and extensible systems that support harmonization, integration, and query across diverse data modalities and linkages to external data sources. Brain-CODE currently supports collaborative research networks focused on various brain conditions, including neurodevelopmental disorders, cerebral palsy, neurodegenerative diseases, epilepsy and mood disorders. These programs are generating large volumes of data that are integrated within Brain-CODE to support scientific inquiry and analytics across multiple brain disorders and modalities. By providing access to very large datasets on patients with different brain disorders and enabling linkages to provincial, national and international databases, Brain-CODE will help to generate new hypotheses about the biological bases of brain disorders, and ultimately promote new discoveries to improve patient care. PMID:29875648

Research on Historic Bim of Built Heritage in Taiwan - a Case Study of Huangxi Academy

NASA Astrophysics Data System (ADS)

Lu, Y. C.; Shih, T. Y.; Yen, Y. N.

2018-05-01

Digital archiving technology for conserving cultural heritage is an important subject nowadays. The Taiwanese Ministry of Culture continues to try to converge the concept and technology of conservation towards international conventions. However, the products from these different technologies are not yet integrated due to the lack of research and development in this field. There is currently no effective schema in HBIM for Taiwanese cultural heritage. The aim of this research is to establish an HBIM schema for Chinese built heritage in Taiwan. The proposed method starts from the perspective of the components of built heritage buildings, up to the investigation of the important properties of the components through important international charters and Taiwanese laws of cultural heritage conservation. Afterwards, object-oriented class diagram and ontology from the scale of components were defined to clarify the concept and increase the interoperability. A historical database was then established for the historical information of components and to bring it into the concept of BIM in order to build a 3D model of heritage objects which can be used for visualization. An integration platform was developed for the users to browse and manipulate the database and 3D model simultaneously. In addition, this research also evaluated the feasibility of this method using the study case at the Huangxi academy located in Taiwan. The conclusion showed that class diagram could help the establishment of database and even its application for different Chinese built heritage objects. The establishment of ontology helped to convey knowledge and increase interoperability. In comparison to traditional documentation methods, the querying result of the platform was more accurate and less prone to human error.

Active in-database processing to support ambient assisted living systems.

PubMed

de Morais, Wagner O; Lundström, Jens; Wickström, Nicholas

2014-08-12

As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare.

Active In-Database Processing to Support Ambient Assisted Living Systems

PubMed Central

de Morais, Wagner O.; Lundström, Jens; Wickström, Nicholas

2014-01-01

As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare. PMID:25120164

ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms

PubMed Central

Pareja, Eduardo; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Bonal, Javier; Tobes, Raquel

2006-01-01

Background Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory proteins and the regulatory DNA signals located in extragenic regions are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and regulatory proteins from bacteria and archaea included in the UniProt database. Description ExtraTrain provides integrated and easily manageable information for 679816 extragenic regions and for the genes delimiting each of them. In addition ExtraTrain supplies a tool to explore extragenic regions, named Palinsight, oriented to detect and search palindromic patterns. This interactive visual tool is totally integrated in the database, allowing the search for regulatory signals in user defined sets of extragenic regions. The 26046 regulatory proteins included in ExtraTrain belong to the families AraC/XylS, ArsR, AsnC, Cold shock domain, CRP-FNR, DeoR, GntR, IclR, LacI, LuxR, LysR, MarR, MerR, NtrC/Fis, OmpR and TetR. The database follows the InterPro criteria to define these families. The information about regulators includes manually curated sets of references specifically associated to regulator entries. In order to achieve a sustainable and maintainable knowledge database ExtraTrain is a platform open to the contribution of knowledge by the scientific community providing a system for the incorporation of textual knowledge. Conclusion ExtraTrain is a new database for exploring Extragenic regions and Transcriptional information in bacteria and archaea. ExtraTrain database is available at . PMID:16539733

A database of archived drilling records of the drill cuttings piles at the North West Hutton oil platform.

PubMed

Marsh, Roy

2003-05-01

Drill cuttings piles are found underneath several hundred oil platforms in the North Sea, and are contaminated with hydrocarbons and chemical products. This study characterised the environmental risk posed by the cuttings pile at the North West Hutton (NWH) oil platform. Data on the drilling fluids and chemical products used over the platform's drilling history were transferred from archived well reports into a custom database, to which were added toxicological and safety data. Although the database contained many gaps, it established that only seven chemical products used at NWH were not in the lowest category of the Offshore Chemicals Notification Scheme, and were used in only small quantities. The study therefore supports the view that the main environmental risk posed by cuttings piles comes from hydrocarbon contamination. The (dated) well records could help future core sampling to be targeted at specific locations in the cuttings piles. Data from many platforms could also be pooled to determine generic 'discharge profiles.' Future study would benefit from the existence, in the public domain, of a standardised, 'legacy' database of chemical products.

Rembrandt: Helping Personalized Medicine Become a Reality Through Integrative Translational Research

PubMed Central

Madhavan, Subha; Zenklusen, Jean-Claude; Kotliarov, Yuri; Sahni, Himanso; Fine, Howard A.; Buetow, Kenneth

2009-01-01

Finding better therapies for the treatment of brain tumors is hampered by the lack of consistently obtained molecular data in a large sample set, and ability to integrate biomedical data from disparate sources enabling translation of therapies from bench to bedside. Hence, a critical factor in the advancement of biomedical research and clinical translation is the ease with which data can be integrated, redistributed and analyzed both within and across functional domains. Novel biomedical informatics infrastructure and tools are essential for developing individualized patient treatment based on the specific genomic signatures in each patient’s tumor. Here we present Rembrandt, Repository of Molecular BRAin Neoplasia DaTa, a cancer clinical genomics database and a web-based data mining and analysis platform aimed at facilitating discovery by connecting the dots between clinical information and genomic characterization data. To date, Rembrandt contains data generated through the Glioma Molecular Diagnostic Initiative from 874 glioma specimens comprising nearly 566 gene expression arrays, 834 copy number arrays and 13,472 clinical phenotype data points. Data can be queried and visualized for a selected gene across all data platforms or for multiple genes in a selected platform. Additionally, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-anomaly pairs to facilitate the discovery of novel biomarkers and therapeutic targets. We believe that REMBRANDT represents a prototype of how high throughput genomic and clinical data can be integrated in a way that will allow expeditious and efficient translation of laboratory discoveries to the clinic. PMID:19208739

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

PubMed Central

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-01

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. PMID:27899624

Neuroimaging Data Sharing on the Neuroinformatics Database Platform

PubMed Central

Book, Gregory A; Stevens, Michael; Assaf, Michal; Glahn, David; Pearlson, Godfrey D

2015-01-01

We describe the Neuroinformatics Database (NiDB), an open-source database platform for archiving, analysis, and sharing of neuroimaging data. Data from the multi-site projects Autism Brain Imaging Data Exchange (ABIDE), Bipolar-Schizophrenia Network on Intermediate Phenotypes parts one and two (B-SNIP1, B-SNIP2), and Monetary Incentive Delay task (MID) are available for download from the public instance of NiDB, with more projects sharing data as it becomes available. As demonstrated by making several large datasets available, NiDB is an extensible platform appropriately suited to archive and distribute shared neuroimaging data. PMID:25888923

The relational database model and multiple multicenter clinical trials.

PubMed

Blumenstein, B A

1989-12-01

The Southwest Oncology Group (SWOG) chose to use a relational database management system (RDBMS) for the management of data from multiple clinical trials because of the underlying relational model's inherent flexibility and the natural way multiple entity types (patients, studies, and participants) can be accommodated. The tradeoffs to using the relational model as compared to using the hierarchical model include added computing cycles due to deferred data linkages and added procedural complexity due to the necessity of implementing protections against referential integrity violations. The SWOG uses its RDBMS as a platform on which to build data operations software. This data operations software, which is written in a compiled computer language, allows multiple users to simultaneously update the database and is interactive with respect to the detection of conditions requiring action and the presentation of options for dealing with those conditions. The relational model facilitates the development and maintenance of data operations software.

Tempest: Accelerated MS/MS Database Search Software for Heterogeneous Computing Platforms.

PubMed

Adamo, Mark E; Gerber, Scott A

2016-09-07

MS/MS database search algorithms derive a set of candidate peptide sequences from in silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU (central processing unit) generates peptide candidates that are asynchronously sent to a discrete GPU (graphics processing unit) to be scored against experimental spectra in parallel. The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

The use of regional platforms for managing electronic health records for the production of regional public health indicators in France

PubMed Central

2012-01-01

Background In France, recent developments in healthcare system organization have aimed at strengthening decision-making and action in public health at the regional level. Firstly, the 2004 Public Health Act, by setting 100 national and regional public health targets, introduced an evaluative approach to public health programs at the national and regional levels. Meanwhile, the implementation of regional platforms for managing electronic health records (EHRs) has also been under assessment to coordinate the deployment of this important instrument of care within each geographic area. In this context, the development and implementation of a regional approach to epidemiological data extracted from EHRs are an opportunity that must be seized as soon as possible. Our article addresses certain design and organizational aspects so that the technical requirements for such use are integrated into regional platforms in France. The article will base itself on organization of the Rhône-Alpes regional health platform. Discussion Different tools being deployed in France allow us to consider the potential of these regional platforms for epidemiology and public health (implementation of a national health identification number and a national information system interoperability framework). The deployment of the Rhône-Alpes regional health platform began in the 2000s in France. By August 2011, 2.6 million patients were identified in this platform. A new development step is emerging because regional decision-makers need to measure healthcare efficiency. To pool heterogeneous information contained in various independent databases, the format, norm and content of the metadata have been defined. Two types of databases will be created according to the nature of the data processed, one for extracting structured data, and the second for extracting non-structured and de-identified free-text documents. Summary Regional platforms for managing EHRs could constitute an important data source for epidemiological surveillance in the context of epidemic alerts, but also in monitoring a number of indicators of infectious and chronic diseases for which no data are yet available in France. PMID:22471902

GIS based solid waste management information system for Nagpur, India.

PubMed

Vijay, Ritesh; Jain, Preeti; Sharma, N; Bhattacharyya, J K; Vaidya, A N; Sohony, R A

2013-01-01

Solid waste management is one of the major problems of today's world and needs to be addressed by proper utilization of technologies and design of effective, flexible and structured information system. Therefore, the objective of this paper was to design and develop a GIS based solid waste management information system as a decision making and planning tool for regularities and municipal authorities. The system integrates geo-spatial features of the city and database of existing solid waste management. GIS based information system facilitates modules of visualization, query interface, statistical analysis, report generation and database modification. It also provides modules like solid waste estimation, collection, transportation and disposal details. The information system is user-friendly, standalone and platform independent.

CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

PubMed

Paananen, Jussi; Storvik, Markus; Wong, Garry

2006-09-22

Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies. We have developed a web-based software resource, called CROPPER that uses the latest genomic information concerning different data identifiers and orthologous genes from the Ensembl database. CROPPER can be used to combine genomic data from different heterogeneous sources, allowing researchers to perform cross-platform/cross-species compendium studies without the need for complex computational tools or the requirement of setting up one's own in-house database. We also present an example of a simple cross-platform/cross-species compendium study based on publicly available Parkinson's disease data derived from different sources. CROPPER is a user-friendly and freely available web-based software resource that can be successfully used for cross-species/cross-platform compendium studies.

The EarthServer Federation: State, Role, and Contribution to GEOSS

NASA Astrophysics Data System (ADS)

Merticariu, Vlad; Baumann, Peter

2016-04-01

The intercontinental EarthServer initiative has established a European datacube platform with proven scalability: known databases exceed 100 TB, and single queries have been split across more than 1,000 cloud nodes. Its service interface being rigorously based on the OGC "Big Geo Data" standards, Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS), a series of clients can dock into the services, ranging from open-source OpenLayers and QGIS over open-source NASA WorldWind to proprietary ESRI ArcGIS. Datacube fusion in a "mix and match" style is supported by the platform technolgy, the rasdaman Array Database System, which transparently federates queries so that users simply approach any node of the federation to access any data item, internally optimized for minimal data transfer. Notably, rasdaman is part of GEOSS GCI. NASA is contributing its Web WorldWind virtual globe for user-friendly data extraction, navigation, and analysis. Integrated datacube / metadata queries are contributed by CITE. Current federation members include ESA (managed by MEEO sr.l.), Plymouth Marine Laboratory (PML), the European Centre for Medium-Range Weather Forecast (ECMWF), Australia's National Computational Infrastructure, and Jacobs University (adding in Planetary Science). Further data centers have expressed interest in joining. We present the EarthServer approach, discuss its underlying technology, and illustrate the contribution this datacube platform can make to GEOSS.

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.

PubMed

Nicolazzi, Ezequiel L; Caprera, Andrea; Nazzicari, Nelson; Cozzi, Paolo; Strozzi, Francesco; Lawley, Cindy; Pirani, Ali; Soans, Chandrasen; Brew, Fiona; Jorjani, Hossein; Evans, Gary; Simpson, Barry; Tosser-Klopp, Gwenola; Brauning, Rudiger; Williams, John L; Stella, Alessandra

2015-04-10

In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information. Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion. This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.

TERRA REF: Advancing phenomics with high resolution, open access sensor and genomics data

NASA Astrophysics Data System (ADS)

LeBauer, D.; Kooper, R.; Burnette, M.; Willis, C.

2017-12-01

Automated plant measurement has the potential to improve understanding of genetic and environmental controls on plant traits (phenotypes). The application of sensors and software in the automation of high throughput phenotyping reflects a fundamental shift from labor intensive hand measurements to drone, tractor, and robot mounted sensing platforms. These tools are expected to speed the rate of crop improvement by enabling plant breeders to more accurately select plants with improved yields, resource use efficiency, and stress tolerance. However, there are many challenges facing high throughput phenomics: sensors and platforms are expensive, currently there are few standard methods of data collection and storage, and the analysis of large data sets requires high performance computers and automated, reproducible computing pipelines. To overcome these obstacles and advance the science of high throughput phenomics, the TERRA Phenotyping Reference Platform (TERRA-REF) team is developing an open-access database of high resolution sensor data. TERRA REF is an integrated field and greenhouse phenotyping system that includes: a reference field scanner with fifteen sensors that can generate terrabytes of data each day at mm resolution; UAV, tractor, and fixed field sensing platforms; and an automated controlled-environment scanner. These platforms will enable investigation of diverse sensing modalities, and the investigation of traits under controlled and field environments. It is the goal of TERRA REF to lower the barrier to entry for academic and industry researchers by providing high-resolution data, open source software, and online computing resources. Our project is unique in that all data will be made fully public in November 2018, and is already available to early adopters through the beta-user program. We will describe the datasets and how to use them as well as the databases and computing pipeline and how these can be reused and remixed in other phenomics pipelines. Finally, we will describe the National Data Service workbench, a cloud computing platform that can access the petabyte scale data while supporting reproducible research.

BanTeC: a software tool for management of corneal transplantation.

PubMed

López-Alvarez, P; Caballero, F; Trias, J; Cortés, U; López-Navidad, A

2005-11-01

Until recently, all cornea information at our tissue bank was managed manually, no specific database or computer tool had been implemented to provide electronic versions of documents and medical reports. The main objective of the BanTeC project was therefore to create a computerized system to integrate and classify all the information and documents used in the center in order to facilitate management of retrieved, transplanted corneal tissues. We used the Windows platform to develop the project. Microsoft Access and Microsoft Jet Engine were used at the database level and Data Access Objects was the chosen data access technology. In short, the BanTeC software seeks to computerize the tissue bank. All the initial stages of the development have now been completed, from specification of needs, program design and implementation of the software components, to the total integration of the final result in the real production environment. BanTeC will allow the generation of statistical reports for analysis to improve our performance.

eSciMart: Web Platform for Scientific Software Marketplace

NASA Astrophysics Data System (ADS)

Kryukov, A. P.; Demichev, A. P.

2016-10-01

In this paper we suggest a design of a web marketplace where users of scientific application software and databases, presented in the form of web services, as well as their providers will have presence simultaneously. The model, which will be the basis for the web marketplace is close to the customer-to-customer (C2C) model, which has been successfully used, for example, on the auction sites such as eBay (ebay.com). Unlike the classical model of C2C the suggested marketplace focuses on application software in the form of web services, and standardization of API through which application software will be integrated into the web marketplace. A prototype of such a platform, entitled eSciMart, is currently being developed at SINP MSU.

RayPlus: a Web-Based Platform for Medical Image Processing.

PubMed

Yuan, Rong; Luo, Ming; Sun, Zhi; Shi, Shuyue; Xiao, Peng; Xie, Qingguo

2017-04-01

Medical image can provide valuable information for preclinical research, clinical diagnosis, and treatment. As the widespread use of digital medical imaging, many researchers are currently developing medical image processing algorithms and systems in order to accommodate a better result to clinical community, including accurate clinical parameters or processed images from the original images. In this paper, we propose a web-based platform to present and process medical images. By using Internet and novel database technologies, authorized users can easily access to medical images and facilitate their workflows of processing with server-side powerful computing performance without any installation. We implement a series of algorithms of image processing and visualization in the initial version of Rayplus. Integration of our system allows much flexibility and convenience for both research and clinical communities.

The Osseus platform: a prototype for advanced web-based distributed simulation

NASA Astrophysics Data System (ADS)

Franceschini, Derrick; Riecken, Mark

2016-05-01

Recent technological advances in web-based distributed computing and database technology have made possible a deeper and more transparent integration of some modeling and simulation applications. Despite these advances towards true integration of capabilities, disparate systems, architectures, and protocols will remain in the inventory for some time to come. These disparities present interoperability challenges for distributed modeling and simulation whether the application is training, experimentation, or analysis. Traditional approaches call for building gateways to bridge between disparate protocols and retaining interoperability specialists. Challenges in reconciling data models also persist. These challenges and their traditional mitigation approaches directly contribute to higher costs, schedule delays, and frustration for the end users. Osseus is a prototype software platform originally funded as a research project by the Defense Modeling & Simulation Coordination Office (DMSCO) to examine interoperability alternatives using modern, web-based technology and taking inspiration from the commercial sector. Osseus provides tools and services for nonexpert users to connect simulations, targeting the time and skillset needed to successfully connect disparate systems. The Osseus platform presents a web services interface to allow simulation applications to exchange data using modern techniques efficiently over Local or Wide Area Networks. Further, it provides Service Oriented Architecture capabilities such that finer granularity components such as individual models can contribute to simulation with minimal effort.

Using Distributed Data over HBase in Big Data Analytics Platform for Clinical Services

PubMed Central

Zamani, Hamid

2017-01-01

Big data analytics (BDA) is important to reduce healthcare costs. However, there are many challenges of data aggregation, maintenance, integration, translation, analysis, and security/privacy. The study objective to establish an interactive BDA platform with simulated patient data using open-source software technologies was achieved by construction of a platform framework with Hadoop Distributed File System (HDFS) using HBase (key-value NoSQL database). Distributed data structures were generated from benchmarked hospital-specific metadata of nine billion patient records. At optimized iteration, HDFS ingestion of HFiles to HBase store files revealed sustained availability over hundreds of iterations; however, to complete MapReduce to HBase required a week (for 10 TB) and a month for three billion (30 TB) indexed patient records, respectively. Found inconsistencies of MapReduce limited the capacity to generate and replicate data efficiently. Apache Spark and Drill showed high performance with high usability for technical support but poor usability for clinical services. Hospital system based on patient-centric data was challenging in using HBase, whereby not all data profiles were fully integrated with the complex patient-to-hospital relationships. However, we recommend using HBase to achieve secured patient data while querying entire hospital volumes in a simplified clinical event model across clinical services. PMID:29375652

Using Distributed Data over HBase in Big Data Analytics Platform for Clinical Services.

PubMed

Chrimes, Dillon; Zamani, Hamid

2017-01-01

Big data analytics (BDA) is important to reduce healthcare costs. However, there are many challenges of data aggregation, maintenance, integration, translation, analysis, and security/privacy. The study objective to establish an interactive BDA platform with simulated patient data using open-source software technologies was achieved by construction of a platform framework with Hadoop Distributed File System (HDFS) using HBase (key-value NoSQL database). Distributed data structures were generated from benchmarked hospital-specific metadata of nine billion patient records. At optimized iteration, HDFS ingestion of HFiles to HBase store files revealed sustained availability over hundreds of iterations; however, to complete MapReduce to HBase required a week (for 10 TB) and a month for three billion (30 TB) indexed patient records, respectively. Found inconsistencies of MapReduce limited the capacity to generate and replicate data efficiently. Apache Spark and Drill showed high performance with high usability for technical support but poor usability for clinical services. Hospital system based on patient-centric data was challenging in using HBase, whereby not all data profiles were fully integrated with the complex patient-to-hospital relationships. However, we recommend using HBase to achieve secured patient data while querying entire hospital volumes in a simplified clinical event model across clinical services.

Precision in robotic rectal surgery using the da Vinci Xi system and integrated table motion, a technical note.

PubMed

Panteleimonitis, Sofoklis; Harper, Mick; Hall, Stuart; Figueiredo, Nuno; Qureshi, Tahseen; Parvaiz, Amjad

2017-09-15

Robotic rectal surgery is becoming increasingly more popular among colorectal surgeons. However, time spent on robotic platform docking, arm clashing and undocking of the platform during the procedure are factors that surgeons often find cumbersome and time consuming. The newest surgical platform, the da Vinci Xi, coupled with integrated table motion can help to overcome these problems. This technical note aims to describe a standardised operative technique of single docking robotic rectal surgery using the da Vinci Xi system and integrated table motion. A stepwise approach of the da Vinci docking process and surgical technique is described accompanied by an intra-operative video that demonstrates this technique. We also present data collected from a prospectively maintained database. 33 consecutive rectal cancer patients (24 male, 9 female) received robotic rectal surgery with the da Vinci Xi during the preparation of this technical note. 29 (88%) patients had anterior resections, and four (12%) had abdominoperineal excisions. There were no conversions, no anastomotic leaks and no mortality. Median operation time was 331 (249-372) min, blood loss 20 (20-45) mls and length of stay 6.5 (4-8) days. 30-day readmission rate and re-operation rates were 3% (n = 1). This standardised technique of single docking robotic rectal surgery with the da Vinci Xi is safe, feasible and reproducible. The technological advances of the new robotic system facilitate the totally robotic single docking approach.

Evaluation of 3-D Air Quality System Remotely-Sensed Aerosol Optical Depth for the Baltimore/Washington Metropolitan Air Shed

NASA Astrophysics Data System (ADS)

Weber, S. A.; Engel-Cox, J. A.; Hoff, R. M.; Prados, A.; Zhang, H.

2008-12-01

Integrating satellite- and ground-based aerosol optical depth (AOD) observations with surface total fine particulate (PM2.5) and sulfate concentrations allows for a more comprehensive understanding of local- and urban-scale air quality. This study evaluates the utility of integrated databases being developed for NOAA and EPA through the 3D-AQS project by examining the relationship between remotely-sensed AOD and PM2.5 concentrations for each platform for the summer of 2004 and the entire year of 2005. We compare results for the Baltimore, MD/Washington, DC metropolitan air shed, incorporating AOD products from the Terra and GOES-12 satellites, AERONET sunphotometer, and ground-based lidar, and PM2.5 concentrations from five surface monitoring sites. The satellite-derived products include AOD from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Multi-angle Imaging Spectroradiometer (MISR), as well as the GOES Aerosol/Smoke Product (GASP). The vertical profile of lidar backscatter is used to retrieve the planetary boundary layer (PBL) height in an attempt to capture only that fraction of the AOD arising from near surface aerosols. Adjusting the AOD data using platform- and season-specific ratios, calculated using the parameters of the regression equations, for two case studies resulted in a more accurate representation of surface PM2.5 concentrations when compared to a constant ratio that is currently being used in the NOAA IDEA product. This work demonstrates that quantitative relationships between remotely-sensed and in-situ aerosol observations in an integrated database can be computed and applied to improve the use of remotely-sensed observations for estimating surface concentrations.

The opportunities and obstacles in developing a vascular birthmark database for clinical and research use.

PubMed

Sharma, Vishal K; Fraulin, Frankie Og; Harrop, A Robertson; McPhalen, Donald F

2011-01-01

Databases are useful tools in clinical settings. The authors review the benefits and challenges associated with the development and implementation of an efficient electronic database for the multidisciplinary Vascular Birthmark Clinic at the Alberta Children's Hospital, Calgary, Alberta. The content and structure of the database were designed using the technical expertise of a data analyst from the Calgary Health Region. Relevant clinical and demographic data fields were included with the goal of documenting ongoing care of individual patients, and facilitating future epidemiological studies of this patient population. After completion of this database, 10 challenges encountered during development were retrospectively identified. Practical solutions for these challenges are presented. THE CHALLENGES IDENTIFIED DURING THE DATABASE DEVELOPMENT PROCESS INCLUDED: identification of relevant data fields; balancing simplicity and user-friendliness with complexity and comprehensive data storage; database expertise versus clinical expertise; software platform selection; linkage of data from the previous spreadsheet to a new data management system; ethics approval for the development of the database and its utilization for research studies; ensuring privacy and limited access to the database; integration of digital photographs into the database; adoption of the database by support staff in the clinic; and maintaining up-to-date entries in the database. There are several challenges involved in the development of a useful and efficient clinical database. Awareness of these potential obstacles, in advance, may simplify the development of clinical databases by others in various surgical settings.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

PubMed

Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Pocock, Matthew; Flanagan, Keith; Hallinan, Jennifer; Wipat, Anil

2016-06-17

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

ClearedLeavesDB: an online database of cleared plant leaf images

PubMed Central

2014-01-01

Background Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers. Description The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database. Conclusions We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at http://clearedleavesdb.org. PMID:24678985

ClearedLeavesDB: an online database of cleared plant leaf images.

PubMed

Das, Abhiram; Bucksch, Alexander; Price, Charles A; Weitz, Joshua S

2014-03-28

Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers. The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database. We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at http://clearedleavesdb.org.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data

PubMed Central

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie

2018-01-01

Abstract Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. PMID:29106630

Omics databases on kidney disease: where they can be found and how to benefit from them.

PubMed

Papadopoulos, Theofilos; Krochmal, Magdalena; Cisek, Katryna; Fernandes, Marco; Husi, Holger; Stevens, Robert; Bascands, Jean-Loup; Schanstra, Joost P; Klein, Julie

2016-06-01

In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.

Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

PubMed

Dubovenko, Alexey; Nikolsky, Yuri; Rakhmatulin, Eugene; Nikolskaya, Tatiana

2017-01-01

Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

Integrated Space Asset Management Database and Modeling

NASA Technical Reports Server (NTRS)

MacLeod, Todd; Gagliano, Larry; Percy, Thomas; Mason, Shane

2015-01-01

Effective Space Asset Management is one key to addressing the ever-growing issue of space congestion. It is imperative that agencies around the world have access to data regarding the numerous active assets and pieces of space junk currently tracked in orbit around the Earth. At the center of this issues is the effective management of data of many types related to orbiting objects. As the population of tracked objects grows, so too should the data management structure used to catalog technical specifications, orbital information, and metadata related to those populations. Marshall Space Flight Center's Space Asset Management Database (SAM-D) was implemented in order to effectively catalog a broad set of data related to known objects in space by ingesting information from a variety of database and processing that data into useful technical information. Using the universal NORAD number as a unique identifier, the SAM-D processes two-line element data into orbital characteristics and cross-references this technical data with metadata related to functional status, country of ownership, and application category. The SAM-D began as an Excel spreadsheet and was later upgraded to an Access database. While SAM-D performs its task very well, it is limited by its current platform and is not available outside of the local user base. Further, while modeling and simulation can be powerful tools to exploit the information contained in SAM-D, the current system does not allow proper integration options for combining the data with both legacy and new M&S tools. This paper provides a summary of SAM-D development efforts to date and outlines a proposed data management infrastructure that extends SAM-D to support the larger data sets to be generated. A service-oriented architecture model using an information sharing platform named SIMON will allow it to easily expand to incorporate new capabilities, including advanced analytics, M&S tools, fusion techniques and user interface for visualizations. In addition, tight control of information sharing policy will increase confidence in the system, which would encourage industry partners to provide commercial data. Combined with the integration of new and legacy M&S tools, a SIMON-based architecture will provide a robust environment that can be extended and expanded indefinitely.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

PubMed

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry

DOE PAGES

Van Berkel, Gary J.; Kertesz, Vilmos

2016-11-15

An “Open Access”-like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database. These tasks were accomplished via the vendorprovided software libraries. Sample classification based on spectral comparison utilized themore » spectral contrast angle method. As a result, using the developed software platform near real-time sample classification is exemplified using a series of commercially available blue ink rollerball pens and vegetable oils. In the case of the inks, full scan positive and negative ion ESI mass spectra were both used for database generation and sample classification. For the vegetable oils, full scan positive ion mode APCI mass spectra were recorded. The overall accuracy of the employed spectral contrast angle statistical model was 95.3% and 98% in case of the inks and oils, respectively, using leave-one-out cross-validation. In conclusion, this work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching.« less

Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Berkel, Gary J.; Kertesz, Vilmos

An “Open Access”-like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database. These tasks were accomplished via the vendorprovided software libraries. Sample classification based on spectral comparison utilized themore » spectral contrast angle method. As a result, using the developed software platform near real-time sample classification is exemplified using a series of commercially available blue ink rollerball pens and vegetable oils. In the case of the inks, full scan positive and negative ion ESI mass spectra were both used for database generation and sample classification. For the vegetable oils, full scan positive ion mode APCI mass spectra were recorded. The overall accuracy of the employed spectral contrast angle statistical model was 95.3% and 98% in case of the inks and oils, respectively, using leave-one-out cross-validation. In conclusion, this work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching.« less

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

PubMed

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

2014-01-01

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

PubMed

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-04

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

PubMed

Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

2010-02-04

Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects. Available on the web at: http://sourceforge.net/projects/cnv.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Po-E; Lo, Chien -Chi; Anderson, Joseph J.

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the easemore » of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.« less

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

PubMed Central

Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J.; Davenport, Karen W.; Bishop-Lilly, Kimberly A.; Xu, Yan; Ahmed, Sanaa; Feng, Shihai; Mokashi, Vishwesh P.; Chain, Patrick S.G.

2017-01-01

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. PMID:27899609

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

DOE PAGES

Li, Po-E; Lo, Chien -Chi; Anderson, Joseph J.; ...

2016-11-24

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the easemore » of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.« less

Literature evidence in open targets - a target validation platform.

PubMed

Kafkas, Şenay; Dunham, Ian; McEntyre, Johanna

2017-06-06

We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-disease associations in documents and ranks the documents based on their confidence from the Europe PMC literature database, by using rules utilising expert-provided heuristic information. The confidence score of a given document represents how valuable the document is in the scope of target validation for a given target-disease association by taking into account the credibility of the association based on the properties of the text. The component serves the platform regularly with the up-to-date data since December, 2015. Currently, there are a total number of 1168365 distinct target-disease associations text mined from >26 million PubMed abstracts and >1.2 million Open Access full text articles. Our comparative analyses on the current available evidence data in the platform revealed that 850179 of these associations are exclusively identified by literature mining. This component helps the platform's users by providing the most relevant literature hits for a given target and disease. The text mining evidence along with the other types of evidence can be explored visually through https://www.targetvalidation.org and all the evidence data is available for download in json format from https://www.targetvalidation.org/downloads/data .

A study on spatial decision support systems for HIV/AIDS prevention based on COM GIS technology

NASA Astrophysics Data System (ADS)

Yang, Kun; Luo, Huasong; Peng, Shungyun; Xu, Quanli

2007-06-01

Based on the deeply analysis of the current status and the existing problems of GIS technology applications in Epidemiology, this paper has proposed the method and process for establishing the spatial decision support systems of AIDS epidemic prevention by integrating the COM GIS, Spatial Database, GPS, Remote Sensing, and Communication technologies, as well as ASP and ActiveX software development technologies. One of the most important issues for constructing the spatial decision support systems of AIDS epidemic prevention is how to integrate the AIDS spreading models with GIS. The capabilities of GIS applications in the AIDS epidemic prevention have been described here in this paper firstly. Then some mature epidemic spreading models have also been discussed for extracting the computation parameters. Furthermore, a technical schema has been proposed for integrating the AIDS spreading models with GIS and relevant geospatial technologies, in which the GIS and model running platforms share a common spatial database and the computing results can be spatially visualized on Desktop or Web GIS clients. Finally, a complete solution for establishing the decision support systems of AIDS epidemic prevention has been offered in this paper based on the model integrating methods and ESRI COM GIS software packages. The general decision support systems are composed of data acquisition sub-systems, network communication sub-systems, model integrating sub-systems, AIDS epidemic information spatial database sub-systems, AIDS epidemic information querying and statistical analysis sub-systems, AIDS epidemic dynamic surveillance sub-systems, AIDS epidemic information spatial analysis and decision support sub-systems, as well as AIDS epidemic information publishing sub-systems based on Web GIS.

Development of water environment information management and water pollution accident response system

NASA Astrophysics Data System (ADS)

Zhang, J.; Ruan, H.

2009-12-01

In recent years, many water pollution accidents occurred with the rapid economical development. In this study, water environment information management and water pollution accident response system are developed based on geographic information system (GIS) techniques. The system integrated spatial database, attribute database, hydraulic model, and water quality model under a user-friendly interface in a GIS environment. System ran in both Client/Server (C/S) and Browser/Server (B/S) platform which focused on model and inquiry respectively. System provided spatial and attribute data inquiry, water quality evaluation, statics, water pollution accident response case management (opening reservoir etc) and 2D and 3D visualization function, and gave assistant information to make decision on water pollution accident response. Polluted plume in Huaihe River were selected to simulate the transport of pollutes.

mantisGRID: a grid platform for DICOM medical images management in Colombia and Latin America.

PubMed

Garcia Ruiz, Manuel; Garcia Chaves, Alvin; Ruiz Ibañez, Carlos; Gutierrez Mazo, Jorge Mario; Ramirez Giraldo, Juan Carlos; Pelaez Echavarria, Alejandro; Valencia Diaz, Edison; Pelaez Restrepo, Gustavo; Montoya Munera, Edwin Nelson; Garcia Loaiza, Bernardo; Gomez Gonzalez, Sebastian

2011-04-01

This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.

Research on spatio-temporal database techniques for spatial information service

NASA Astrophysics Data System (ADS)

Zhao, Rong; Wang, Liang; Li, Yuxiang; Fan, Rongshuang; Liu, Ping; Li, Qingyuan

2007-06-01

Geographic data should be described by spatial, temporal and attribute components, but the spatio-temporal queries are difficult to be answered within current GIS. This paper describes research into the development and application of spatio-temporal data management system based upon GeoWindows GIS software platform which was developed by Chinese Academy of Surveying and Mapping (CASM). Faced the current and practical requirements of spatial information application, and based on existing GIS platform, one kind of spatio-temporal data model which integrates vector and grid data together was established firstly. Secondly, we solved out the key technique of building temporal data topology, successfully developed a suit of spatio-temporal database management system adopting object-oriented methods. The system provides the temporal data collection, data storage, data management and data display and query functions. Finally, as a case study, we explored the application of spatio-temporal data management system with the administrative region data of multi-history periods of China as the basic data. With all the efforts above, the GIS capacity of management and manipulation in aspect of time and attribute of GIS has been enhanced, and technical reference has been provided for the further development of temporal geographic information system (TGIS).

Bringing Web 2.0 to bioinformatics.

PubMed

Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

2009-01-01

Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

The Design and Implementation of Network Teaching Platform Basing on .NET

NASA Astrophysics Data System (ADS)

Yanna, Ren

This paper addresses the problem that students under traditional teaching model have poor operation ability and studies in depth the network teaching platform in domestic colleges and universities, proposing the design concept of network teaching platform of NET + C # + SQL excellent course and designing the overall structure, function module and back-end database of the platform. This paper emphatically expounds the use of MD5 encryption techniques in order to solve data security problems and the assessment of student learning using ADO.NET database access technology as well as the mathematical formula. The example shows that the network teaching platform developed by using WEB application technology has higher safety and availability, and thus improves the students' operation ability.

Computer-Aided Systems Engineering for Flight Research Projects Using a Workgroup Database

NASA Technical Reports Server (NTRS)

Mizukami, Masahi

2004-01-01

An online systems engineering tool for flight research projects has been developed through the use of a workgroup database. Capabilities are implemented for typical flight research systems engineering needs in document library, configuration control, hazard analysis, hardware database, requirements management, action item tracking, project team information, and technical performance metrics. Repetitive tasks are automated to reduce workload and errors. Current data and documents are instantly available online and can be worked on collaboratively. Existing forms and conventional processes are used, rather than inventing or changing processes to fit the tool. An integrated tool set offers advantages by automatically cross-referencing data, minimizing redundant data entry, and reducing the number of programs that must be learned. With a simplified approach, significant improvements are attained over existing capabilities for minimal cost. By using a workgroup-level database platform, personnel most directly involved in the project can develop, modify, and maintain the system, thereby saving time and money. As a pilot project, the system has been used to support an in-house flight experiment. Options are proposed for developing and deploying this type of tool on a more extensive basis.

GARNET--gene set analysis with exploration of annotation relations.

PubMed

Rho, Kyoohyoung; Kim, Bumjin; Jang, Youngjun; Lee, Sanghyun; Bae, Taejeong; Seo, Jihae; Seo, Chaehwa; Lee, Jihyun; Kang, Hyunjung; Yu, Ungsik; Kim, Sunghoon; Lee, Sanghyuk; Kim, Wan Kyu

2011-02-15

Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information. GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).

The International Experimental Thermal Hydraulic Systems database – TIETHYS: A new NEA validation tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rohatgi, Upendra S.

Nuclear reactor codes require validation with appropriate data representing the plant for specific scenarios. The thermal-hydraulic data is scattered in different locations and in different formats. Some of the data is in danger of being lost. A relational database is being developed to organize the international thermal hydraulic test data for various reactor concepts and different scenarios. At the reactor system level, that data is organized to include separate effect tests and integral effect tests for specific scenarios and corresponding phenomena. The database relies on the phenomena identification sections of expert developed PIRTs. The database will provide a summary ofmore » appropriate data, review of facility information, test description, instrumentation, references for the experimental data and some examples of application of the data for validation. The current database platform includes scenarios for PWR, BWR, VVER, and specific benchmarks for CFD modelling data and is to be expanded to include references for molten salt reactors. There are place holders for high temperature gas cooled reactors, CANDU and liquid metal reactors. This relational database is called The International Experimental Thermal Hydraulic Systems (TIETHYS) database and currently resides at Nuclear Energy Agency (NEA) of the OECD and is freely open to public access. Going forward the database will be extended to include additional links and data as they become available. https://www.oecd-nea.org/tiethysweb/« less

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

Readiness of Sub-Saharan Africa Healthcare Systems for the New Pandemic, Diabetes: A Systematic Review

PubMed Central

2018-01-01

Background Effective health systems are needed to care for the coming surge of diabetics in sub-Saharan Africa (SSA). Objective We conducted a systematic review of literature to determine the capacity of SSA health systems to manage diabetes. Methodology We used three different databases (Embase, Scopus, and PubMed) to search for studies, published from 2004 to 2017, on diabetes care in SSA. Results Fifty-five articles met the inclusion criteria, covering the different aspects related to diabetes care such as availability of drugs and diagnostic tools, the capacity of healthcare workers, and the integration of diabetes care into HIV and TB platforms. Conclusion Although chronic care health systems in SSA have developed significantly in the last decade, the capacity for managing diabetes remains in its infancy. We identified pilot projects to enhance these capacities. The scale-up of these pilot interventions and the integration of diabetes care into existing robust chronic disease platforms may be a feasible approach to begin to tackle the upcoming pandemic in diabetes. Nonetheless, much more work needs to be done to address the health system-wide deficiencies in diabetes care. More research is also needed to determine how to integrate diabetes care into the healthcare system in SSA. PMID:29670916

Human Disease Insight: An integrated knowledge-based platform for disease-gene-drug information.

PubMed

Tasleem, Munazzah; Ishrat, Romana; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2016-01-01

The scope of the Human Disease Insight (HDI) database is not limited to researchers or physicians as it also provides basic information to non-professionals and creates disease awareness, thereby reducing the chances of patient suffering due to ignorance. HDI is a knowledge-based resource providing information on human diseases to both scientists and the general public. Here, our mission is to provide a comprehensive human disease database containing most of the available useful information, with extensive cross-referencing. HDI is a knowledge management system that acts as a central hub to access information about human diseases and associated drugs and genes. In addition, HDI contains well-classified bioinformatics tools with helpful descriptions. These integrated bioinformatics tools enable researchers to annotate disease-specific genes and perform protein analysis, search for biomarkers and identify potential vaccine candidates. Eventually, these tools will facilitate the analysis of disease-associated data. The HDI provides two types of search capabilities and includes provisions for downloading, uploading and searching disease/gene/drug-related information. The logistical design of the HDI allows for regular updating. The database is designed to work best with Mozilla Firefox and Google Chrome and is freely accessible at http://humandiseaseinsight.com. Copyright © 2015 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

MEMOSys: Bioinformatics platform for genome-scale metabolic models

PubMed Central

2011-01-01

Background Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. Results MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. Conclusions We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys. PMID:21276275

InverPep: A database of invertebrate antimicrobial peptides.

PubMed

Gómez, Esteban A; Giraldo, Paula; Orduz, Sergio

2017-03-01

The aim of this work was to construct InverPep, a database specialised in experimentally validated antimicrobial peptides (AMPs) from invertebrates. AMP data contained in InverPep were manually curated from other databases and the scientific literature. MySQL was integrated with the development platform Laravel; this framework allows to integrate programming in PHP with HTML and was used to design the InverPep web page's interface. InverPep contains 18 separated fields, including InverPep code, phylum and species source, peptide name, sequence, peptide length, secondary structure, molar mass, charge, isoelectric point, hydrophobicity, Boman index, aliphatic index and percentage of hydrophobic amino acids. CALCAMPI, an algorithm to calculate the physicochemical properties of multiple peptides simultaneously, was programmed in PERL language. To date, InverPep contains 702 experimentally validated AMPs from invertebrate species. All of the peptides contain information associated with their source, physicochemical properties, secondary structure, biological activity and links to external literature. Most AMPs in InverPep have a length between 10 and 50 amino acids, a positive charge, a Boman index between 0 and 2 kcal/mol, and 30-50% hydrophobic amino acids. InverPep includes 33 AMPs not reported in other databases. Besides, CALCAMPI and statistical analysis of InverPep data is presented. The InverPep database is available in English and Spanish. InverPep is a useful database to study invertebrate AMPs and its information could be used for the design of new peptides. The user-friendly interface of InverPep and its information can be freely accessed via a web-based browser at http://ciencias.medellin.unal.edu.co/gruposdeinvestigacion/prospeccionydisenobiomoleculas/InverPep/public/home_en. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb).

PubMed

Baldwin, Thomas T; Basenko, Evelina; Harb, Omar; Brown, Neil A; Urban, Martin; Hammond-Kosack, Kim E; Bregitzer, Phil P

2018-06-01

There is no comprehensive storage for generated mutants of Fusarium graminearum or data associated with these mutants. Instead, researchers relied on several independent and non-integrated databases. FgMutantDb was designed as a simple spreadsheet that is accessible globally on the web that will function as a centralized source of information on F. graminearum mutants. FgMutantDb aids in the maintenance and sharing of mutants within a research community. It will serve also as a platform for disseminating prepublication results as well as negative results that often go unreported. Additionally, the highly curated information on mutants in FgMutantDb will be shared with other databases (FungiDB, Ensembl, PhytoPath, and PHI-base) through updating reports. Here we describe the creation and potential usefulness of FgMutantDb to the F. graminearum research community, and provide a tutorial on its use. This type of database could be easily emulated for other fungal species. Published by Elsevier Inc.

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

PubMed

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

PubMed Central

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information. PMID:28234924

MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

PubMed Central

Montague, Elizabeth; Stanberry, Larissa; Higdon, Roger; Janko, Imre; Lee, Elaine; Anderson, Nathaniel; Choiniere, John; Stewart, Elizabeth; Yandl, Gregory; Broomall, William; Kolker, Natali

2014-01-01

Abstract Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding. PMID:24910945

MetPetDB: A database for metamorphic geochemistry

NASA Astrophysics Data System (ADS)

Spear, Frank S.; Hallett, Benjamin; Pyle, Joseph M.; Adalı, Sibel; Szymanski, Boleslaw K.; Waters, Anthony; Linder, Zak; Pearce, Shawn O.; Fyffe, Matthew; Goldfarb, Dennis; Glickenhouse, Nickolas; Buletti, Heather

2009-12-01

We present a data model for the initial implementation of MetPetDB, a geochemical database specific to metamorphic rock samples. The database is designed around the concept of preservation of spatial relationships, at all scales, of chemical analyses and their textural setting. Objects in the database (samples) represent physical rock samples; each sample may contain one or more subsamples with associated geochemical and image data. Samples, subsamples, geochemical data, and images are described with attributes (some required, some optional); these attributes also serve as search delimiters. All data in the database are classified as published (i.e., archived or published data), public or private. Public and published data may be freely searched and downloaded. All private data is owned; permission to view, edit, download and otherwise manipulate private data may be granted only by the data owner; all such editing operations are recorded by the database to create a data version log. The sharing of data permissions among a group of collaborators researching a common sample is done by the sample owner through the project manager. User interaction with MetPetDB is hosted by a web-based platform based upon the Java servlet application programming interface, with the PostgreSQL relational database. The database web portal includes modules that allow the user to interact with the database: registered users may save and download public and published data, upload private data, create projects, and assign permission levels to project collaborators. An Image Viewer module provides for spatial integration of image and geochemical data. A toolkit consisting of plotting and geochemical calculation software for data analysis and a mobile application for viewing the public and published data is being developed. Future issues to address include population of the database, integration with other geochemical databases, development of the analysis toolkit, creation of data models for derivative data, and building a community-wide user base. It is believed that this and other geochemical databases will enable more productive collaborations, generate more efficient research efforts, and foster new developments in basic research in the field of solid earth geochemistry.

HIPdb: a database of experimentally validated HIV inhibiting peptides.

PubMed

Qureshi, Abid; Thakur, Nishant; Kumar, Manoj

2013-01-01

Besides antiretroviral drugs, peptides have also demonstrated potential to inhibit the Human immunodeficiency virus (HIV). For example, T20 has been discovered to effectively block the HIV entry and was approved by the FDA as a novel anti-HIV peptide (AHP). We have collated all experimental information on AHPs at a single platform. HIPdb is a manually curated database of experimentally verified HIV inhibiting peptides targeting various steps or proteins involved in the life cycle of HIV e.g. fusion, integration, reverse transcription etc. This database provides experimental information of 981 peptides. These are of varying length obtained from natural as well as synthetic sources and tested on different cell lines. Important fields included are peptide sequence, length, source, target, cell line, inhibition/IC(50), assay and reference. The database provides user friendly browse, search, sort and filter options. It also contains useful services like BLAST and 'Map' for alignment with user provided sequences. In addition, predicted structure and physicochemical properties of the peptides are also included. HIPdb database is freely available at http://crdd.osdd.net/servers/hipdb. Comprehensive information of this database will be helpful in selecting/designing effective anti-HIV peptides. Thus it may prove a useful resource to researchers for peptide based therapeutics development.

Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures

PubMed Central

2010-01-01

Background Papaver somniferum (opium poppy) is the source for several pharmaceutical benzylisoquinoline alkaloids including morphine, the codeine and sanguinarine. In response to treatment with a fungal elicitor, the biosynthesis and accumulation of sanguinarine is induced along with other plant defense responses in opium poppy cell cultures. The transcriptional induction of alkaloid metabolism in cultured cells provides an opportunity to identify components of this process via the integration of deep transcriptome and proteome databases generated using next-generation technologies. Results A cDNA library was prepared for opium poppy cell cultures treated with a fungal elicitor for 10 h. Using 454 GS-FLX Titanium pyrosequencing, 427,369 expressed sequence tags (ESTs) with an average length of 462 bp were generated. Assembly of these sequences yielded 93,723 unigenes, of which 23,753 were assigned Gene Ontology annotations. Transcripts encoding all known sanguinarine biosynthetic enzymes were identified in the EST database, 5 of which were represented among the 50 most abundant transcripts. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) of total protein extracts from cell cultures treated with a fungal elicitor for 50 h facilitated the identification of 1,004 proteins. Proteins were fractionated by one-dimensional SDS-PAGE and digested with trypsin prior to LC-MS/MS analysis. Query of an opium poppy-specific EST database substantially enhanced peptide identification. Eight out of 10 known sanguinarine biosynthetic enzymes and many relevant primary metabolic enzymes were represented in the peptide database. Conclusions The integration of deep transcriptome and proteome analyses provides an effective platform to catalogue the components of secondary metabolism, and to identify genes encoding uncharacterized enzymes. The establishment of corresponding transcript and protein databases generated by next-generation technologies in a system with a well-defined metabolite profile facilitates an improved linkage between genes, enzymes, and pathway components. The proteome database represents the most relevant alkaloid-producing enzymes, compared with the much deeper and more complete transcriptome library. The transcript database contained full-length mRNAs encoding most alkaloid biosynthetic enzymes, which is a key requirement for the functional characterization of novel gene candidates. PMID:21083930

VSDMIP: virtual screening data management on an integrated platform

NASA Astrophysics Data System (ADS)

Gil-Redondo, Rubén; Estrada, Jorge; Morreale, Antonio; Herranz, Fernando; Sancho, Javier; Ortiz, Ángel R.

2009-03-01

A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.

Andromeda: a peptide search engine integrated into the MaxQuant environment.

PubMed

Cox, Jürgen; Neuhauser, Nadin; Michalski, Annette; Scheltema, Richard A; Olsen, Jesper V; Mann, Matthias

2011-04-01

A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.

TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

PubMed

Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

2018-01-04

Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

EST-PAC a web package for EST annotation and protein sequence prediction

PubMed Central

Strahm, Yvan; Powell, David; Lefèvre, Christophe

2006-01-01

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics. PMID:17147782

DialysisNet: Application for Integrating and Management Data Sources of Hemodialysis Information by Continuity of Care Record.

PubMed

Ku, Ho Suk; Kim, Sungho; Kim, HyeHyeon; Chung, Hee-Joon; Park, Yu Rang; Kim, Ju Han

2014-04-01

Health Avatar Beans was for the management of chronic kidney disease and end-stage renal disease (ESRD). This article is about the DialysisNet system in Health Avatar Beans for the seamless management of ESRD based on the personal health record. For hemodialysis data modeling, we identified common data elements for hemodialysis information (CDEHI). We used ASTM continuity of care record (CCR) and ISO/IEC 11179 for the compliance method with a standard model for the CDEHI. According to the contents of the ASTM CCR, we mapped the CDHEI to the contents and created the metadata from that. It was transformed and parsed into the database and verified according to the ASTM CCR/XML schema definition (XSD). DialysisNet was created as an iPad application. The contents of the CDEHI were categorized for effective management. For the evaluation of information transfer, we used CarePlatform, which was developed for data access. The metadata of CDEHI in DialysisNet was exchanged by the CarePlatform with semantic interoperability. The CDEHI was separated into a content list for individual patient data, a contents list for hemodialysis center data, consultation and transfer form, and clinical decision support data. After matching to the CCR, the CDEHI was transformed to metadata, and it was transformed to XML and proven according to the ASTM CCR/XSD. DialysisNet has specific consideration of visualization, graphics, images, statistics, and database. We created the DialysisNet application, which can integrate and manage data sources for hemodialysis information based on CCR standards.

SeqHound: biological sequence and structure database as a platform for bioinformatics research

PubMed Central

2002-01-01

Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit. PMID:12401134

Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry.

PubMed

Van Berkel, Gary J; Kertesz, Vilmos

2017-02-15

An "Open Access"-like mass spectrometric platform to fully utilize the simplicity of the manual open port sampling interface for rapid characterization of unprocessed samples by liquid introduction atmospheric pressure ionization mass spectrometry has been lacking. The in-house developed integrated software with a simple, small and relatively low-cost mass spectrometry system introduced here fills this void. Software was developed to operate the mass spectrometer, to collect and process mass spectrometric data files, to build a database and to classify samples using such a database. These tasks were accomplished via the vendor-provided software libraries. Sample classification based on spectral comparison utilized the spectral contrast angle method. Using the developed software platform near real-time sample classification is exemplified using a series of commercially available blue ink rollerball pens and vegetable oils. In the case of the inks, full scan positive and negative ion ESI mass spectra were both used for database generation and sample classification. For the vegetable oils, full scan positive ion mode APCI mass spectra were recorded. The overall accuracy of the employed spectral contrast angle statistical model was 95.3% and 98% in case of the inks and oils, respectively, using leave-one-out cross-validation. This work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes

PubMed Central

Kim, Mara; Cooper, Brian A.; Venkat, Rohit; Phillips, Julie B.; Eidem, Haley R.; Hirbo, Jibril; Nutakki, Sashank; Williams, Scott M.; Muglia, Louis J.; Capra, J. Anthony; Petren, Kenneth; Abbot, Patrick; Rokas, Antonis; McGary, Kriston L.

2016-01-01

Mammalian gestation and pregnancy are fast evolving processes that involve the interaction of the fetal, maternal and paternal genomes. Version 1.0 of the GEneSTATION database (http://genestation.org) integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. GEneSTATION is built using tools from the Generic Model Organism Database project, including the biology-aware database CHADO, new tools for rapid data integration, and algorithms that streamline synthesis and user access. GEneSTATION contains curated life history information on pregnancy and reproduction from 23 high-quality mammalian genomes. For every human gene, GEneSTATION contains diverse evolutionary (e.g. gene age, population genetic and molecular evolutionary statistics), organismal (e.g. tissue-specific gene and protein expression, differential gene expression, disease phenotype), and molecular data types (e.g. Gene Ontology Annotation, protein interactions), as well as links to many general (e.g. Entrez, PubMed) and pregnancy disease-specific (e.g. PTBgene, dbPTB) databases. By facilitating the synthesis of diverse functional and evolutionary data in pregnancy-associated tissues and phenotypes and enabling their quick, intuitive, accurate and customized meta-analysis, GEneSTATION provides a novel platform for comprehensive investigation of the function and evolution of mammalian pregnancy. PMID:26567549

Semantically Interoperable XML Data

PubMed Central

Vergara-Niedermayr, Cristobal; Wang, Fusheng; Pan, Tony; Kurc, Tahsin; Saltz, Joel

2013-01-01

XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups. PMID:25298789

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

PubMed

Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

EasyKSORD: A Platform of Keyword Search Over Relational Databases

NASA Astrophysics Data System (ADS)

Peng, Zhaohui; Li, Jing; Wang, Shan

Keyword Search Over Relational Databases (KSORD) enables casual users to use keyword queries (a set of keywords) to search relational databases just like searching the Web, without any knowledge of the database schema or any need of writing SQL queries. Based on our previous work, we design and implement a novel KSORD platform named EasyKSORD for users and system administrators to use and manage different KSORD systems in a novel and simple manner. EasyKSORD supports advanced queries, efficient data-graph-based search engines, multiform result presentations, and system logging and analysis. Through EasyKSORD, users can search relational databases easily and read search results conveniently, and system administrators can easily monitor and analyze the operations of KSORD and manage KSORD systems much better.

P2P proteomics -- data sharing for enhanced protein identification

PubMed Central

2012-01-01

Background In order to tackle the important and challenging problem in proteomics of identifying known and new protein sequences using high-throughput methods, we propose a data-sharing platform that uses fully distributed P2P technologies to share specifications of peer-interaction protocols and service components. By using such a platform, information to be searched is no longer centralised in a few repositories but gathered from experiments in peer proteomics laboratories, which can subsequently be searched by fellow researchers. Methods The system distributively runs a data-sharing protocol specified in the Lightweight Communication Calculus underlying the system through which researchers interact via message passing. For this, researchers interact with the system through particular components that link to database querying systems based on BLAST and/or OMSSA and GUI-based visualisation environments. We have tested the proposed platform with data drawn from preexisting MS/MS data reservoirs from the 2006 ABRF (Association of Biomolecular Resource Facilities) test sample, which was extensively tested during the ABRF Proteomics Standards Research Group 2006 worldwide survey. In particular we have taken the data available from a subset of proteomics laboratories of Spain's National Institute for Proteomics, ProteoRed, a network for the coordination, integration and development of the Spanish proteomics facilities. Results and Discussion We performed queries against nine databases including seven ProteoRed proteomics laboratories, the NCBI Swiss-Prot database and the local database of the CSIC/UAB Proteomics Laboratory. A detailed analysis of the results indicated the presence of a protein that was supported by other NCBI matches and highly scored matches in several proteomics labs. The analysis clearly indicated that the protein was a relatively high concentrated contaminant that could be present in the ABRF sample. This fact is evident from the information that could be derived from the proposed P2P proteomics system, however it is not straightforward to arrive to the same conclusion by conventional means as it is difficult to discard organic contamination of samples. The actual presence of this contaminant was only stated after the ABRF study of all the identifications reported by the laboratories. PMID:22293032

Real-time Monitoring of Subsea Gas Pipelines, Offshore Platforms, and Ship Inspection Scores Using an Automatic Identification System

NASA Astrophysics Data System (ADS)

Artana, K. B.; Pitana, T.; Dinariyana, D. P.; Ariana, M.; Kristianto, D.; Pratiwi, E.

2018-06-01

The aim of this research is to develop an algorithm and application that can perform real-time monitoring of the safety operation of offshore platforms and subsea gas pipelines as well as determine the need for ship inspection using data obtained from automatic identification system (AIS). The research also focuses on the integration of shipping database, AIS data, and others to develop a prototype for designing a real-time monitoring system of offshore platforms and pipelines. A simple concept is used in the development of this prototype, which is achieved by using an overlaying map that outlines the coordinates of the offshore platform and subsea gas pipeline with the ship's coordinates (longitude/latitude) as detected by AIS. Using such information, we can then build an early warning system (EWS) relayed through short message service (SMS), email, or other means when the ship enters the restricted and exclusion zone of platforms and pipelines. The ship inspection system is developed by combining several attributes. Then, decision analysis software is employed to prioritize the vessel's four attributes, including ship age, ship type, classification, and flag state. Results show that the EWS can increase the safety level of offshore platforms and pipelines, as well as the efficient use of patrol boats in monitoring the safety of the facilities. Meanwhile, ship inspection enables the port to prioritize the ship to be inspected in accordance with the priority ranking inspection score.

Framework Design of Unified Cross-Authentication Based on the Fourth Platform Integrated Payment

NASA Astrophysics Data System (ADS)

Yong, Xu; Yujin, He

The essay advances a unified authentication based on the fourth integrated payment platform. The research aims at improving the compatibility of the authentication in electronic business and providing a reference for the establishment of credit system by seeking a way to carry out a standard unified authentication on a integrated payment platform. The essay introduces the concept of the forth integrated payment platform and finally put forward the whole structure and different components. The main issue of the essay is about the design of the credit system of the fourth integrated payment platform and the PKI/CA structure design.

The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va

Computational framework to support integration of biomolecular and clinical data within a translational approach.

PubMed

Miyoshi, Newton Shydeo Brandão; Pinheiro, Daniel Guariz; Silva, Wilson Araújo; Felipe, Joaquim Cezar

2013-06-06

The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.

Publishing Data on Physical Samples Using the GeoLink Ontology and Linked Data Platforms

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K. A.; Song, L.; Carter, M. R.; Hsu, L.

2015-12-01

Interdisciplinary Earth Data Alliance (IEDA), one of partners in EarthCube GeoLink project, seeks to explore the extent to which the use of GeoLink reusable Ontology Design Patterns (ODPs) and linked data platforms in IEDA data infrastructure can make research data more easily accessible and valuable. Linked data for the System for Earth Sample Registration (SESAR) is the first effort of IEDA to show how linked data enhance the presentation of IEDA data system architecture. SESAR Linked Data maps each table and column in SESAR database to RDF class and property based on GeoLink view, which build on the top of GeoLink ODPs. Then, uses D2RQ dumping the contents of SESAR database into RDF triples on the basis of mapping results. And, the dumped RDF triples is loaded into GRAPHDB, an RDF graph database, as permanent data in the form of atomic facts expressed as subjects, predicates and objects which provide support for semantic interoperability between IEDA and other GeoLink partners. Finally, an integrated browsing and searching interface build on Callimachus, a highly scalable platform for publishing linked data, is introduced to make sense of data stored in triplestore. Drill down and through features are built in the interface to help users locating content efficiently. The drill down feature enables users to explore beyond the summary information in the instance list of a specific class and into the detail from the specific instance page. The drill through feature enables users to jump from one instance to another one by simply clicking the link of the latter nested in the former region. Additionally, OpenLayers map is embedded into the interface to enhance the attractiveness of the presentation of instance which has geospatial information. Furthermore, by linking instances in the SESAR datasets to matching or corresponding instances in external sets, the presentation has been enriched with additional information about related classes like person, cruise, etc.

The multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) high performance computing infrastructure: applications in neuroscience and neuroinformatics research

PubMed Central

Goscinski, Wojtek J.; McIntosh, Paul; Felzmann, Ulrich; Maksimenko, Anton; Hall, Christopher J.; Gureyev, Timur; Thompson, Darren; Janke, Andrew; Galloway, Graham; Killeen, Neil E. B.; Raniga, Parnesh; Kaluza, Owen; Ng, Amanda; Poudel, Govinda; Barnes, David G.; Nguyen, Toan; Bonnington, Paul; Egan, Gary F.

2014-01-01

The Multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) is a national imaging and visualization facility established by Monash University, the Australian Synchrotron, the Commonwealth Scientific Industrial Research Organization (CSIRO), and the Victorian Partnership for Advanced Computing (VPAC), with funding from the National Computational Infrastructure and the Victorian Government. The MASSIVE facility provides hardware, software, and expertise to drive research in the biomedical sciences, particularly advanced brain imaging research using synchrotron x-ray and infrared imaging, functional and structural magnetic resonance imaging (MRI), x-ray computer tomography (CT), electron microscopy and optical microscopy. The development of MASSIVE has been based on best practice in system integration methodologies, frameworks, and architectures. The facility has: (i) integrated multiple different neuroimaging analysis software components, (ii) enabled cross-platform and cross-modality integration of neuroinformatics tools, and (iii) brought together neuroimaging databases and analysis workflows. MASSIVE is now operational as a nationally distributed and integrated facility for neuroinfomatics and brain imaging research. PMID:24734019

GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.

PubMed

Young, Nelson; Chang, Zhan; Wishart, David S

2004-04-12

GelScape is a web-based tool that permits facile, interactive annotation, comparison, manipulation and storage of protein gel images. It uses Java applet-servlet technology to allow rapid, remote image handling and image processing in a platform-independent manner. It supports many of the features found in commercial, stand-alone gel analysis software including spot annotation, spot integration, gel warping, image resizing, HTML image mapping, image overlaying as well as the storage of gel image and gel annotation data in compliance with Federated Gel Database requirements.

Remote monitoring of cardiovascular implanted electronic devices: a paradigm shift for the 21st century.

PubMed

Cronin, Edmond M; Varma, Niraj

2012-07-01

Traditional follow-up of cardiac implantable electronic devices involves the intermittent download of largely nonactionable data. Remote monitoring represents a paradigm shift from episodic office-based follow-up to continuous monitoring of device performance and patient and disease state. This lessens device clinical burden and may also lead to cost savings, although data on economic impact are only beginning to emerge. Remote monitoring technology has the potential to improve the outcomes through earlier detection of arrhythmias and compromised device integrity, and possibly predict heart failure hospitalizations through integration of heart failure diagnostics and hemodynamic monitors. Remote monitoring platforms are also huge databases of patients and devices, offering unprecedented opportunities to investigate real-world outcomes. Here, the current status of the field is described and future directions are predicted.

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K. Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-01

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. PMID:26467476

The Qatar National Historic Environment Record: a Platform for the Development of a Fully-Integrated Cultural Heritage Management Application

NASA Astrophysics Data System (ADS)

Cuttler, R. T. H.; Tonner, T. W. W.; Al-Naimi, F. A.; Dingwall, L. M.; Al-Hemaidi, N.

2013-07-01

The development of the Qatar National Historic Environment Record (QNHER) by the Qatar Museums Authority and the University of Birmingham in 2008 was based on a customised, bilingual Access database and ArcGIS. While both platforms are stable and well supported, neither was designed for the documentation and retrieval of cultural heritage data. As a result it was decided to develop a custom application using Open Source code. The core module of this application is now completed and is orientated towards the storage and retrieval of geospatial heritage data for the curation of heritage assets. Based on MIDAS Heritage data standards and regionally relevant thesauri, it is a truly bilingual system. Significant attention has been paid to the user interface, which is userfriendly and intuitive. Based on a suite of web services and accessed through a web browser, the system makes full use of internet resources such as Google Maps and Bing Maps. The application avoids long term vendor ''tie-ins'' and as a fully integrated data management system, is now an important tool for both cultural resource managers and heritage researchers in Qatar.

An integrated telemedicine platform for the assessment of affective physiological states

PubMed Central

Katsis, Christos D; Ganiatsas, George; Fotiadis, Dimitrios I

2006-01-01

AUBADE is an integrated platform built for the affective assessment of individuals. The system performs evaluation of the emotional state by classifying vectors of features extracted from: facial Electromyogram, Respiration, Electrodermal Activity and Electrocardiogram. The AUBADE system consists of: (a) a multisensorial wearable, (b) a data acquisition and wireless communication module, (c) a feature extraction module, (d) a 3D facial animation module which is used for the projection of the obtained data through a generic 3D face model; whereas the end-user will be able to view the facial expression of the subject in real time, (e) an intelligent emotion recognition module, and (f) the AUBADE databases where the acquired signals along with the subject's animation videos are saved. The system is designed to be applied to human subjects operating under extreme stress conditions, in particular car racing drivers, and also to patients suffering from neurological and psychological disorders. AUBADE's classification accuracy into five predefined emotional classes (high stress, low stress, disappointment, euphoria and neutral face) is 86.0%. The pilot system applications and components are being tested and evaluated on Maserati's car. racing drivers. PMID:16879757

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.

PubMed

Li, Po-E; Lo, Chien-Chi; Anderson, Joseph J; Davenport, Karen W; Bishop-Lilly, Kimberly A; Xu, Yan; Ahmed, Sanaa; Feng, Shihai; Mokashi, Vishwesh P; Chain, Patrick S G

2017-01-09

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

SCALEUS: Semantic Web Services Integration for Biomedical Applications.

PubMed

Sernadela, Pedro; González-Castro, Lorena; Oliveira, José Luís

2017-04-01

In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies.

PubMed

Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas

2016-09-23

The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users' own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences

PubMed Central

Stephens, Susie M.; Chen, Jake Y.; Davidson, Marcel G.; Thomas, Shiby; Trute, Barry M.

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html PMID:15608287

The eBioKit, a stand-alone educational platform for bioinformatics.

PubMed

Hernández-de-Diego, Rafael; de Villiers, Etienne P; Klingström, Tomas; Gourlé, Hadrien; Conesa, Ana; Bongcam-Rudloff, Erik

2017-09-01

Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.

Identification of beer spoilage microorganisms using the MALDI Biotyper platform.

PubMed

Turvey, Michelle Elizabeth; Weiland, Florian; Meneses, Jon; Sterenberg, Nick; Hoffmann, Peter

2016-03-01

Beer spoilage microorganisms present a major risk for the brewing industry and can lead to cost-intensive recall of contaminated products and damage to brand reputation. The applicability of molecular profiling using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) in combination with Biotyper software was investigated for the identification of beer spoilage microorganisms from routine brewery quality control samples. Reference mass spectrum profiles for three of the most common bacterial beer spoilage microorganisms (Lactobacillus lindneri, Lactobacillus brevis and Pediococcus damnosus), four commercially available brewing yeast strains (top- and bottom-fermenting) and Dekkera/Brettanomyces bruxellensis wild yeast were established, incorporated into the Biotyper reference library and validated by successful identification after inoculation into beer. Each bacterial species could be accurately identified and distinguished from one another and from over 5600 other microorganisms present in the Biotyper database. In addition, wild yeast contaminations were rapidly detected and distinguished from top- and bottom-fermenting brewing strains. The applicability and integration of mass spectrometry profiling using the Biotyper platform into existing brewery quality assurance practices within industry were assessed by analysing routine microbiology control samples from a local brewery, where contaminating microorganisms could be reliably identified. Brewery-isolated microorganisms not present in the Biotyper database were further analysed for identification using LC-MS/MS methods. This renders the Biotyper platform a promising candidate for biological quality control testing within the brewing industry as a more rapid, high-throughput and cost-effective technology that can be tailored for the detection of brewery-specific spoilage organisms from the local environment.

The eBioKit, a stand-alone educational platform for bioinformatics

PubMed Central

Conesa, Ana; Bongcam-Rudloff, Erik

2017-01-01

Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative. PMID:28910280

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

PubMed Central

2010-01-01

Background Root and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)—food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community. Description The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers. The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3663 genes 5959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant species for comparative analysis of plant splicing patterns. Conclusions RoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables. PMID:20691054

Implementation and Evaluation of a Mobile Mapping System Based on Integrated Range and Intensity Images for Traffic Signs Localization

NASA Astrophysics Data System (ADS)

Shahbazi, M.; Sattari, M.; Homayouni, S.; Saadatseresht, M.

2012-07-01

Recent advances in positioning techniques have made it possible to develop Mobile Mapping Systems (MMS) for detection and 3D localization of various objects from a moving platform. On the other hand, automatic traffic sign recognition from an equipped mobile platform has recently been a challenging issue for both intelligent transportation and municipal database collection. However, there are several inevitable problems coherent to all the recognition methods completely relying on passive chromatic or grayscale images. This paper presents the implementation and evaluation of an operational MMS. Being distinct from the others, the developed MMS comprises one range camera based on Photonic Mixer Device (PMD) technology and one standard 2D digital camera. The system benefits from certain algorithms to detect, recognize and localize the traffic signs by fusing the shape, color and object information from both range and intensity images. As the calibrating stage, a self-calibration method based on integrated bundle adjustment via joint setup with the digital camera is applied in this study for PMD camera calibration. As the result, an improvement of 83 % in RMS of range error and 72 % in RMS of coordinates residuals for PMD camera, over that achieved with basic calibration is realized in independent accuracy assessments. Furthermore, conventional photogrammetric techniques based on controlled network adjustment are utilized for platform calibration. Likewise, the well-known Extended Kalman Filtering (EKF) is applied to integrate the navigation sensors, namely GPS and INS. The overall acquisition system along with the proposed techniques leads to 90 % true positive recognition and the average of 12 centimetres 3D positioning accuracy.

Implementation and Evaluation of a Mobile Mapping System Based on Integrated Range and Intensity Images for Traffic Signs Localization

NASA Astrophysics Data System (ADS)

Shahbazi, M.; Sattari, M.; Homayouni, S.; Saadatseresht, M.

2012-07-01

Recent advances in positioning techniques have made it possible to develop Mobile Mapping Systems (MMS) for detection and 3D localization of various objects from a moving platform. On the other hand, automatic traffic sign recognition from an equipped mobile platform has recently been a challenging issue for both intelligent transportation and municipal database collection. However, there are several inevitable problems coherent to all the recognition methods completely relying on passive chromatic or grayscale images. This paper presents the implementation and evaluation of an operational MMS. Being distinct from the others, the developed MMS comprises one range camera based on Photonic Mixer Device (PMD) technology and one standard 2D digital camera. The system benefits from certain algorithms to detect, recognize and localize the traffic signs by fusing the shape, color and object information from both range and intensity images. As the calibrating stage, a self-calibration method based on integrated bundle adjustment via joint setup with the digital camera is applied in this study for PMD camera calibration. As the result, an improvement of 83% in RMS of range error and 72% in RMS of coordinates residuals for PMD camera, over that achieved with basic calibration is realized in independent accuracy assessments. Furthermore, conventional photogrammetric techniques based on controlled network adjustment are utilized for platform calibration. Likewise, the well-known Extended Kalman Filtering (EKF) is applied to integrate the navigation sensors, namely GPS and INS. The overall acquisition system along with the proposed techniques leads to 90% true positive recognition and the average of 12 centimetres 3D positioning accuracy.

Design Research of TIANDITU (Map Worl)-Based Geographic Information System for Travelling Service

NASA Astrophysics Data System (ADS)

Zhang, J.; Zhang, H.; Wang, C.

2014-04-01

TIANDITU (Map World) is the public version of the National Platform for Common Geospatial Information Service, and the travelling channel is TIANDITU-based geographic information platform for travelling service. With the development of tourism, traditional ways for providing travelling information cannot meet the needs of travelers. As such, the travelling channel of TIANDITU focuses on providing travel information abundantly and precisely, which integrated the geographic information data of TIANDITU Version 2.0 and the authoritative information resources from China National Tourism Administration. Furthermore, spatial positioning, category and information query of various travelling information were offered for the public in the travelling channel. This research mainly involves three important parts: the system design, key technologies of the system design and application examples. Firstly, this paper introduced the design of TIANDITU-based geographic information system for travelling service, and the general and database design were described in detail. The designs for general, database and travelling service above should consider lots of factors which illustrated in the paper in order to guarantee the efficient service. The process of system construction, the content of geographic information for travelling and system functions of geographic information for travelling are also proposed via diagram in this part. Then several key technologies were discussed, including the travelling information integration for main node and among nodes, general architecture design and management system for travelling channel, web portals and system interface. From the perspective of main technologies, this part describes how TIANDITU travelling channel can realize various functions and reach the requirements from different users. Finally, three application examples about travelling information query were listed shortly. The functions and search results are shown clearly in this part. In all, TIANDITU-based geographic information system for travelling service aimed to integrate the travelling information resources from national, provincial and municipal levels, and finally realized to provide "one stop" travelling service for users in the end.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients.

PubMed

Ma, Kevin C; Fernandez, James R; Amezcua, Lilyana; Lerner, Alex; Shiroishi, Mark S; Liu, Brent J

2015-12-01

MRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients' progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. An imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists' contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. The MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients

PubMed Central

Ma, Kevin C.; Fernandez, James R.; Amezcua, Lilyana; Lerner, Alex; Shiroishi, Mark S.; Liu, Brent J.

2016-01-01

Purpose MRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients' progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. Method An imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists' contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. Summary The MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record. PMID:26564667

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria

PubMed Central

Koutero, Mikael; Tchitchek, Nicolas; Cerutti, Franck; Lechat, Pierre; Maillet, Nicolas; Hoede, Claire; Chiapello, Hélène; Gaspin, Christine

2017-01-01

ABSTRACT As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach. PMID:28317029

Development of cloud-operating platform for detention facility design

NASA Astrophysics Data System (ADS)

Tun Lee, Kwan; Hung, Meng-Chiu; Tseng, Wei-Fan; Chan, Yi-Ping

2017-04-01

In the past 20 years, the population of Taiwan has accumulated in urban areas. The land development has changed the hydrological environment and resulted in the increase of surface runoff and shortened the time to peak discharge. The change of runoff characteristics increases the flood risk and reduces resilient ability of the city during flood. Considering that engineering measures may not be easy to implement in populated cities, detention facilities set on building basements have been proposed to compromise the increase of surface runoff resulting from development activities. In this study, a web-based operational platform has been developed to integrate the GIS technologies, hydrological analyses, as well as relevant regulations for the design of detention facilities. The design procedure embedded in the system includes a prior selection of type and size of the detention facility, integrated hydrological analysis for the developing site, and inspection of relevant regulations. After login the platform, designers can access the system database to retrieve road maps, land use coverages, and storm sewer information. Once the type, size, inlet, and outlet of the detention facility are assigned, the system can acquire the rainfall intensity-duration-frequency information from adjacent rain gauges to perform hydrological analyses for the developing site. The increase of the runoff volume due to the development and the reduction of the outflow peak through the construction of the detention facility can be estimated. The outflow peak at the target site is then checked with relevant regulations to confirm the suitability of the detention facility design. The proposed web-based platform can provide a concise layout of the detention facility and the drainageway of the developing site on a graphical interface. The design information can also be delivered directly through a web link to authorities for inspecting to simplify the complex administrative procedures.

Flexible Software Architecture for Visualization and Seismic Data Analysis

NASA Astrophysics Data System (ADS)

Petunin, S.; Pavlov, I.; Mogilenskikh, D.; Podzyuban, D.; Arkhipov, A.; Baturuin, N.; Lisin, A.; Smith, A.; Rivers, W.; Harben, P.

2007-12-01

Research in the field of seismology requires software and signal processing utilities for seismogram manipulation and analysis. Seismologists and data analysts often encounter a major problem in the use of any particular software application specific to seismic data analysis: the tuning of commands and windows to the specific waveforms and hot key combinations so as to fit their familiar informational environment. The ability to modify the user's interface independently from the developer requires an adaptive code structure. An adaptive code structure also allows for expansion of software capabilities such as new signal processing modules and implementation of more efficient algorithms. Our approach is to use a flexible "open" architecture for development of geophysical software. This report presents an integrated solution for organizing a logical software architecture based on the Unix version of the Geotool software implemented on the Microsoft NET 2.0 platform. Selection of this platform greatly expands the variety and number of computers that can implement the software, including laptops that can be utilized in field conditions. It also facilitates implementation of communication functions for seismic data requests from remote databases through the Internet. The main principle of the new architecture for Geotool is that scientists should be able to add new routines for digital waveform analysis via software plug-ins that utilize the basic Geotool display for GUI interaction. The use of plug-ins allows the efficient integration of diverse signal-processing software, including software still in preliminary development, into an organized platform without changing the fundamental structure of that platform itself. An analyst's use of Geotool is tracked via a metadata file so that future studies can reconstruct, and alter, the original signal processing operations. The work has been completed in the framework of a joint Russian- American project.

DNAtraffic--a new database for systems biology of DNA dynamics during the cell life.

PubMed

Kuchta, Krzysztof; Barszcz, Daniela; Grzesiuk, Elzbieta; Pomorski, Pawel; Krwawicz, Joanna

2012-01-01

DNAtraffic (http://dnatraffic.ibb.waw.pl/) is dedicated to be a unique comprehensive and richly annotated database of genome dynamics during the cell life. It contains extensive data on the nomenclature, ontology, structure and function of proteins related to the DNA integrity mechanisms such as chromatin remodeling, histone modifications, DNA repair and damage response from eight organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on the diseases related to the assembled human proteins. DNAtraffic is richly annotated in the systemic information on the nomenclature, chemistry and structure of DNA damage and their sources, including environmental agents or commonly used drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA network analysis. Database includes illustrations of pathways, damage, proteins and drugs. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines, it has to be extensively linked to numerous external data sources. Our database represents the result of the manual annotation work aimed at making the DNAtraffic much more useful for a wide range of systems biology applications.

DNAtraffic—a new database for systems biology of DNA dynamics during the cell life

PubMed Central

Kuchta, Krzysztof; Barszcz, Daniela; Grzesiuk, Elzbieta; Pomorski, Pawel; Krwawicz, Joanna

2012-01-01

DNAtraffic (http://dnatraffic.ibb.waw.pl/) is dedicated to be a unique comprehensive and richly annotated database of genome dynamics during the cell life. It contains extensive data on the nomenclature, ontology, structure and function of proteins related to the DNA integrity mechanisms such as chromatin remodeling, histone modifications, DNA repair and damage response from eight organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on the diseases related to the assembled human proteins. DNAtraffic is richly annotated in the systemic information on the nomenclature, chemistry and structure of DNA damage and their sources, including environmental agents or commonly used drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA network analysis. Database includes illustrations of pathways, damage, proteins and drugs. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines, it has to be extensively linked to numerous external data sources. Our database represents the result of the manual annotation work aimed at making the DNAtraffic much more useful for a wide range of systems biology applications. PMID:22110027

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

The making of a pan-European organ transplant registry.

PubMed

Smits, Jacqueline M; Niesing, Jan; Breidenbach, Thomas; Collett, Dave

2013-03-01

A European patient registry to track the outcomes of organ transplant recipients does not exist. As knowledge gleaned from large registries has already led to the creation of standards of care that gained widespread support from patients and healthcare providers, the European Union initiated a project that would enable the creation of a European Registry linking currently existing national databases. This report contains a description of all functional, technical, and legal prerequisites, which upon fulfillment should allow for the seamless sharing of national longitudinal data across temporal, geographical, and subspecialty boundaries. To create a platform that can effortlessly link multiple databases and maintain the integrity of the existing national databases crucial elements were described during the project. These elements are: (i) use of a common dictionary, (ii) use of a common database and refined data uploading technology, (iii) use of standard methodology to allow uniform protocol driven and meaningful long-term follow-up analyses, (iv) use of a quality assurance mechanism to guarantee completeness and accuracy of the data collected, and (v) establishment of a solid legal framework that allows for safe data exchange. © 2012 The Authors Transplant International © 2012 European Society for Organ Transplantation. Published by Blackwell Publishing Ltd.

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

PubMed

Gacesa, Ranko; Zucko, Jurica; Petursdottir, Solveig K; Gudmundsdottir, Elisabet Eik; Fridjonsson, Olafur H; Diminic, Janko; Long, Paul F; Cullum, John; Hranueli, Daslav; Hreggvidsson, Gudmundur O; Starcevic, Antonio

2017-06-01

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya . The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

The Method of Multiple Spatial Planning Basic Map

NASA Astrophysics Data System (ADS)

Zhang, C.; Fang, C.

2018-04-01

The "Provincial Space Plan Pilot Program" issued in December 2016 pointed out that the existing space management and control information management platforms of various departments were integrated, and a spatial planning information management platform was established to integrate basic data, target indicators, space coordinates, and technical specifications. The planning and preparation will provide supportive decision support, digital monitoring and evaluation of the implementation of the plan, implementation of various types of investment projects and space management and control departments involved in military construction projects in parallel to approve and approve, and improve the efficiency of administrative approval. The space planning system should be set up to delimit the control limits for the development of production, life and ecological space, and the control of use is implemented. On the one hand, it is necessary to clarify the functional orientation between various kinds of planning space. On the other hand, it is necessary to achieve "multi-compliance" of various space planning. Multiple spatial planning intergration need unified and standard basic map(geographic database and technical specificaton) to division of urban, agricultural, ecological three types of space and provide technical support for the refinement of the space control zoning for the relevant planning. The article analysis the main space datum, the land use classification standards, base map planning, planning basic platform main technical problems. Based on the geographic conditions, the results of the census preparation of spatial planning map, and Heilongjiang, Hainan many rules combined with a pilot application.

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

PubMed

Edwards, J D; Baldo, A M; Mueller, L A

2016-01-01

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

The Comprehensive Antibiotic Resistance Database

PubMed Central

McArthur, Andrew G.; Waglechner, Nicholas; Nizam, Fazmin; Yan, Austin; Azad, Marisa A.; Baylay, Alison J.; Bhullar, Kirandeep; Canova, Marc J.; De Pascale, Gianfranco; Ejim, Linda; Kalan, Lindsay; King, Andrew M.; Koteva, Kalinka; Morar, Mariya; Mulvey, Michael R.; O'Brien, Jonathan S.; Pawlowski, Andrew C.; Piddock, Laura J. V.; Spanogiannopoulos, Peter; Sutherland, Arlene D.; Tang, Irene; Taylor, Patricia L.; Thaker, Maulik; Wang, Wenliang; Yan, Marie; Yu, Tennison

2013-01-01

The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment. PMID:23650175

Development of user-friendly and interactive data collection system for cerebral palsy.

PubMed

Raharjo, I; Burns, T G; Venugopalan, J; Wang, M D

2016-02-01

Cerebral palsy (CP) is a permanent motor disorder that appears in early age and it requires multiple tests to assess the physical and mental capabilities of the patients. Current medical record data collection systems, e.g., EPIC, employed for CP are very general, difficult to navigate, and prone to errors. The data cannot easily be extracted which limits data analysis on this rich source of information. To overcome these limitations, we designed and prototyped a database with a graphical user interface geared towards clinical research specifically in CP. The platform with MySQL and Java framework is reliable, secure, and can be easily integrated with other programming languages for data analysis such as MATLAB. This database with GUI design is a promising tool for data collection and can be applied in many different fields aside from CP to infer useful information out of the vast amount of data being collected.

Development of user-friendly and interactive data collection system for cerebral palsy

PubMed Central

Raharjo, I.; Burns, T. G.; Venugopalan, J.; Wang., M. D.

2016-01-01

Cerebral palsy (CP) is a permanent motor disorder that appears in early age and it requires multiple tests to assess the physical and mental capabilities of the patients. Current medical record data collection systems, e.g., EPIC, employed for CP are very general, difficult to navigate, and prone to errors. The data cannot easily be extracted which limits data analysis on this rich source of information. To overcome these limitations, we designed and prototyped a database with a graphical user interface geared towards clinical research specifically in CP. The platform with MySQL and Java framework is reliable, secure, and can be easily integrated with other programming languages for data analysis such as MATLAB. This database with GUI design is a promising tool for data collection and can be applied in many different fields aside from CP to infer useful information out of the vast amount of data being collected. PMID:28133638

Management and assimilation of diverse, distributed watershed datasets

NASA Astrophysics Data System (ADS)

Varadharajan, C.; Faybishenko, B.; Versteeg, R.; Agarwal, D.; Hubbard, S. S.; Hendrix, V.

2016-12-01

The U.S. Department of Energy's (DOE) Watershed Function Scientific Focus Area (SFA) seeks to determine how perturbations to mountainous watersheds (e.g., floods, drought, early snowmelt) impact the downstream delivery of water, nutrients, carbon, and metals over seasonal to decadal timescales. We are building a software platform that enables integration of diverse and disparate field, laboratory, and simulation datasets, of various types including hydrological, geological, meteorological, geophysical, geochemical, ecological and genomic datasets across a range of spatial and temporal scales within the Rifle floodplain and the East River watershed, Colorado. We are using agile data management and assimilation approaches, to enable web-based integration of heterogeneous, multi-scale dataSensor-based observations of water-level, vadose zone and groundwater temperature, water quality, meteorology as well as biogeochemical analyses of soil and groundwater samples have been curated and archived in federated databases. Quality Assurance and Quality Control (QA/QC) are performed on priority datasets needed for on-going scientific analyses, and hydrological and geochemical modeling. Automated QA/QC methods are used to identify and flag issues in the datasets. Data integration is achieved via a brokering service that dynamically integrates data from distributed databases via web services, based on user queries. The integrated results are presented to users in a portal that enables intuitive search, interactive visualization and download of integrated datasets. The concepts, approaches and codes being used are shared across various data science components of various large DOE-funded projects such as the Watershed Function SFA, Next Generation Ecosystem Experiment (NGEE) Tropics, Ameriflux/FLUXNET, and Advanced Simulation Capability for Environmental Management (ASCEM), and together contribute towards DOE's cyberinfrastructure for data management and model-data integration.

TCMSP: a database of systems pharmacology for drug discovery from herbal medicines.

PubMed

Ru, Jinlong; Li, Peng; Wang, Jinan; Zhou, Wei; Li, Bohui; Huang, Chao; Li, Pidong; Guo, Zihu; Tao, Weiyang; Yang, Yinfeng; Xu, Xue; Li, Yan; Wang, Yonghua; Yang, Ling

2014-01-01

Modern medicine often clashes with traditional medicine such as Chinese herbal medicine because of the little understanding of the underlying mechanisms of action of the herbs. In an effort to promote integration of both sides and to accelerate the drug discovery from herbal medicines, an efficient systems pharmacology platform that represents ideal information convergence of pharmacochemistry, ADME properties, drug-likeness, drug targets, associated diseases and interaction networks, are urgently needed. The traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) was built based on the framework of systems pharmacology for herbal medicines. It consists of all the 499 Chinese herbs registered in the Chinese pharmacopoeia with 29,384 ingredients, 3,311 targets and 837 associated diseases. Twelve important ADME-related properties like human oral bioavailability, half-life, drug-likeness, Caco-2 permeability, blood-brain barrier and Lipinski's rule of five are provided for drug screening and evaluation. TCMSP also provides drug targets and diseases of each active compound, which can automatically establish the compound-target and target-disease networks that let users view and analyze the drug action mechanisms. It is designed to fuel the development of herbal medicines and to promote integration of modern medicine and traditional medicine for drug discovery and development. The particular strengths of TCMSP are the composition of the large number of herbal entries, and the ability to identify drug-target networks and drug-disease networks, which will help revealing the mechanisms of action of Chinese herbs, uncovering the nature of TCM theory and developing new herb-oriented drugs. TCMSP is freely available at http://sm.nwsuaf.edu.cn/lsp/tcmsp.php.

The Rare Diseases Clinical Research Network's organization and approach to observational research and health outcomes research.

PubMed

Krischer, Jeffrey P; Gopal-Srivastava, Rashmi; Groft, Stephen C; Eckstein, David J

2014-08-01

Established in 2003 by the Office of Rare Diseases Research (ORDR), in collaboration with several National Institutes of Health (NIH) Institutes/Centers, the Rare Diseases Clinical Research Network (RDCRN) consists of multiple clinical consortia conducting research in more than 200 rare diseases. The RDCRN supports longitudinal or natural history, pilot, Phase I, II, and III, case-control, cross-sectional, chart review, physician survey, bio-repository, and RDCRN Contact Registry (CR) studies. To date, there have been 24,684 participants enrolled on 120 studies from 446 sites worldwide. An additional 11,533 individuals participate in the CR. Through a central data management and coordinating center (DMCC), the RDCRN's platform for the conduct of observational research encompasses electronic case report forms, federated databases, and an online CR for epidemiological and survey research. An ORDR-governed data repository (through dbGaP, a database for genotype and phenotype information from the National Library of Medicine) has been created. DMCC coordinates with ORDR to register and upload study data to dbGaP for data sharing with the scientific community. The platform provided by the RDCRN DMCC has supported 128 studies, six of which were successfully conducted through the online CR, with 2,352 individuals accrued and a median enrollment time of just 2 months. The RDCRN has built a powerful suite of web-based tools that provide for integration of federated and online database support that can accommodate a large number of rare diseases on a global scale. RDCRN studies have made important advances in the diagnosis and treatment of rare diseases.

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

PubMed Central

Prakash, Peralam Yegneswaran; Irinyi, Laszlo; Halliday, Catriona; Chen, Sharon; Robert, Vincent

2017-01-01

ABSTRACT The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform. PMID:28179406

Apparatus, method and system to control accessibility of platform resources based on an integrity level

DOEpatents

Jenkins, Chris; Pierson, Lyndon G.

2016-10-25

Techniques and mechanism to selectively provide resource access to a functional domain of a platform. In an embodiment, the platform includes both a report domain to monitor the functional domain and a policy domain to identify, based on such monitoring, a transition of the functional domain from a first integrity level to a second integrity level. In response to a change in integrity level, the policy domain may configure the enforcement domain to enforce against the functional domain one or more resource accessibility rules corresponding to the second integrity level. In another embodiment, the policy domain automatically initiates operations in aid of transitioning the platform from the second integrity level to a higher integrity level.

New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research.

PubMed

Torous, John; Kiang, Mathew V; Lorme, Jeanette; Onnela, Jukka-Pekka

2016-05-05

A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health.

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

PubMed

Neinstein, Aaron; Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-03-01

Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research

PubMed Central

Torous, John; Kiang, Mathew V; Lorme, Jeanette

2016-01-01

Background A longstanding barrier to progress in psychiatry, both in clinical settings and research trials, has been the persistent difficulty of accurately and reliably quantifying disease phenotypes. Mobile phone technology combined with data science has the potential to offer medicine a wealth of additional information on disease phenotypes, but the large majority of existing smartphone apps are not intended for use as biomedical research platforms and, as such, do not generate research-quality data. Objective Our aim is not the creation of yet another app per se but rather the establishment of a platform to collect research-quality smartphone raw sensor and usage pattern data. Our ultimate goal is to develop statistical, mathematical, and computational methodology to enable us and others to extract biomedical and clinical insights from smartphone data. Methods We report on the development and early testing of Beiwe, a research platform featuring a study portal, smartphone app, database, and data modeling and analysis tools designed and developed specifically for transparent, customizable, and reproducible biomedical research use, in particular for the study of psychiatric and neurological disorders. We also outline a proposed study using the platform for patients with schizophrenia. Results We demonstrate the passive data capabilities of the Beiwe platform and early results of its analytical capabilities. Conclusions Smartphone sensors and phone usage patterns, when coupled with appropriate statistical learning tools, are able to capture various social and behavioral manifestations of illnesses, in naturalistic settings, as lived and experienced by patients. The ubiquity of smartphones makes this type of moment-by-moment quantification of disease phenotypes highly scalable and, when integrated within a transparent research platform, presents tremendous opportunities for research, discovery, and patient health. PMID:27150677

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management

PubMed Central

Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-01-01

Objective Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. Materials and Methods An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Results Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application (“app”), Blip, to visualize the data. Tidepool’s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. Discussion By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. Conclusion The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool’s open source, cloud model for health data interoperability is applicable to other healthcare use cases. PMID:26338218

Results from a new 193nm die-to-database reticle inspection platform

NASA Astrophysics Data System (ADS)

Broadbent, William H.; Alles, David S.; Giusti, Michael T.; Kvamme, Damon F.; Shi, Rui-fang; Sousa, Weston L.; Walsh, Robert; Xiong, Yalin

2010-05-01

A new 193nm wavelength high resolution reticle defect inspection platform has been developed for both die-to-database and die-to-die inspection modes. In its initial configuration, this innovative platform has been designed to meet the reticle qualification requirements of the IC industry for the 22nm logic and 3xhp memory generations (and shrinks) with planned extensions to the next generation. The 22nm/3xhp IC generation includes advanced 193nm optical lithography using conventional RET, advanced computational lithography, and double patterning. Further, EUV pilot line lithography is beginning. This advanced 193nm inspection platform has world-class performance and the capability to meet these diverse needs in optical and EUV lithography. The architecture of the new 193nm inspection platform is described. Die-to-database inspection results are shown on a variety of reticles from industry sources; these reticles include standard programmed defect test reticles, as well as advanced optical and EUV product and product-like reticles. Results show high sensitivity and low false and nuisance detections on complex optical reticle designs and small feature size EUV reticles. A direct comparison with the existing industry standard 257nm wavelength inspection system shows measurable sensitivity improvement for small feature sizes

Arkheia: Data Management and Communication for Open Computational Neuroscience

PubMed Central

Antolík, Ján; Davison, Andrew P.

2018-01-01

Two trends have been unfolding in computational neuroscience during the last decade. First, a shift of focus to increasingly complex and heterogeneous neural network models, with a concomitant increase in the level of collaboration within the field (whether direct or in the form of building on top of existing tools and results). Second, a general trend in science toward more open communication, both internally, with other potential scientific collaborators, and externally, with the wider public. This multi-faceted development toward more integrative approaches and more intense communication within and outside of the field poses major new challenges for modelers, as currently there is a severe lack of tools to help with automatic communication and sharing of all aspects of a simulation workflow to the rest of the community. To address this important gap in the current computational modeling software infrastructure, here we introduce Arkheia. Arkheia is a web-based open science platform for computational models in systems neuroscience. It provides an automatic, interactive, graphical presentation of simulation results, experimental protocols, and interactive exploration of parameter searches, in a web browser-based application. Arkheia is focused on automatic presentation of these resources with minimal manual input from users. Arkheia is written in a modular fashion with a focus on future development of the platform. The platform is designed in an open manner, with a clearly defined and separated API for database access, so that any project can write its own backend translating its data into the Arkheia database format. Arkheia is not a centralized platform, but allows any user (or group of users) to set up their own repository, either for public access by the general population, or locally for internal use. Overall, Arkheia provides users with an automatic means to communicate information about not only their models but also individual simulation results and the entire experimental context in an approachable graphical manner, thus facilitating the user's ability to collaborate in the field and outreach to a wider audience. PMID:29556187

Arkheia: Data Management and Communication for Open Computational Neuroscience.

PubMed

Antolík, Ján; Davison, Andrew P

2018-01-01

Two trends have been unfolding in computational neuroscience during the last decade. First, a shift of focus to increasingly complex and heterogeneous neural network models, with a concomitant increase in the level of collaboration within the field (whether direct or in the form of building on top of existing tools and results). Second, a general trend in science toward more open communication, both internally, with other potential scientific collaborators, and externally, with the wider public. This multi-faceted development toward more integrative approaches and more intense communication within and outside of the field poses major new challenges for modelers, as currently there is a severe lack of tools to help with automatic communication and sharing of all aspects of a simulation workflow to the rest of the community. To address this important gap in the current computational modeling software infrastructure, here we introduce Arkheia. Arkheia is a web-based open science platform for computational models in systems neuroscience. It provides an automatic, interactive, graphical presentation of simulation results, experimental protocols, and interactive exploration of parameter searches, in a web browser-based application. Arkheia is focused on automatic presentation of these resources with minimal manual input from users. Arkheia is written in a modular fashion with a focus on future development of the platform. The platform is designed in an open manner, with a clearly defined and separated API for database access, so that any project can write its own backend translating its data into the Arkheia database format. Arkheia is not a centralized platform, but allows any user (or group of users) to set up their own repository, either for public access by the general population, or locally for internal use. Overall, Arkheia provides users with an automatic means to communicate information about not only their models but also individual simulation results and the entire experimental context in an approachable graphical manner, thus facilitating the user's ability to collaborate in the field and outreach to a wider audience.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

DOE PAGES

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna; ...

2016-10-30

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

Development of imaging biomarkers and generation of big data.

PubMed

Alberich-Bayarri, Ángel; Hernández-Navarro, Rafael; Ruiz-Martínez, Enrique; García-Castro, Fabio; García-Juan, David; Martí-Bonmatí, Luis

2017-06-01

Several image processing algorithms have emerged to cover unmet clinical needs but their application to radiological routine with a clear clinical impact is still not straightforward. Moving from local to big infrastructures, such as Medical Imaging Biobanks (millions of studies), or even more, Federations of Medical Imaging Biobanks (in some cases totaling to hundreds of millions of studies) require the integration of automated pipelines for fast analysis of pooled data to extract clinically relevant conclusions, not uniquely linked to medical imaging, but in combination to other information such as genetic profiling. A general strategy for the development of imaging biomarkers and their integration in the cloud for the quantitative management and exploitation in large databases is herein presented. The proposed platform has been successfully launched and is being validated nowadays among the early adopters' community of radiologists, clinicians, and medical imaging researchers.

Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies.

PubMed

Pozdeyev, Nikita; Yoo, Minjae; Mackie, Ryan; Schweppe, Rebecca E; Tan, Aik Choon; Haugen, Bryan R

2016-08-09

The consistency of in vitro drug sensitivity data is of key importance for cancer pharmacogenomics. Previous attempts to correlate drug sensitivities from the large pharmacogenomics databases, such as the Cancer Cell Line Encyclopedia (CCLE) and the Genomics of Drug Sensitivity in Cancer (GDSC), have produced discordant results. We developed a new drug sensitivity metric, the area under the dose response curve adjusted for the range of tested drug concentrations, which allows integration of heterogeneous drug sensitivity data from the CCLE, the GDSC, and the Cancer Therapeutics Response Portal (CTRP). We show that there is moderate to good agreement of drug sensitivity data for many targeted therapies, particularly kinase inhibitors. The results of this largest cancer cell line drug sensitivity data analysis to date are accessible through the online portal, which serves as a platform for high power pharmacogenomics analysis.

Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

PubMed

Chang, Wenling E; Peterson, Matthew W; Garay, Christopher D; Korves, Tonia

2016-09-15

Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only for research but for biosurveillance and public health. However, current freely available tools for analyzing this data are geared towards bioinformaticians and/or do not provide summaries and visualizations needed to readily interpret results. We designed a platform to easily access and summarize data about pathogen samples. The software includes a PostgreSQL database that captures metadata useful for disease outbreak investigations, and scripts for downloading and parsing data from NCBI BioSample and BioProject into the database. The software provides a user interface to query metadata and obtain standardized results in an exportable, tab-delimited format. To visually summarize results, the user interface provides a 2D histogram for user-selected metadata types and mapping of geolocated entries. The software is built on the LabKey data platform, an open-source data management platform, which enables developers to add functionalities. We demonstrate the use of the software in querying for a pathogen serovar and for genome sequence identifiers. This software enables users to create a local database for pathogen metadata, populate it with data from NCBI, easily query the data, and obtain visual summaries. Some of the components, such as the database, are modular and can be incorporated into other data platforms. The source code is freely available for download at https://github.com/wchangmitre/bioattribution .

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis

PubMed Central

2013-01-01

Background Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data. Results We developed inTB, a web-based system for integrated warehousing and analysis of clinical, socio-demographic and molecular data for Mycobacterium sp. isolates. As a database it can organize and display data from any of the standard genotyping methods (SNP, MIRU-VNTR, RFLP and spoligotype), as well as an extensive array of clinical and socio-demographic variables that are used in multiple countries to characterize the disease. Through the inTB interface it is possible to insert and download data, browse the database and search specific parameters. New isolates are automatically classified into strains according to an internal reference, and data uploaded or typed in is checked for internal consistency. As an analysis framework, the system provides simple, point and click analysis tools that allow multiple types of data plotting, as well as simple ways to download data for external analysis. Individual trees for each genotyping method are available, as well as a super tree combining all of them. The integrative nature of inTB grants the user the ability to generate trees for filtered subsets of data crossing molecular and clinical/socio-demografic information. inTB is built on open source software, can be easily installed locally and easily adapted to other diseases. Its design allows for use by research laboratories, hospitals or public health authorities. The full source code as well as ready to use packages is available at http://www.evocell.org/inTB. Conclusions To the best of our knowledge, this is the only system capable of integrating different types of molecular data with clinical and socio-demographic data, empowering researchers and clinicians with easy to use analysis tools that were not possible before. PMID:24001185

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.

PubMed

Soares, Patrícia; Alves, Renato J; Abecasis, Ana B; Penha-Gonçalves, Carlos; Gomes, M Gabriela M; Pereira-Leal, José B

2013-08-30

Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data. We developed inTB, a web-based system for integrated warehousing and analysis of clinical, socio-demographic and molecular data for Mycobacterium sp. isolates. As a database it can organize and display data from any of the standard genotyping methods (SNP, MIRU-VNTR, RFLP and spoligotype), as well as an extensive array of clinical and socio-demographic variables that are used in multiple countries to characterize the disease. Through the inTB interface it is possible to insert and download data, browse the database and search specific parameters. New isolates are automatically classified into strains according to an internal reference, and data uploaded or typed in is checked for internal consistency. As an analysis framework, the system provides simple, point and click analysis tools that allow multiple types of data plotting, as well as simple ways to download data for external analysis. Individual trees for each genotyping method are available, as well as a super tree combining all of them. The integrative nature of inTB grants the user the ability to generate trees for filtered subsets of data crossing molecular and clinical/socio-demografic information. inTB is built on open source software, can be easily installed locally and easily adapted to other diseases. Its design allows for use by research laboratories, hospitals or public health authorities. The full source code as well as ready to use packages is available at http://www.evocell.org/inTB. To the best of our knowledge, this is the only system capable of integrating different types of molecular data with clinical and socio-demographic data, empowering researchers and clinicians with easy to use analysis tools that were not possible before.

QUALITATIVE AND QUANTITATIVE METHODS OF SUICIDE RESEARCH IN OLD AGE.

PubMed

Ojagbemi, A

2017-06-01

This paper examines the merits of the qualitative and quantitative methods of suicide research in the elderly using two studies identified through a free search of the Pubmed database for articles that might have direct bearing on suicidality in the elderly. The studies have been purposively selected for critical appraisal because they meaningfully reflect the quantitative and qualitative divide as well as the social, economic, and cultural boundaries between the elderly living in sub-Saharan Africa and Europe. The paper concludes that an integration of both the qualitative and quantitative research approaches may provide a better platform for unraveling the complex phenomenon of suicide in the elderly.

Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

PubMed Central

Gražulis, Saulius; Daškevič, Adriana; Merkys, Andrius; Chateigner, Daniel; Lutterotti, Luca; Quirós, Miguel; Serebryanaya, Nadezhda R.; Moeck, Peter; Downs, Robert T.; Le Bail, Armel

2012-01-01

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge. PMID:22070882

G-DOC: A Systems Medicine Platform for Personalized Oncology1

PubMed Central

Madhavan, Subha; Gusev, Yuriy; Harris, Michael; Tanenbaum, David M; Gauba, Robinder; Bhuvaneshwar, Krithika; Shinohara, Andrew; Rosso, Kevin; Carabet, Lavinia A; Song, Lei; Riggins, Rebecca B; Dakshanamurthy, Sivanesan; Wang, Yue; Byers, Stephen W; Clarke, Robert; Weiner, Louis M

2011-01-01

Currently, cancer therapy remains limited by a “one-size-fits-all” approach, whereby treatment decisions are based mainly on the clinical stage of disease, yet fail to reference the individual's underlying biology and its role driving malignancy. Identifying better personalized therapies for cancer treatment is hindered by the lack of high-quality “omics” data of sufficient size to produce meaningful results and the ability to integrate biomedical data from disparate technologies. Resolving these issues will help translation of therapies from research to clinic by helping clinicians develop patient-specific treatments based on the unique signatures of patient's tumor. Here we describe the Georgetown Database of Cancer (G-DOC), a Web platform that enables basic and clinical research by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment. While several rich data repositories for high-dimensional research data exist in the public domain, most focus on a single-data type and do not support integration across multiple technologies. Currently, G-DOC contains data from more than 2500 breast cancer patients and 800 gastrointestinal cancer patients, G-DOC includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major “omics” types: DNA, mRNA, microRNA, and metabolites. We believe that G-DOC will help facilitate systems medicine by providing identification of trends and patterns in integrated data sets and hence facilitate the use of better targeted therapies for cancer. A set of representative usage scenarios is provided to highlight the technical capabilities of this resource. PMID:21969811

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform.

PubMed

Prakash, Peralam Yegneswaran; Irinyi, Laszlo; Halliday, Catriona; Chen, Sharon; Robert, Vincent; Meyer, Wieland

2017-04-01

The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform. Copyright © 2017 American Society for Microbiology.

A method and software framework for enriching private biomedical sources with data from public online repositories.

PubMed

Anguita, Alberto; García-Remesal, Miguel; Graf, Norbert; Maojo, Victor

2016-04-01

Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the information about the identified entities-e.g. scientific literature, published clinical trial results, etc. While semantic integration techniques have traditionally focused on providing homogeneous access to private datasets-thus helping automate the first part of the research, and there exist different solutions for browsing public data, there is still a need for tools that facilitate merging public repositories with private datasets. This paper presents a framework that automatically locates public data of interest to the researcher and semantically integrates it with existing private datasets. The framework has been designed as an extension of traditional data integration systems, and has been validated with an existing data integration platform from a European research project by integrating a private biological dataset with data from the National Center for Biotechnology Information (NCBI). Copyright © 2016 Elsevier Inc. All rights reserved.

JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies.

PubMed

Angers-Loustau, Alexandre; Petrillo, Mauro; Bonfini, Laura; Gatto, Francesco; Rosa, Sabrina; Patak, Alexandre; Kreysa, Joachim

2014-12-30

The polymerase chain reaction (PCR) is the current state of the art technique for DNA-based detection of Genetically Modified Organisms (GMOs). A typical control strategy starts by analyzing a sample for the presence of target sequences (GM-elements) known to be present in many GMOs. Positive findings from this "screening" are then confirmed with GM (event) specific test methods. A reliable knowledge of which GMOs are detected by combinations of GM-detection methods is thus crucial to minimize the verification efforts. In this article, we describe a novel platform that links the information of two unique databases built and maintained by the European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) at the Joint Research Centre (JRC) of the European Commission, one containing the sequence information of known GM-events and the other validated PCR-based detection and identification methods. The new platform compiles in silico determinations of the detection of a wide range of GMOs by the available detection methods using existing scripts that simulate PCR amplification and, when present, probe binding. The correctness of the information has been verified by comparing the in silico conclusions to experimental results for a subset of forty-nine GM events and six methods. The JRC GMO-Matrix is unique for its reliance on DNA sequence data and its flexibility in integrating novel GMOs and new detection methods. Users can mine the database using a set of web interfaces that thus provide a valuable support to GMO control laboratories in planning and evaluating their GMO screening strategies. The platform is accessible at http://gmo-crl.jrc.ec.europa.eu/jrcgmomatrix/ .

A service platform architecture design towards a light integration of heterogeneous systems in the wellbeing domain.

PubMed

Yang, Yaojin; Ahtinen, Aino; Lahteenmaki, Jaakko; Nyman, Petri; Paajanen, Henrik; Peltoniemi, Teijo; Quiroz, Carlos

2007-01-01

System integration is one of the major challenges for building wellbeing or healthcare related information systems. In this paper, we are going to share our experiences on how to design a service platform called Nuadu service platform, for providing integrated services in occupational health promotion and health risk management through two heterogeneous systems. Our design aims for a light integration covering the layers, from data through service up to presentation, while maintaining the integrity of the underlying systems.

A Symphony of Software.

ERIC Educational Resources Information Center

Currents, 2002

2002-01-01

Offers a descriptive table of databases that help higher education institutions orchestrate advancement operations. Information includes vendor, contact, software, price, database engine/server platform, recommended reporting tools, record capacity, and client type. (EV)

P185-M Protein Identification and Validation of Results in Workflows that Integrate over Various Instruments, Datasets, Search Engines

PubMed Central

Hufnagel, P.; Glandorf, J.; Körting, G.; Jabs, W.; Schweiger-Hufnagel, U.; Hahner, S.; Lubeck, M.; Suckau, D.

2007-01-01

Analysis of complex proteomes often results in long protein lists, but falls short in measuring the validity of identification and quantification results on a greater number of proteins. Biological and technical replicates are mandatory, as is the combination of the MS data from various workflows (gels, 1D-LC, 2D-LC), instruments (TOF/TOF, trap, qTOF or FTMS), and search engines. We describe a database-driven study that combines two workflows, two mass spectrometers, and four search engines with protein identification following a decoy database strategy. The sample was a tryptically digested lysate (10,000 cells) of a human colorectal cancer cell line. Data from two LC-MALDI-TOF/TOF runs and a 2D-LC-ESI-trap run using capillary and nano-LC columns were submitted to the proteomics software platform ProteinScape. The combined MALDI data and the ESI data were searched using Mascot (Matrix Science), Phenyx (GeneBio), ProteinSolver (Bruker and Protagen), and Sequest (Thermo) against a decoy database generated from IPI-human in order to obtain one protein list across all workflows and search engines at a defined maximum false-positive rate of 5%. ProteinScape combined the data to one LC-MALDI and one LC-ESI dataset. The initial separate searches from the two combined datasets generated eight independent peptide lists. These were compiled into an integrated protein list using the ProteinExtractor algorithm. An initial evaluation of the generated data led to the identification of approximately 1200 proteins. Result integration on a peptide level allowed discrimination of protein isoforms that would not have been possible with a mere combination of protein lists.

Study of Mobile GIS Application on the Field of GPR in the Road Disease Detection

NASA Astrophysics Data System (ADS)

Liao, Q.; Yang, F.

2013-12-01

With the reflection principle of pulsed electromagnetic waves, ground penetrating radar (GPR) is available to measure depth of the pavement layer, reflecting different hidden danger underground. Currently, GPR has been widely used in road engineering with the constantly improved ability of detection and diagnosis to road diseases. The sum of road disease data of a region, a city, and even a wider range will be a very informative database, so we need a more convenient way to achieve data query intuitively. As mobile internet develops continuously, application of mobile terminal device plays a more important role in information platform. Mobile GIS, with smartphone as its terminal, is supported by the mobile Internet, GPS or base station as its positioning method. In this article, based on Android Platform and using C/S pattern, the LBS application of road diseases information which integrates Baidu Map API and database technology was discussed. After testing, it can display and query the real-time and historical road diseases data, the classification of data on a phone intuitively and easily. Because of the location technique and high portability of smart phone, the spot investigations of road diseases become easier. Though, the system needs further improvement, especially with the improving of the mobile phone performance, the system can also add the function of analysis to the disease data, thus forming a set of service system with more applicable.

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

PubMed

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-04

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.

PubMed

Venkatesan, Aravind; Kim, Jee-Hyub; Talo, Francesco; Ide-Smith, Michele; Gobeill, Julien; Carter, Jacob; Batista-Navarro, Riza; Ananiadou, Sophia; Ruch, Patrick; McEntyre, Johanna

2016-01-01

The tremendous growth in biological data has resulted in an increase in the number of research papers being published. This presents a great challenge for scientists in searching and assimilating facts described in those papers. Particularly, biological databases depend on curators to add highly precise and useful information that are usually extracted by reading research articles. Therefore, there is an urgent need to find ways to improve linking literature to the underlying data, thereby minimising the effort in browsing content and identifying key biological concepts.   As part of the development of Europe PMC, we have developed a new platform, SciLite, which integrates text-mined annotations from different sources and overlays those outputs on research articles. The aim is to aid researchers and curators using Europe PMC in finding key concepts more easily and provide links to related resources or tools, bridging the gap between literature and biological data.

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data

PubMed Central

Talo, Francesco; Ide-Smith, Michele; Gobeill, Julien; Carter, Jacob; Batista-Navarro, Riza; Ananiadou, Sophia; Ruch, Patrick; McEntyre, Johanna

2017-01-01

The tremendous growth in biological data has resulted in an increase in the number of research papers being published. This presents a great challenge for scientists in searching and assimilating facts described in those papers. Particularly, biological databases depend on curators to add highly precise and useful information that are usually extracted by reading research articles. Therefore, there is an urgent need to find ways to improve linking literature to the underlying data, thereby minimising the effort in browsing content and identifying key biological concepts.   As part of the development of Europe PMC, we have developed a new platform, SciLite, which integrates text-mined annotations from different sources and overlays those outputs on research articles. The aim is to aid researchers and curators using Europe PMC in finding key concepts more easily and provide links to related resources or tools, bridging the gap between literature and biological data. PMID:28948232

Advances in Data Management in Remote Sensing and Climate Modeling

NASA Astrophysics Data System (ADS)

Brown, P. G.

2014-12-01

Recent commercial interest in "Big Data" information systems has yielded little more than a sense of deja vu among scientists whose work has always required getting their arms around extremely large databases, and writing programs to explore and analyze it. On the flip side, there are some commercial DBMS startups building "Big Data" platform using techniques taken from earth science, astronomy, high energy physics and high performance computing. In this talk, we will introduce one such platform; Paradigm4's SciDB, the first DBMS designed from the ground up to combine the kinds of quality-of-service guarantees made by SQL DBMS platforms—high level data model, query languages, extensibility, transactions—with the kinds of functionality familiar to scientific users—arrays as structural building blocks, integrated linear algebra, and client language interfaces that minimize the learning curve. We will review how SciDB is used to manage and analyze earth science data by several teams of scientific users.

Effective 3-D surface modeling for geographic information systems

NASA Astrophysics Data System (ADS)

Yüksek, K.; Alparslan, M.; Mendi, E.

2013-11-01

In this work, we propose a dynamic, flexible and interactive urban digital terrain platform (DTP) with spatial data and query processing capabilities of Geographic Information Systems (GIS), multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized Directional Replacement Policy (DRP) based buffer management scheme. Polyhedron structures are used in Digital Surface Modeling (DSM) and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g. X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

A platform for discovery: The University of Pennsylvania Integrated Neurodegenerative Disease Biobank

PubMed Central

Toledo, Jon B.; Van Deerlin, Vivianna M.; Lee, Edward B.; Suh, EunRan; Baek, Young; Robinson, John L.; Xie, Sharon X.; McBride, Jennifer; Wood, Elisabeth M.; Schuck, Theresa; Irwin, David J.; Gross, Rachel G.; Hurtig, Howard; McCluskey, Leo; Elman, Lauren; Karlawish, Jason; Schellenberg, Gerard; Chen-Plotkin, Alice; Wolk, David; Grossman, Murray; Arnold, Steven E.; Shaw, Leslie M.; Lee, Virginia M.-Y.; Trojanowski, John Q.

2014-01-01

Neurodegenerative diseases (NDs) are defined by the accumulation of abnormal protein deposits in the central nervous system (CNS), and only neuropathological examination enables a definitive diagnosis. Brain banks and their associated scientific programs have shaped the actual knowledge of NDs, identifying and characterizing the CNS deposits that define new diseases, formulating staging schemes, and establishing correlations between neuropathological changes and clinical features. However, brain banks have evolved to accommodate the banking of biofluids as well as DNA and RNA samples. Moreover, the value of biobanks is greatly enhanced if they link all the multidimensional clinical and laboratory information of each case, which is accomplished, optimally, using systematic and standardized operating procedures, and in the framework of multidisciplinary teams with the support of a flexible and user-friendly database system that facilitates the sharing of information of all the teams in the network. We describe a biobanking system that is a platform for discovery research at the Center for Neurodegenerative Disease Research at the University of Pennsylvania. PMID:23978324

Effective 3-D surface modeling for geographic information systems

NASA Astrophysics Data System (ADS)

Yüksek, K.; Alparslan, M.; Mendi, E.

2016-01-01

In this work, we propose a dynamic, flexible and interactive urban digital terrain platform with spatial data and query processing capabilities of geographic information systems, multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized directional replacement policy (DRP) based buffer management scheme. Polyhedron structures are used in digital surface modeling and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g., X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

Background and Data Configuration Process of a Nationwide Population-Based Study Using the Korean National Health Insurance System

PubMed Central

Song, Sun Ok; Jung, Chang Hee; Song, Young Duk; Park, Cheol-Young; Kwon, Hyuk-Sang; Cha, Bong Soo; Park, Joong-Yeol; Lee, Ki-Up

2014-01-01

Background The National Health Insurance Service (NHIS) recently signed an agreement to provide limited open access to the databases within the Korean Diabetes Association for the benefit of Korean subjects with diabetes. Here, we present the history, structure, contents, and way to use data procurement in the Korean National Health Insurance (NHI) system for the benefit of Korean researchers. Methods The NHIS in Korea is a single-payer program and is mandatory for all residents in Korea. The three main healthcare programs of the NHI, Medical Aid, and long-term care insurance (LTCI) provide 100% coverage for the Korean population. The NHIS in Korea has adopted a fee-for-service system to pay health providers. Researchers can obtain health information from the four databases of the insured that contain data on health insurance claims, health check-ups and LTCI. Results Metabolic disease as chronic disease is increasing with aging society. NHIS data is based on mandatory, serial population data, so, this might show the time course of disease and predict some disease progress, and also be used in primary and secondary prevention of disease after data mining. Conclusion The NHIS database represents the entire Korean population and can be used as a population-based database. The integrated information technology of the NHIS database makes it a world-leading population-based epidemiology and disease research platform. PMID:25349827

Background and data configuration process of a nationwide population-based study using the korean national health insurance system.

PubMed

Song, Sun Ok; Jung, Chang Hee; Song, Young Duk; Park, Cheol-Young; Kwon, Hyuk-Sang; Cha, Bong Soo; Park, Joong-Yeol; Lee, Ki-Up; Ko, Kyung Soo; Lee, Byung-Wan

2014-10-01

The National Health Insurance Service (NHIS) recently signed an agreement to provide limited open access to the databases within the Korean Diabetes Association for the benefit of Korean subjects with diabetes. Here, we present the history, structure, contents, and way to use data procurement in the Korean National Health Insurance (NHI) system for the benefit of Korean researchers. The NHIS in Korea is a single-payer program and is mandatory for all residents in Korea. The three main healthcare programs of the NHI, Medical Aid, and long-term care insurance (LTCI) provide 100% coverage for the Korean population. The NHIS in Korea has adopted a fee-for-service system to pay health providers. Researchers can obtain health information from the four databases of the insured that contain data on health insurance claims, health check-ups and LTCI. Metabolic disease as chronic disease is increasing with aging society. NHIS data is based on mandatory, serial population data, so, this might show the time course of disease and predict some disease progress, and also be used in primary and secondary prevention of disease after data mining. The NHIS database represents the entire Korean population and can be used as a population-based database. The integrated information technology of the NHIS database makes it a world-leading population-based epidemiology and disease research platform.

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)

PubMed Central

Weber, Griffin; Mendis, Michael; Gainer, Vivian; Chueh, Henry C; Churchill, Susanne; Kohane, Isaac

2010-01-01

Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases (“data marts”) can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software. PMID:20190053

Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.

PubMed

Hu, Hai; Brzeski, Henry; Hutchins, Joe; Ramaraj, Mohan; Qu, Long; Xiong, Richard; Kalathil, Surendran; Kato, Rand; Tenkillaya, Santhosh; Carney, Jerry; Redd, Rosann; Arkalgudvenkata, Sheshkumar; Shahzad, Kashif; Scott, Richard; Cheng, Hui; Meadow, Stephen; McMichael, John; Sheu, Shwu-Lin; Rosendale, David; Kvecher, Leonid; Ahern, Stephen; Yang, Song; Zhang, Yonghong; Jordan, Rick; Somiari, Stella B; Hooke, Jeffrey; Shriver, Craig D; Somiari, Richard I; Liebman, Michael N

2004-10-01

The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

General pathologist-helper: The new medical app about general pathology.

PubMed

Fernández-Vega, Iván

2015-01-01

Smartphone applications (apps) have become increasingly prevalent in medicine. Due to most pathologists, pathology trainees, technicians, and medical students use smartphones; apps can be a different way for general pathology education. "General pathologist-helper (GP-HELPER)" is a novel app developed as a reference tool in general pathology and especially for general pathologists, developed for Android and iOS platforms. "GP-HELPER," was created using Mobincube website platform. This tool also integrates "FORUM GP-HELPER," an external website created using Miarroba website (http://forum-gp-helper.mboards.com) and "COMMUNITY GP-HELPER" a multichannel chat created using Chatango website platform. The application was released in July 2015, and it is been periodically updated since then. The app has permanent information (offline data) about different pathology protocols (TNM latest edition, protocols regarding management of tumors of unknown primary origin, and flowcharts for some of the most difficult tumors to diagnose) and a database with more than 5000 immunohistochemistry results from different tumors. Online data have links to more than 1100 reference pathology video lectures, 250 antibodies information, more than 70 pathology association websites, 46 pathology providers, and 78 outstanding pathology journal websites. Besides this information, the app has two interactive places such as "FORUM GP-HELPER" and "COMMUNITY GP-HELPER" that let users to stay in touch everywhere and every time. Expert consult section is also available. "GP-HELPER" pretends to integrate offline and online data about pathology with two interactive external places in order to represent a reference tool for general pathologists and associate members.

A web platform for integrated surface water - groundwater modeling and data management

NASA Astrophysics Data System (ADS)

Fatkhutdinov, Aybulat; Stefan, Catalin; Junghanns, Ralf

2016-04-01

Model-based decision support systems are considered to be reliable and time-efficient tools for resources management in various hydrology related fields. However, searching and acquisition of the required data, preparation of the data sets for simulations as well as post-processing, visualization and publishing of the simulations results often requires significantly more work and time than performing the modeling itself. The purpose of the developed software is to combine data storage facilities, data processing instruments and modeling tools in a single platform which potentially can reduce time required for performing simulations, hence decision making. The system is developed within the INOWAS (Innovative Web Based Decision Support System for Water Sustainability under a Changing Climate) project. The platform integrates spatially distributed catchment scale rainfall - runoff, infiltration and groundwater flow models with data storage, processing and visualization tools. The concept is implemented in a form of a web-GIS application and is build based on free and open source components, including the PostgreSQL database management system, Python programming language for modeling purposes, Mapserver for visualization and publishing the data, Openlayers for building the user interface and others. Configuration of the system allows performing data input, storage, pre- and post-processing and visualization in a single not disturbed workflow. In addition, realization of the decision support system in the form of a web service provides an opportunity to easily retrieve and share data sets as well as results of simulations over the internet, which gives significant advantages for collaborative work on the projects and is able to significantly increase usability of the decision support system.

Digital database of channel cross-section surveys, Mount St. Helens, Washington

USGS Publications Warehouse

Mosbrucker, Adam R.; Spicer, Kurt R.; Major, Jon J.; Saunders, Dennis R.; Christianson, Tami S.; Kingsbury, Cole G.

2015-08-06

Stream-channel cross-section survey data are a fundamental component to studies of fluvial geomorphology. Such data provide important parameters required by many open-channel flow models, sediment-transport equations, sediment-budget computations, and flood-hazard assessments. At Mount St. Helens, Washington, the long-term response of channels to the May 18, 1980, eruption, which dramatically altered the hydrogeomorphic regime of several drainages, is documented by an exceptional time series of repeat stream-channel cross-section surveys. More than 300 cross sections, most established shortly following the eruption, represent more than 100 kilometers of surveyed topography. Although selected cross sections have been published previously in print form, we present a comprehensive digital database that includes geospatial and tabular data. Furthermore, survey data are referenced to a common geographic projection and to common datums. Database design, maintenance, and data dissemination are accomplished through a geographic information system (GIS) platform, which integrates survey data acquired with theodolite, total station, and global navigation satellite system (GNSS) instrumentation. Users can interactively perform advanced queries and geospatial time-series analysis. An accuracy assessment provides users the ability to quantify uncertainty within these data. At the time of publication, this project is ongoing. Regular database updates are expected; users are advised to confirm they are using the latest version.

Development of a web-based video management and application processing system

NASA Astrophysics Data System (ADS)

Chan, Shermann S.; Wu, Yi; Li, Qing; Zhuang, Yueting

2001-07-01

How to facilitate efficient video manipulation and access in a web-based environment is becoming a popular trend for video applications. In this paper, we present a web-oriented video management and application processing system, based on our previous work on multimedia database and content-based retrieval. In particular, we extend the VideoMAP architecture with specific web-oriented mechanisms, which include: (1) Concurrency control facilities for the editing of video data among different types of users, such as Video Administrator, Video Producer, Video Editor, and Video Query Client; different users are assigned various priority levels for different operations on the database. (2) Versatile video retrieval mechanism which employs a hybrid approach by integrating a query-based (database) mechanism with content- based retrieval (CBR) functions; its specific language (CAROL/ST with CBR) supports spatio-temporal semantics of video objects, and also offers an improved mechanism to describe visual content of videos by content-based analysis method. (3) Query profiling database which records the `histories' of various clients' query activities; such profiles can be used to provide the default query template when a similar query is encountered by the same kind of users. An experimental prototype system is being developed based on the existing VideoMAP prototype system, using Java and VC++ on the PC platform.

Alignment of high-throughput sequencing data inside in-memory databases.

PubMed

Firnkorn, Daniel; Knaup-Gregori, Petra; Lorenzo Bermejo, Justo; Ganzinger, Matthias

2014-01-01

In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.

An adaptable XML based approach for scientific data management and integration

NASA Astrophysics Data System (ADS)

Wang, Fusheng; Thiel, Florian; Furrer, Daniel; Vergara-Niedermayr, Cristobal; Qin, Chen; Hackenberg, Georg; Bourgue, Pierre-Emmanuel; Kaltschmidt, David; Wang, Mo

2008-03-01

Increased complexity of scientific research poses new challenges to scientific data management. Meanwhile, scientific collaboration is becoming increasing important, which relies on integrating and sharing data from distributed institutions. We develop SciPort, a Web-based platform on supporting scientific data management and integration based on a central server based distributed architecture, where researchers can easily collect, publish, and share their complex scientific data across multi-institutions. SciPort provides an XML based general approach to model complex scientific data by representing them as XML documents. The documents capture not only hierarchical structured data, but also images and raw data through references. In addition, SciPort provides an XML based hierarchical organization of the overall data space to make it convenient for quick browsing. To provide generalization, schemas and hierarchies are customizable with XML-based definitions, thus it is possible to quickly adapt the system to different applications. While each institution can manage documents on a Local SciPort Server independently, selected documents can be published to a Central Server to form a global view of shared data across all sites. By storing documents in a native XML database, SciPort provides high schema extensibility and supports comprehensive queries through XQuery. By providing a unified and effective means for data modeling, data access and customization with XML, SciPort provides a flexible and powerful platform for sharing scientific data for scientific research communities, and has been successfully used in both biomedical research and clinical trials.

An Adaptable XML Based Approach for Scientific Data Management and Integration.

PubMed

Wang, Fusheng; Thiel, Florian; Furrer, Daniel; Vergara-Niedermayr, Cristobal; Qin, Chen; Hackenberg, Georg; Bourgue, Pierre-Emmanuel; Kaltschmidt, David; Wang, Mo

2008-02-20

Increased complexity of scientific research poses new challenges to scientific data management. Meanwhile, scientific collaboration is becoming increasing important, which relies on integrating and sharing data from distributed institutions. We develop SciPort, a Web-based platform on supporting scientific data management and integration based on a central server based distributed architecture, where researchers can easily collect, publish, and share their complex scientific data across multi-institutions. SciPort provides an XML based general approach to model complex scientific data by representing them as XML documents. The documents capture not only hierarchical structured data, but also images and raw data through references. In addition, SciPort provides an XML based hierarchical organization of the overall data space to make it convenient for quick browsing. To provide generalization, schemas and hierarchies are customizable with XML-based definitions, thus it is possible to quickly adapt the system to different applications. While each institution can manage documents on a Local SciPort Server independently, selected documents can be published to a Central Server to form a global view of shared data across all sites. By storing documents in a native XML database, SciPort provides high schema extensibility and supports comprehensive queries through XQuery. By providing a unified and effective means for data modeling, data access and customization with XML, SciPort provides a flexible and powerful platform for sharing scientific data for scientific research communities, and has been successfully used in both biomedical research and clinical trials.

The PyCASSO database: spatially resolved stellar population properties for CALIFA galaxies

NASA Astrophysics Data System (ADS)

de Amorim, A. L.; García-Benito, R.; Cid Fernandes, R.; Cortijo-Ferrero, C.; González Delgado, R. M.; Lacerda, E. A. D.; López Fernández, R.; Pérez, E.; Vale Asari, N.

2017-11-01

The Calar Alto Legacy Integral Field Area (CALIFA) survey, a pioneer in integral field spectroscopy legacy projects, has fostered many studies exploring the information encoded on the spatially resolved data on gaseous and stellar features in the optical range of galaxies. We describe a value-added catalogue of stellar population properties for CALIFA galaxies analysed with the spectral synthesis code starlight and processed with the pycasso platform. Our public database (http://pycasso.ufsc.br/, mirror at http://pycasso.iaa.es/) comprises 445 galaxies from the CALIFA Data Release 3 with COMBO data. The catalogue provides maps for the stellar mass surface density, mean stellar ages and metallicities, stellar dust attenuation, star formation rates, and kinematics. Example applications both for individual galaxies and for statistical studies are presented to illustrate the power of this data set. We revisit and update a few of our own results on mass density radial profiles and on the local mass-metallicity relation. We also show how to employ the catalogue for new investigations, and show a pseudo Schmidt-Kennicutt relation entirely made with information extracted from the stellar continuum. Combinations to other databases are also illustrated. Among other results, we find a very good agreement between star formation rate surface densities derived from the stellar continuum and the H α emission. This public catalogue joins the scientific community's effort towards transparency and reproducibility, and will be useful for researchers focusing on (or complementing their studies with) stellar properties of CALIFA galaxies.

A Web-Based Data Collection Platform for Multisite Randomized Behavioral Intervention Trials: Development, Key Software Features, and Results of a User Survey.

PubMed

Modi, Riddhi A; Mugavero, Michael J; Amico, Rivet K; Keruly, Jeanne; Quinlivan, Evelyn Byrd; Crane, Heidi M; Guzman, Alfredo; Zinski, Anne; Montue, Solange; Roytburd, Katya; Church, Anna; Willig, James H

2017-06-16

Meticulous tracking of study data must begin early in the study recruitment phase and must account for regulatory compliance, minimize missing data, and provide high information integrity and/or reduction of errors. In behavioral intervention trials, participants typically complete several study procedures at different time points. Among HIV-infected patients, behavioral interventions can favorably affect health outcomes. In order to empower newly diagnosed HIV positive individuals to learn skills to enhance retention in HIV care, we developed the behavioral health intervention Integrating ENGagement and Adherence Goals upon Entry (iENGAGE) funded by the National Institute of Allergy and Infectious Diseases (NIAID), where we deployed an in-clinic behavioral health intervention in 4 urban HIV outpatient clinics in the United States. To scale our intervention strategy homogenously across sites, we developed software that would function as a behavioral sciences research platform. This manuscript aimed to: (1) describe the design and implementation of a Web-based software application to facilitate deployment of a multisite behavioral science intervention; and (2) report on results of a survey to capture end-user perspectives of the impact of this platform on the conduct of a behavioral intervention trial. In order to support the implementation of the NIAID-funded trial iENGAGE, we developed software to deploy a 4-site behavioral intervention for new clinic patients with HIV/AIDS. We integrated the study coordinator into the informatics team to participate in the software development process. Here, we report the key software features and the results of the 25-item survey to evaluate user perspectives on research and intervention activities specific to the iENGAGE trial (N=13). The key features addressed are study enrollment, participant randomization, real-time data collection, facilitation of longitudinal workflow, reporting, and reusability. We found 100% user agreement (13/13) that participation in the database design and/or testing phase made it easier to understand user roles and responsibilities and recommended participation of research teams in developing databases for future studies. Users acknowledged ease of use, color flags, longitudinal work flow, and data storage in one location as the most useful features of the software platform and issues related to saving participant forms, security restrictions, and worklist layout as least useful features. The successful development of the iENGAGE behavioral science research platform validated an approach of early and continuous involvement of the study team in design development. In addition, we recommend post-hoc collection of data from users as this led to important insights on how to enhance future software and inform standard clinical practices. Clinicaltrials.gov NCT01900236; (https://clinicaltrials.gov/ct2/show/NCT01900236 (Archived by WebCite at http://www.webcitation.org/6qAa8ld7v). ©Riddhi A Modi, Michael J Mugavero, Rivet K Amico, Jeanne Keruly, Evelyn Byrd Quinlivan, Heidi M Crane, Alfredo Guzman, Anne Zinski, Solange Montue, Katya Roytburd, Anna Church, James H Willig. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 16.06.2017.

An Innovative, No-cost, Evidence-Based Smartphone Platform for Resident Evaluation.

PubMed

Green, John M

Timely performance evaluation and feedback are critical to resident development. However, formulating and delivering this information disrupts physician workflow, leading to low participation. This study was designed to determine if a locally developed smartphone platform would integrate regular evaluation into daily processes and thus increase faculty participation in timely resident evaluation. Formal, documented resident operative and patient interaction evaluations were compiled over an 8-month study period. The study was divided into two 4-month phases. No changes to the existing evaluation methods were made during Phase 1. Phase 2 began after a washout period of 2 weeks and coincided with the launch of a smartphone-based platform. The platform uses a combination of Likert scale questions and the Dreyfus model of skill acquisition to describe competence levels in technical and nontechnical skills. The instrument inflicts minimal effect on surgeon workflow, with the aim of integrating resident evaluation into daily processes. The number of different faculty members performing evaluations, resident level (postgraduate year), type of interaction or procedure, and competency data were compiled. All evaluations were tracked by the program director as they were automatically uploaded into a database. Faculty members were introduced to the new platform at the beginning of Phase 2, and previous methods of evaluation continued to be encouraged and were considered valid throughout both phases of the study. Data were analyzed using Fisher exact test for specific PGY level, and chi-square test was used for overall program analysis. Statistical significance was set at p < 0.05. Total faculty engagement, that is, number of faculty members completing evaluations, increased from 13% (5/38) in Phase 1 to 53% (20/38) in Phase 2. During Phase 1, all evaluations consisted of online forms through the department's established system or e-mails to the program director. Evaluations were completed in 0.9% (15/1599) of cases residents completed in Phase 1 versus 12% (217/1812) of those in Phase 2. During Phase 2, evaluations were conducted exclusively using the new platform. This was done based on participant's choice. Total numbers of residents and core faculty members did not change between Phases 1 and 2. A smartphone-based platform can be created with existing technology at no cost. It is adaptable and can be updated in real-time and can employ validated scales to build an evaluation portfolio for learners assessing technical and nontechnical skills. Furthermore, and perhaps most importantly, it can be designed to integrate into existing workflow patterns to increase faculty participation. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

The Stanford MediaServer Project: strategies for building a flexible digital media platform to support biomedical education and research.

PubMed Central

Durack, Jeremy C.; Chao, Chih-Chien; Stevenson, Derek; Andriole, Katherine P.; Dev, Parvati

2002-01-01

Medical media collections are growing at a pace that exceeds the value they currently provide as research and educational resources. To address this issue, the Stanford MediaServer was designed to promote innovative multimedia-based application development. The nucleus of the MediaServer platform is a digital media database strategically designed to meet the information needs of many biomedical disciplines. Key features include an intuitive web-based interface for collaboratively populating the media database, flexible creation of media collections for diverse and specialized purposes, and the ability to construct a variety of end-user applications from the same database to support biomedical education and research. PMID:12463820

The Stanford MediaServer Project: strategies for building a flexible digital media platform to support biomedical education and research.

PubMed

Durack, Jeremy C; Chao, Chih-Chien; Stevenson, Derek; Andriole, Katherine P; Dev, Parvati

2002-01-01

Medical media collections are growing at a pace that exceeds the value they currently provide as research and educational resources. To address this issue, the Stanford MediaServer was designed to promote innovative multimedia-based application development. The nucleus of the MediaServer platform is a digital media database strategically designed to meet the information needs of many biomedical disciplines. Key features include an intuitive web-based interface for collaboratively populating the media database, flexible creation of media collections for diverse and specialized purposes, and the ability to construct a variety of end-user applications from the same database to support biomedical education and research.

Development and applications of the EntomopathogenID MLSA database for use in agricultural systems

USDA-ARS?s Scientific Manuscript database

The current study reports the development and application of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal was to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identi...

Overcoming Dietary Assessment Challenges in Low-Income Countries: Technological Solutions Proposed by the International Dietary Data Expansion (INDDEX) Project.

PubMed

Coates, Jennifer C; Colaiezzi, Brooke A; Bell, Winnie; Charrondiere, U Ruth; Leclercq, Catherine

2017-03-16

An increasing number of low-income countries (LICs) exhibit high rates of malnutrition coincident with rising rates of overweight and obesity. Individual-level dietary data are needed to inform effective responses, yet dietary data from large-scale surveys conducted in LICs remain extremely limited. This discussion paper first seeks to highlight the barriers to collection and use of individual-level dietary data in LICs. Second, it introduces readers to new technological developments and research initiatives to remedy this situation, led by the International Dietary Data Expansion (INDDEX) Project. Constraints to conducting large-scale dietary assessments include significant costs, time burden, technical complexity, and limited investment in dietary research infrastructure, including the necessary tools and databases required to collect individual-level dietary data in large surveys. To address existing bottlenecks, the INDDEX Project is developing a dietary assessment platform for LICs, called INDDEX24, consisting of a mobile application integrated with a web database application, which is expected to facilitate seamless data collection and processing. These tools will be subject to rigorous testing including feasibility, validation, and cost studies. To scale up dietary data collection and use in LICs, the INDDEX Project will also invest in food composition databases, an individual-level dietary data dissemination platform, and capacity development activities. Although the INDDEX Project activities are expected to improve the ability of researchers and policymakers in low-income countries to collect, process, and use dietary data, the global nutrition community is urged to commit further significant investments in order to adequately address the range and scope of challenges described in this paper.

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics

PubMed Central

Ramirez-Gonzalez, Ricardo H.; Leggett, Richard M.; Waite, Darren; Thanki, Anil; Drou, Nizar; Caccamo, Mario; Davey, Robert

2014-01-01

Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages. PMID:24627795

Overcoming Dietary Assessment Challenges in Low-Income Countries: Technological Solutions Proposed by the International Dietary Data Expansion (INDDEX) Project

PubMed Central

Coates, Jennifer C.; Colaiezzi, Brooke A.; Bell, Winnie; Charrondiere, U. Ruth; Leclercq, Catherine

2017-01-01

An increasing number of low-income countries (LICs) exhibit high rates of malnutrition coincident with rising rates of overweight and obesity. Individual-level dietary data are needed to inform effective responses, yet dietary data from large-scale surveys conducted in LICs remain extremely limited. This discussion paper first seeks to highlight the barriers to collection and use of individual-level dietary data in LICs. Second, it introduces readers to new technological developments and research initiatives to remedy this situation, led by the International Dietary Data Expansion (INDDEX) Project. Constraints to conducting large-scale dietary assessments include significant costs, time burden, technical complexity, and limited investment in dietary research infrastructure, including the necessary tools and databases required to collect individual-level dietary data in large surveys. To address existing bottlenecks, the INDDEX Project is developing a dietary assessment platform for LICs, called INDDEX24, consisting of a mobile application integrated with a web database application, which is expected to facilitate seamless data collection and processing. These tools will be subject to rigorous testing including feasibility, validation, and cost studies. To scale up dietary data collection and use in LICs, the INDDEX Project will also invest in food composition databases, an individual-level dietary data dissemination platform, and capacity development activities. Although the INDDEX Project activities are expected to improve the ability of researchers and policymakers in low-income countries to collect, process, and use dietary data, the global nutrition community is urged to commit further significant investments in order to adequately address the range and scope of challenges described in this paper. PMID:28300759

Digital Image Support in the ROADNet Real-time Monitoring Platform

NASA Astrophysics Data System (ADS)

Lindquist, K. G.; Hansen, T. S.; Newman, R. L.; Vernon, F. L.; Nayak, A.; Foley, S.; Fricke, T.; Orcutt, J.; Rajasekar, A.

2004-12-01

The ROADNet real-time monitoring infrastructure has allowed researchers to integrate geophysical monitoring data from a wide variety of signal domains. Antelope-based data transport, relational-database buffering and archiving, backup/replication/archiving through the Storage Resource Broker, and a variety of web-based distribution tools create a powerful monitoring platform. In this work we discuss our use of the ROADNet system for the collection and processing of digital image data. Remote cameras have been deployed at approximately 32 locations as of September 2004, including the SDSU Santa Margarita Ecological Reserve, the Imperial Beach pier, and the Pinon Flats geophysical observatory. Fire monitoring imagery has been obtained through a connection to the HPWREN project. Near-real-time images obtained from the R/V Roger Revelle include records of seafloor operations by the JASON submersible, as part of a maintenance mission for the H2O underwater seismic observatory. We discuss acquisition mechanisms and the packet architecture for image transport via Antelope orbservers, including multi-packet support for arbitrarily large images. Relational database storage supports archiving of timestamped images, image-processing operations, grouping of related images and cameras, support for motion-detect triggers, thumbnail images, pre-computed video frames, support for time-lapse movie generation and storage of time-lapse movies. Available ROADNet monitoring tools include both orbserver-based display of incoming real-time images and web-accessible searching and distribution of images and movies driven by the relational database (http://mercali.ucsd.edu/rtapps/rtimbank.php). An extension to the Kepler Scientific Workflow System also allows real-time image display via the Ptolemy project. Custom time-lapse movies may be made from the ROADNet web pages.

MouseNet database: digital management of a large-scale mutagenesis project.

PubMed

Pargent, W; Heffner, S; Schäble, K F; Soewarto, D; Fuchs, H; Hrabé de Angelis, M

2000-07-01

The Munich ENU Mouse Mutagenesis Screen is a large-scale mutant production, phenotyping, and mapping project. It encompasses two animal breeding facilities and a number of screening groups located in the general area of Munich. A central database is required to manage and process the immense amount of data generated by the mutagenesis project. This database, which we named MouseNet(c), runs on a Sybase platform and will finally store and process all data from the entire project. In addition, the system comprises a portfolio of functions needed to support the workflow management of the core facility and the screening groups. MouseNet(c) will make all of the data available to the participating screening groups, and later to the international scientific community. MouseNet(c) will consist of three major software components:* Animal Management System (AMS)* Sample Tracking System (STS)* Result Documentation System (RDS)MouseNet(c) provides the following major advantages:* being accessible from different client platforms via the Internet* being a full-featured multi-user system (including access restriction and data locking mechanisms)* relying on a professional RDBMS (relational database management system) which runs on a UNIX server platform* supplying workflow functions and a variety of plausibility checks.

DICOM image integration into an electronic medical record using thin viewing clients

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Taira, Ricky K.

1998-07-01

Purpose -- To integrate radiological DICOM images into our currently existing web-browsable Electronic Medical Record (MINDscape). Over the last five years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A text-based view of this data called the Mini Medical Record (MMR) has been available for three years. MINDscape, unlike the text based MMR, provides a platform independent, web browser view of the MIND dataset that can easily be linked to other information resources on the network. We have now added the integration of radiological images into MINDscape through a DICOM webserver. Methods/New Work -- we have integrated a commercial webserver that acts as a DICOM Storage Class Provider to our, computed radiography (CR), computed tomography (CT), digital fluoroscopy (DF), magnetic resonance (MR) and ultrasound (US) scanning devices. These images can be accessed through CGI queries or by linking the image server database using ODBC or SQL gateways. This allows the use of dynamic HTML links to the images on the DICOM webserver from MINDscape, so that the radiology reports already resident in the MIND repository can be married with the associated images through the unique examination accession number generated by our Radiology Information System (RIS). The web browser plug-in used provides a wavelet decompression engine (up to 16-bits per pixel) and performs the following image manipulation functions: window/level, flip, invert, sort, rotate, zoom, cine-loop and save as JPEG. Results -- Radiological DICOM image sets (CR, CT, MR and US) are displayed with associated exam reports for referring physician and clinicians anywhere within the widespread academic medical center on PCs, Macs, X-terminals and Unix computers. This system is also being used for home teleradiology application. Conclusion -- Radiological DICOM images can be made available medical center wide to physicians quickly using low-cost and ubiquitous, thin client browsing technology and wavelet compression.

GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project.

PubMed

Jeong, Seul-Ki; Hancock, William S; Paik, Young-Ki

2015-09-04

Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.

A Web-GIS Procedure Based on Satellite Multi-Spectral and Airborne LIDAR Data to Map the Road blockage Due to seismic Damages of Built-Up Urban Areas

NASA Astrophysics Data System (ADS)

Costanzo, Antonio; Montuori, Antonio; Silva, Juan Pablo; Silvestri, Malvina; Musacchio, Massimo; Buongiorno, Maria Fabrizia; Stramondo, Salvatore

2016-08-01

In this work, a web-GIS procedure to map the risk of road blockage in urban environments through the combined use of space-borne and airborne remote sensing sensors is presented. The methodology concerns (1) the provision of a geo-database through the integration of space-borne multispectral images and airborne LiDAR data products; (2) the modeling of building vulnerability, based on the corresponding 3D geometry and construction time information; (3) the GIS-based mapping of road closure due to seismic- related building collapses based on the building characteristic height and the width of the road. Experimental results, gathered for the Cosenza urban area, allow demonstrating the benefits of both the proposed approach and the GIS-based integration of multi-platforms remote sensing sensors and techniques for seismic road assessment purposes.

Knowledge-based assistance in costing the space station DMS

NASA Technical Reports Server (NTRS)

Henson, Troy; Rone, Kyle

1988-01-01

The Software Cost Engineering (SCE) methodology developed over the last two decades at IBM Systems Integration Division (SID) in Houston is utilized to cost the NASA Space Station Data Management System (DMS). An ongoing project to capture this methodology, which is built on a foundation of experiences and lessons learned, has resulted in the development of an internal-use-only, PC-based prototype that integrates algorithmic tools with knowledge-based decision support assistants. This prototype Software Cost Engineering Automation Tool (SCEAT) is being employed to assist in the DMS costing exercises. At the same time, DMS costing serves as a forcing function and provides a platform for the continuing, iterative development, calibration, and validation and verification of SCEAT. The data that forms the cost engineering database is derived from more than 15 years of development of NASA Space Shuttle software, ranging from low criticality, low complexity support tools to highly complex and highly critical onboard software.

SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock.

PubMed

Nicolazzi, Ezequiel Luis; Picciolini, Matteo; Strozzi, Francesco; Schnabel, Robert David; Lawley, Cindy; Pirani, Ali; Brew, Fiona; Stella, Alessandra

2014-02-11

Currently, six commercial whole-genome SNP chips are available for cattle genotyping, produced by two different genotyping platforms. Technical issues need to be addressed to combine data that originates from the different platforms, or different versions of the same array generated by the manufacturer. For example: i) genome coordinates for SNPs may refer to different genome assemblies; ii) reference genome sequences are updated over time changing the positions, or even removing sequences which contain SNPs; iii) not all commercial SNP ID's are searchable within public databases; iv) SNPs can be coded using different formats and referencing different strands (e.g. A/B or A/C/T/G alleles, referencing forward/reverse, top/bottom or plus/minus strand); v) Due to new information being discovered, higher density chips do not necessarily include all the SNPs present in the lower density chips; and, vi) SNP IDs may not be consistent across chips and platforms. Most researchers and breed associations manage SNP data in real-time and thus require tools to standardise data in a user-friendly manner. Here we present SNPchiMp, a MySQL database linked to an open access web-based interface. Features of this interface include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). In addition, SNPchiMp can retrieve this information on subsets of SNPs, accessing such data either via physical position on a supported assembly, or by a list of SNP IDs, rs or ss identifiers. This tool combines many different sources of information, that otherwise are time consuming to obtain and difficult to integrate. The SNPchiMp not only provides the information in a user-friendly format, but also enables researchers to perform a large number of operations with a few clicks of the mouse. This significantly reduces the time needed to execute the large number of operations required to manage SNP data.

Structurally Integrated Photoluminescent Chemical and Biological Sensors: An Organic Light-Emitting Diode-Based Platform

NASA Astrophysics Data System (ADS)

Shinar, J.; Shinar, R.

The chapter describes the development, advantages, challenges, and potential of an emerging, compact photoluminescence-based sensing platform for chemical and biological analytes, including multiple analytes. In this platform, the excitation source is an array of organic light-emitting device (OLED) pixels that is structurally integrated with the sensing component. Steps towards advanced integration with additionally a thin-film-based photodetector are also described. The performance of the OLED-based sensing platform is examined for gas-phase and dissolved oxygen, glucose, lactate, ethanol, hydrazine, and anthrax lethal factor.

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

SERS diagnostic platforms, methods and systems microarrays, biosensors and biochips

DOEpatents

Vo-Dinh, Tuan [Knoxville, TN

2007-09-11

A Raman integrated sensor system for the detection of targets including biotargets includes at least one sampling platform, at least one receptor probe disposed on the sampling platform, and an integrated circuit detector system communicably connected to the receptor. The sampling platform is preferably a Raman active surface-enhanced scattering (SERS) platform, wherein the Raman sensor is a SERS sensor. The receptors can include at least one protein receptor and at least one nucleic acid receptor.

Integration of upper air data in the MeteoSwiss Data Warehouse

NASA Astrophysics Data System (ADS)

Musa, M.; Haeberli, Ch.; Ruffieux, D.

2010-09-01

Over the last 10 years MeteoSwiss established a Data Warehouse in order to get one single, integrated data platform for all kinds of meteorological and climatological data. In the MeteoSwiss Data Warehouse data and metadata are hold in a metadata driven relational database. To reach this goal, we started with the integration of the actual and historical data from our surface stations in a first step, including routines for aggregation and calculation and the implementation of enhanced Quality Control tools. In 2008 we started with the integration of actual and historical upper air data like soundings (PTU, Wind and Ozone), any kind of profilers like wind profiler or radiometer, profiles calculated from numerical weather models and AMDAR data in the Data Warehouse. The dataset includes also high resolution sounding data from the station Payerne and TEMP data from 20 European stations since 1942. A critical point was to work out a concept for the general architecture which could deal with all different types of data. While integrating the data itself all metadata of the aerological station Payerne was transferred and imported in the central metadata repository of the Data Warehouse. The implementation of the real time and daily QC tools as well as the routines for aggregation and calculation were realized in an analog way as for the surface data. The Quality Control tools include plausibility tests like limit tests, consistency tests in the same level and vertical consistency tests. From the beginning it was the aim to support the MeteoSwiss integration strategy which deals with all aspects of integration like various observing technologies and platforms, observing systems outside MeteoSwiss and the data and metadata itself. This kind of integration comprises all aspects of "Enterprise Data Integration". After the integration, the historical as well as the actual upper air data are now available for the climatologists and meteorologists with standardized access for data retrieving and visualization. We are convinced making these data accessible for the scientist is a good contribution to a better understanding of high resolution climatology.

New Database Manipulation Tools in the Easy-Learning On-Line Platform

ERIC Educational Resources Information Center

Radescu, Radu; Davidescu, Andrei; Pupezescu, Valentin

2011-01-01

The present paper deals with the new ORM (object-relational mapping) tool introduced in the easy-learning platform. Propel 1.5 is the latest version of Propel, one of the ORMs fully compatible with the Symfony framework, and in comparison with the older versions and it has drastically improved the way the easy-learning platform can manipulate its…

Research on application information system integration platform in medicine manufacturing enterprise.

PubMed

Deng, Wu; Zhao, Huimin; Zou, Li; Li, Yuanyuan; Li, Zhengguang

2012-08-01

Computer and information technology popularizes in the medicine manufacturing enterprise for its potentials in working efficiency and service quality. In allusion to the explosive data and information of application system in current medicine manufacturing enterprise, we desire to propose a novel application information system integration platform in medicine manufacturing enterprise, which based on a combination of RFID technology and SOA, to implement information sharing and alternation. This method exploits the application integration platform across service interface layer to invoke the RFID middleware. The loose coupling in integration solution is realized by Web services. The key techniques in RFID event components and expanded role-based security access mechanism are studied in detail. Finally, a case study is implemented and tested to evidence our understanding on application system integration platform in medicine manufacturing enterprise.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

PubMed

Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

2016-01-01

Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016. Published by Oxford University Press.

Recent advances in proteomics of cereals.

PubMed

Bansal, Monika; Sharma, Madhu; Kanwar, Priyanka; Goyal, Aakash

Cereals contribute a major part of human nutrition and are considered as an integral source of energy for human diets. With genomic databases already available in cereals such as rice, wheat, barley, and maize, the focus has now moved to proteome analysis. Proteomics studies involve the development of appropriate databases based on developing suitable separation and purification protocols, identification of protein functions, and can confirm their functional networks based on already available data from other sources. Tremendous progress has been made in the past decade in generating huge data-sets for covering interactions among proteins, protein composition of various organs and organelles, quantitative and qualitative analysis of proteins, and to characterize their modulation during plant development, biotic, and abiotic stresses. Proteomics platforms have been used to identify and improve our understanding of various metabolic pathways. This article gives a brief review of efforts made by different research groups on comparative descriptive and functional analysis of proteomics applications achieved in the cereal science so far.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources

PubMed Central

Guha, Rajarshi; Nguyen, Dac-Trung; Southall, Noel; Jadhav, Ajit

2012-01-01

Over the last 20 years, there has been an explosion in the amount and type of biological and chemical data that has been made publicly available in a variety of online databases. While this means that vast amounts of information can be found online, there is no guarantee that it can be found easily (or at all). A scientist searching for a specific piece of information is faced with a daunting task - many databases have overlapping content, use their own identifiers and, in some cases, have arcane and unintuitive user interfaces. In this overview, a variety of well known data sources for chemical and biological information are highlighted, focusing on those most useful for chemical biology research. The issue of using multiple data sources together and the associated problems such as identifier disambiguation are highlighted. A brief discussion is then provided on Tripod, a recently developed platform that supports the integration of arbitrary data sources, providing users a simple interface to search across a federated collection of resources. PMID:26609498

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Current and future trends in marine image annotation software

NASA Astrophysics Data System (ADS)

Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.

2016-12-01

Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images. Integration into available MIAS is currently limited to semi-automated processes of pixel recognition through computer-vision modules that compile expert-based knowledge. Important topics aiding the choice of a specific software are outlined, the ideal software is discussed and future trends are presented.

Agile data management for curation of genomes to watershed datasets

NASA Astrophysics Data System (ADS)

Varadharajan, C.; Agarwal, D.; Faybishenko, B.; Versteeg, R.

2015-12-01

A software platform is being developed for data management and assimilation [DMA] as part of the U.S. Department of Energy's Genomes to Watershed Sustainable Systems Science Focus Area 2.0. The DMA components and capabilities are driven by the project science priorities and the development is based on agile development techniques. The goal of the DMA software platform is to enable users to integrate and synthesize diverse and disparate field, laboratory, and simulation datasets, including geological, geochemical, geophysical, microbiological, hydrological, and meteorological data across a range of spatial and temporal scales. The DMA objectives are (a) developing an integrated interface to the datasets, (b) storing field monitoring data, laboratory analytical results of water and sediments samples collected into a database, (c) providing automated QA/QC analysis of data and (d) working with data providers to modify high-priority field and laboratory data collection and reporting procedures as needed. The first three objectives are driven by user needs, while the last objective is driven by data management needs. The project needs and priorities are reassessed regularly with the users. After each user session we identify development priorities to match the identified user priorities. For instance, data QA/QC and collection activities have focused on the data and products needed for on-going scientific analyses (e.g. water level and geochemistry). We have also developed, tested and released a broker and portal that integrates diverse datasets from two different databases used for curation of project data. The development of the user interface was based on a user-centered design process involving several user interviews and constant interaction with data providers. The initial version focuses on the most requested feature - i.e. finding the data needed for analyses through an intuitive interface. Once the data is found, the user can immediately plot and download data through the portal. The resulting product has an interface that is more intuitive and presents the highest priority datasets that are needed by the users. Our agile approach has enabled us to build a system that is keeping pace with the science needs while utilizing limited resources.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes.

PubMed

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. The database is available for free at http://mail.nbfgr.res.in/fbis/

CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.

PubMed

Hernandez-Prieto, Miguel A; Futschik, Matthias E

2012-01-01

Synechocystis sp. PCC6803 is one of the best studied cyanobacteria and an important model organism for our understanding of photosynthesis. The early availability of its complete genome sequence initiated numerous transcriptome studies, which have generated a wealth of expression data. Analysis of the accumulated data can be a powerful tool to study transcription in a comprehensive manner and to reveal underlying regulatory mechanisms, as well as to annotate genes whose functions are yet unknown. However, use of divergent microarray platforms, as well as distributed data storage make meta-analyses of Synechocystis expression data highly challenging, especially for researchers with limited bioinformatic expertise and resources. To facilitate utilisation of the accumulated expression data for a wider research community, we have developed CyanoEXpress, a web database for interactive exploration and visualisation of transcriptional response patterns in Synechocystis. CyanoEXpress currently comprises expression data for 3073 genes and 178 environmental and genetic perturbations obtained in 31 independent studies. At present, CyanoEXpress constitutes the most comprehensive collection of expression data available for Synechocystis and can be freely accessed. The database is available for free at http://cyanoexpress.sysbiolab.eu.

The research and development of water resources management information system based on ArcGIS

NASA Astrophysics Data System (ADS)

Cui, Weiqun; Gao, Xiaoli; Li, Yuzhi; Cui, Zhencai

According to that there are large amount of data, complexity of data type and format in the water resources management, we built the water resources calculation model and established the water resources management information system based on the advanced ArcGIS and Visual Studio.NET development platform. The system can integrate the spatial data and attribute data organically, and manage them uniformly. It can analyze spatial data, inquire by map and data bidirectionally, provide various charts and report forms automatically, link multimedia information, manage database etc. . So it can provide spatial and static synthetical information services for study, management and decision of water resources, regional geology and eco-environment etc..

Bringing the human genome and the revolution in bioinformatics to the medical school classroom: a case report from Washington University School of Medicine.

PubMed

Magee, J; Gordon, J I; Whelan, A

2001-08-01

The human genome project is revolutionizing medical research and the practice of clinical medicine. To understand and participate in this revolution, physicians must be fluent in human genomics and bioinformatics. At Washington University School of Medicine (WUSM), the authors designed a module for teaching these skills to first-year students. The module uses clinical cases as a platform for accessing information stored in GenBank, Online Mendelian Inheritance in Man (OMIM), and PubMed databases at the National Center for Biotechnology Information (NCBI). This module, which is also designed to reinforce problem-solving skills, has been integrated into WUSM's first-year medical genetics course.

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

PubMed

Paez-Espino, David; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M; Nielsen, Torben; Huntemann, Marcel; K Reddy, T B; Pavlopoulos, Georgios A; Sullivan, Matthew B; Campbell, Barbara J; Chen, Feng; McMahon, Katherine; Hallam, Steve J; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean M; Streit, Wolfgang R; Webster, John; Handley, Kim M; Salekdeh, Ghasem H; Tsesmetzis, Nicolas; Setubal, Joao C; Pope, Phillip B; Liu, Wen-Tso; Rivers, Adam R; Ivanova, Natalia N; Kyrpides, Nikos C

2017-01-04

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mobile Food Ordering Application using Android OS Platform

NASA Astrophysics Data System (ADS)

Yosep Ricky, Michael

2014-03-01

The purpose of this research is making an ordering food application based on Android with New Order, Order History, Restaurant Profile, Order Status, Tracking Order, and Setting Profile features. The research method used in this research is water model of System Development Life Cycle (SDLC) method with following phases: requirement definition, analyzing and determining the features needed in developing application and making the detail definition of each features, system and software design, designing the flow of developing application by using storyboard design, user experience design, Unified Modeling Language (UML) design, and database structure design, implementation an unit testing, making database and translating the result of designs to programming language code then doing unit testing, integration and System testing, integrating unit program to one unit system then doing system testing, operation and maintenance, operating the result of system testing and if any changes and reparations needed then the previous phases could be back. The result of this research is an ordering food application based on Android for customer and courier user, and a website for restaurant and admin user. The conclusion of this research is to help customer in making order easily, to give detail information needed by customer, to help restaurant in receiving order, and to help courier while doing delivery.

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species ▿ ‡ #

PubMed Central

Gillespie, Joseph J.; Wattam, Alice R.; Cammer, Stephen A.; Gabbard, Joseph L.; Shukla, Maulik P.; Dalay, Oral; Driscoll, Timothy; Hix, Deborah; Mane, Shrinivasrao P.; Mao, Chunhong; Nordberg, Eric K.; Scott, Mark; Schulman, Julie R.; Snyder, Eric E.; Sullivan, Daniel E.; Wang, Chunxia; Warren, Andrew; Williams, Kelly P.; Xue, Tian; Seung Yoo, Hyun; Zhang, Chengdong; Zhang, Yan; Will, Rebecca; Kenyon, Ronald W.; Sobral, Bruno W.

2011-01-01

Funded by the National Institute of Allergy and Infectious Diseases, the Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided. PMID:21896772

Using realist review to inform intervention development: methodological illustration and conceptual platform for collaborative care in offender mental health.

PubMed

Pearson, M; Brand, S L; Quinn, C; Shaw, J; Maguire, M; Michie, S; Briscoe, S; Lennox, C; Stirzaker, A; Kirkpatrick, T; Byng, R

2015-09-28

This paper reports how we used a realist review, as part of a wider project to improve collaborative mental health care for prisoners with common mental health problems, to develop a conceptual platform. The importance of offenders gaining support for their mental health, and the need for practitioners across the health service, the criminal justice system, and the third sector to work together to achieve this is recognised internationally. However, the literature does not provide coherent analyses of how these ambitions can be achieved. This paper demonstrates how a realist review can be applied to inform complex intervention development that spans different locations, organisations, professions, and care sectors. We applied and developed a realist review for the purposes of intervention development, using a three-stage process. (1) An iterative database search strategy (extending beyond criminal justice and offender health) and groups of academics, practitioners, and people with lived experience were used to identify explanatory accounts (n = 347). (2) From these accounts, we developed consolidated explanatory accounts (n = 75). (3) The identified interactions between practitioners and offenders (within their organisational, social, and cultural contexts) were specified in a conceptual platform. We also specify, step by step, how these explanatory accounts were documented, consolidated, and built into a conceptual platform. This addresses an important methodological gap for social scientists and intervention developers about how to develop and articulate programme and implementation theory underpinning complex interventions. An integrated person-centred system is proposed to improve collaborative mental health care for offenders with common mental health problems (near to and after release) by achieving consistency between the goals of different sectors and practitioners, enabling practitioners to apply scientific and experiential knowledge in working judiciously and reflectively, and building systems and aligning resources that are centred on offenders' health and social care needs. As part of a broader programme of work, a realist review can make an important contribution to the specification of theoretically informed interventions that have the potential to improve health outcomes. Our conceptual platform has potential application in related systems of health and social care where integrated, and person-centred care is a goal.

The climate4impact platform: Providing, tailoring and facilitating climate model data access

NASA Astrophysics Data System (ADS)

Pagé, Christian; Pagani, Andrea; Plieger, Maarten; Som de Cerff, Wim; Mihajlovski, Andrej; de Vreede, Ernst; Spinuso, Alessandro; Hutjes, Ronald; de Jong, Fokke; Bärring, Lars; Vega, Manuel; Cofiño, Antonio; d'Anca, Alessandro; Fiore, Sandro; Kolax, Michael

2017-04-01

One of the main objectives of climate4impact is to provide standardized web services and tools that are reusable in other portals. These services include web processing services, web coverage services and web mapping services (WPS, WCS and WMS). Tailored portals can be targeted to specific communities and/or countries/regions while making use of those services. Easier access to climate data is very important for the climate change impact communities. To fulfill this objective, the climate4impact (http://climate4impact.eu/) web portal and services has been developed, targeting climate change impact modellers, impact and adaptation consultants, as well as other experts using climate change data. It provides to users harmonized access to climate model data through tailored services. It features static and dynamic documentation, Use Cases and best practice examples, an advanced search interface, an integrated authentication and authorization system with the Earth System Grid Federation (ESGF), a visualization interface with ADAGUC web mapping tools. In the latest version, statistical downscaling services, provided by the Santander Meteorology Group Downscaling Portal, were integrated. An innovative interface to integrate statistical downscaling services will be released in the upcoming version. The latter will be a big step in bridging the gap between climate scientists and the climate change impact communities. The climate4impact portal builds on the infrastructure of an international distributed database that has been set to disseminate the results from the global climate model results of the Coupled Model Intercomparison project Phase 5 (CMIP5). This database, the ESGF, is an international collaboration that develops, deploys and maintains software infrastructure for the management, dissemination, and analysis of climate model data. The European FP7 project IS-ENES, Infrastructure for the European Network for Earth System modelling, supports the European contribution to ESGF and contributes to the ESGF open source effort, notably through the development of search, monitoring, quality control, and metadata services. In its second phase, IS-ENES2 supports the implementation of regional climate model results from the international Coordinated Regional Downscaling Experiments (CORDEX). These services were extended within the European FP7 Climate Information Portal for Copernicus (CLIPC) project, and some could be later integrated into the European Copernicus platform.

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reviewing Clinical Effectiveness of Active Training Strategies of Platform-Based Ankle Rehabilitation Robots.

PubMed

Zeng, Xiangfeng; Zhu, Guoli; Zhang, Mingming; Xie, Sheng Q

2018-01-01

This review aims to provide a systematical investigation of clinical effectiveness of active training strategies applied in platform-based ankle robots. English-language studies published from Jan 1980 to Aug 2017 were searched from four databases using key words of "Ankle ∗ " AND "Robot ∗ " AND "Effect ∗ OR Improv ∗ OR Increas ∗ ." Following an initial screening, three rounds of discrimination were successively conducted based on the title, the abstract, and the full paper. A total of 21 studies were selected with 311 patients involved; of them, 13 studies applied a single group while another eight studies used different groups for comparison to verify the therapeutic effect. Virtual-reality (VR) game training was applied in 19 studies, while two studies used proprioceptive neuromuscular facilitation (PNF) training. Active training techniques delivered by platform ankle rehabilitation robots have been demonstrated with great potential for clinical applications. Training strategies are mostly combined with one another by considering rehabilitation schemes and motion ability of ankle joints. VR game environment has been commonly used with active ankle training. Bioelectrical signals integrated with VR game training can implement intelligent identification of movement intention and assessment. These further provide the foundation for advanced interactive training strategies that can lead to enhanced training safety and confidence for patients and better treatment efficacy.

Boutiques: a flexible framework to integrate command-line applications in computing platforms.

PubMed

Glatard, Tristan; Kiar, Gregory; Aumentado-Armstrong, Tristan; Beck, Natacha; Bellec, Pierre; Bernard, Rémi; Bonnet, Axel; Brown, Shawn T; Camarasu-Pop, Sorina; Cervenansky, Frédéric; Das, Samir; Ferreira da Silva, Rafael; Flandin, Guillaume; Girard, Pascal; Gorgolewski, Krzysztof J; Guttmann, Charles R G; Hayot-Sasson, Valérie; Quirion, Pierre-Olivier; Rioux, Pierre; Rousseau, Marc-Étienne; Evans, Alan C

2018-05-01

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

VA's Integrated Imaging System on three platforms.

PubMed

Dayhoff, R E; Maloney, D L; Majurski, W J

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability.

VA's Integrated Imaging System on three platforms.

PubMed Central

Dayhoff, R. E.; Maloney, D. L.; Majurski, W. J.

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability. PMID:1482983

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

PubMed Central

Yi, Ming; Horton, Jay D; Cohen, Jonathan C; Hobbs, Helen H; Stephens, Robert M

2006-01-01

Background Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. Result WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. Conclusion This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at . PMID:16423281

Design of web platform for science and engineering in the model of open market

NASA Astrophysics Data System (ADS)

Demichev, A. P.; Kryukov, A. P.

2016-09-01

This paper presents a design and operation algorithms of a web-platform for convenient, secure and effective remote interaction on the principles of the open market of users and providers of scientific application software and databases.

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

A web-based relational database for monitoring and analyzing mosquito population dynamics.

PubMed

Sucaet, Yves; Van Hemert, John; Tucker, Brad; Bartholomay, Lyric

2008-07-01

Mosquito population dynamics have been monitored on an annual basis in the state of Iowa since 1969. The primary goal of this project was to integrate light trap data from these efforts into a centralized back-end database and interactive website that is available through the internet at http://iowa-mosquito.ent.iastate.edu. For comparative purposes, all data were categorized according to the week of the year and normalized according to the number of traps running. Users can readily view current, weekly mosquito abundance compared with data from previous years. Additional interactive capabilities facilitate analyses of the data based on mosquito species, distribution, or a time frame of interest. All data can be viewed in graphical and tabular format and can be downloaded to a comma separated value (CSV) file for import into a spreadsheet or more specialized statistical software package. Having this long-term dataset in a centralized database/website is useful for informing mosquito and mosquito-borne disease control and for exploring the ecology of the species represented therein. In addition to mosquito population dynamics, this database is available as a standardized platform that could be modified and applied to a multitude of projects that involve repeated collection of observational data. The development and implementation of this tool provides capacity for the user to mine data from standard spreadsheets into a relational database and then view and query the data in an interactive website.

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.

PubMed

Piñero, Janet; Queralt-Rosinach, Núria; Bravo, Àlex; Deu-Pons, Jordi; Bauer-Mehren, Anna; Baron, Martin; Sanz, Ferran; Furlong, Laura I

2015-01-01

DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380,000 associations between >16,000 genes and 13,000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/ © The Author(s) 2015. Published by Oxford University Press.

Helicopter synthetic vision based DVE processing for all phases of flight

NASA Astrophysics Data System (ADS)

O'Brien, Patrick; Baughman, David C.; Wallace, H. Bruce

2013-05-01

Helicopters experience nearly 10 times the accident rate of fixed wing platforms, due largely to the nature of their mission, frequently requiring operations in close proximity to terrain and obstacles. Degraded visual environments (DVE), including brownout or whiteout conditions generated by rotor downwash, result in loss of situational awareness during the most critical phase of flight, and contribute significantly to this accident rate. Considerable research into sensor and system solutions to address DVE has been conducted in recent years; however, the promise of a Synthetic Vision Avionics Backbone (SVAB) extends far beyond DVE, enabling improved situational awareness and mission effectiveness during all phases of flight and in all visibility conditions. The SVAB fuses sensor information with high resolution terrain databases and renders it in synthetic vision format for display to the crew. Honeywell was awarded the DARPA MFRF Technical Area 2 contract in 2011 to develop an SVAB1. This work includes creation of a common sensor interface, development of SVAB hardware and software, and flight demonstration on a Black Hawk helicopter. A "sensor agnostic" SVAB allows platform and mission diversity with efficient upgrade path, even while research continues into new and improved sensors for use in DVE conditions. Through careful integration of multiple sources of information such as sensors, terrain and obstacle databases, mission planning information, and aircraft state information, operations in all conditions and phases of flight can be enhanced. This paper describes the SVAB and its functionality resulting from the DARPA contract as well as Honeywell RD investment.

Internal validation of the DNAscan/ANDE™ Rapid DNA Analysis™ platform and its associated PowerPlex® 16 high content DNA biochip cassette for use as an expert system with reference buccal swabs.

PubMed

Moreno, Lilliana I; Brown, Alice L; Callaghan, Thomas F

2017-07-01

Rapid DNA platforms are fully integrated systems capable of producing and analyzing short tandem repeat (STR) profiles from reference sample buccal swabs in less than two hours. The technology requires minimal user interaction and experience making it possible for high quality profiles to be generated outside an accredited laboratory. The automated production of point of collection reference STR profiles could eliminate the time delay for shipment and analysis of arrestee samples at centralized laboratories. Furthermore, point of collection analysis would allow searching against profiles from unsolved crimes during the normal booking process once the infrastructure to immediately search the Combined DNA Index System (CODIS) database from the booking station is established. The DNAscan/ANDE™ Rapid DNA Analysis™ System developed by Network Biosystems was evaluated for robustness and reliability in the production of high quality reference STR profiles for database enrollment and searching applications. A total of 193 reference samples were assessed for concordance of the CODIS 13 loci. Studies to evaluate contamination, reproducibility, precision, stutter, peak height ratio, noise and sensitivity were also performed. The system proved to be robust, consistent and dependable. Results indicated an overall success rate of 75% for the 13 CODIS core loci and more importantly no incorrect calls were identified. The DNAscan/ANDE™ could be confidently used without human interaction in both laboratory and non-laboratory settings to generate reference profiles. Published by Elsevier B.V.

The development and implementation of MOSAIQ Integration Platform (MIP) based on the radiotherapy workflow

NASA Astrophysics Data System (ADS)

Yang, Xin; He, Zhen-yu; Jiang, Xiao-bo; Lin, Mao-sheng; Zhong, Ning-shan; Hu, Jiang; Qi, Zhen-yu; Bao, Yong; Li, Qiao-qiao; Li, Bao-yue; Hu, Lian-ying; Lin, Cheng-guang; Gao, Yuan-hong; Liu, Hui; Huang, Xiao-yan; Deng, Xiao-wu; Xia, Yun-fei; Liu, Meng-zhong; Sun, Ying

2017-03-01

To meet the special demands in China and the particular needs for the radiotherapy department, a MOSAIQ Integration Platform CHN (MIP) based on the workflow of radiation therapy (RT) has been developed, as a supplement system to the Elekta MOSAIQ. The MIP adopts C/S (client-server) structure mode, and its database is based on the Treatment Planning System (TPS) and MOSAIQ SQL Server 2008, running on the hospital local network. Five network servers, as a core hardware, supply data storage and network service based on the cloud services. The core software, using C# programming language, is developed based on Microsoft Visual Studio Platform. The MIP server could offer network service, including entry, query, statistics and print information for about 200 workstations at the same time. The MIP was implemented in the past one and a half years, and some practical patient-oriented functions were developed. And now the MIP is almost covering the whole workflow of radiation therapy. There are 15 function modules, such as: Notice, Appointment, Billing, Document Management (application/execution), System Management, and so on. By June of 2016, recorded data in the MIP are as following: 13546 patients, 13533 plan application, 15475 RT records, 14656 RT summaries, 567048 billing records and 506612 workload records, etc. The MIP based on the RT workflow has been successfully developed and clinically implemented with real-time performance, data security, stable operation. And it is demonstrated to be user-friendly and is proven to significantly improve the efficiency of the department. It is a key to facilitate the information sharing and department management. More functions can be added or modified for further enhancement its potentials in research and clinical practice.

A platform to integrate climate information and rural telemedicine in Malawi

NASA Astrophysics Data System (ADS)

Lowe, R.; Chadza, T.; Chirombo, J.; Fonda, C.; Muyepa, A.; Nkoloma, M.; Pietrosemoli, E.; Radicella, S. M.; Tompkins, A. M.; Zennaro, M.

2012-04-01

It is commonly accepted that climate plays a role in the transmission of many infectious diseases, particularly those transmitted by mosquitoes such as malaria, which is one of the most important causes of mortality and morbidity in developing countries. Due to time lags involved in the climate-disease transmission system, lagged observed climate variables could provide some predictive lead for forecasting disease epidemics. This lead time could be extended by using forecasts of the climate in disease prediction models. This project aims to implement a platform for the dissemination of climate-driven disease risk forecasts, using a telemedicine approach. A pilot project has been established in Malawi, where a 162 km wireless link has been installed, spanning from Blantyre City to remote health facilities in the district of Mangochi in the Southern region, bordering Lake Malawi. This long Wi-Fi technology allows rural health facilities to upload real-time disease cases as they occur to an online health information system (DHIS2); a national medical database repository administered by the Ministry of Health. This technology provides a real-time data logging system for disease incidence monitoring and facilitates the flow of information between local and national levels. This platform allows statistical and dynamical disease prediction models to be rapidly updated with real-time climate and epidemiological information. This permits health authorities to target timely interventions ahead of an imminent increase in malaria incidence. By integrating meteorological and health information systems in a statistical-dynamical prediction model, we show that a long-distance Wi-Fi link is a practical and inexpensive means to enable the rapid analysis of real-time information in order to target disease prevention and control measures and mobilise resources at the local level.

Data Mining and Knowledge Discovery tools for exploiting big Earth-Observation data

NASA Astrophysics Data System (ADS)

Espinoza Molina, D.; Datcu, M.

2015-04-01

The continuous increase in the size of the archives and in the variety and complexity of Earth-Observation (EO) sensors require new methodologies and tools that allow the end-user to access a large image repository, to extract and to infer knowledge about the patterns hidden in the images, to retrieve dynamically a collection of relevant images, and to support the creation of emerging applications (e.g.: change detection, global monitoring, disaster and risk management, image time series, etc.). In this context, we are concerned with providing a platform for data mining and knowledge discovery content from EO archives. The platform's goal is to implement a communication channel between Payload Ground Segments and the end-user who receives the content of the data coded in an understandable format associated with semantics that is ready for immediate exploitation. It will provide the user with automated tools to explore and understand the content of highly complex images archives. The challenge lies in the extraction of meaningful information and understanding observations of large extended areas, over long periods of time, with a broad variety of EO imaging sensors in synergy with other related measurements and data. The platform is composed of several components such as 1.) ingestion of EO images and related data providing basic features for image analysis, 2.) query engine based on metadata, semantics and image content, 3.) data mining and knowledge discovery tools for supporting the interpretation and understanding of image content, 4.) semantic definition of the image content via machine learning methods. All these components are integrated and supported by a relational database management system, ensuring the integrity and consistency of Terabytes of Earth Observation data.

FORCEnet Net Centric Architecture - A Standards View

DTIC Science & Technology

2006-06-01

SHARED SERVICES NETWORKING/COMMUNICATIONS STORAGE COMPUTING PLATFORM DATA INTERCHANGE/INTEGRATION DATA MANAGEMENT APPLICATION...R V I C E P L A T F O R M S E R V I C E F R A M E W O R K USER-FACING SERVICES SHARED SERVICES NETWORKING/COMMUNICATIONS STORAGE COMPUTING PLATFORM...E F R A M E W O R K USER-FACING SERVICES SHARED SERVICES NETWORKING/COMMUNICATIONS STORAGE COMPUTING PLATFORM DATA INTERCHANGE/INTEGRATION

Mems: Platform for Large-Scale Integrated Vacuum Electronic Circuits

DTIC Science & Technology

2017-03-20

SECURITY CLASSIFICATION OF: The objective of the LIVEC advanced study project was to develop a platform for large-scale integrated vacuum electronic ...Distribution Unlimited UU UU UU UU 20-03-2017 1-Jul-2014 30-Jun-2015 Final Report: MEMS Platform for Large-Scale Integrated Vacuum Electronic ... Electronic Circuits (LIVEC) Contract No: W911NF-14-C-0093 COR Dr. James Harvey U.S. ARO RTP, NC 27709-2211 Phone: 702-696-2533 e-mail

Integrated Web-Based Immersive Exploration of the Coordinated Canyon Experiment Data using Open Source STOQS Software

NASA Astrophysics Data System (ADS)

McCann, M. P.; Gwiazda, R.; O'Reilly, T. C.; Maier, K. L.; Lundsten, E. M.; Parsons, D. R.; Paull, C. K.

2017-12-01

The Coordinated Canyon Experiment (CCE) in Monterey Submarine Canyon has produced a wealth of oceanographic measurements whose analysis will improve understanding of turbidity current processes. Exploration of this data set, consisting of over 60 parameters from 15 platforms, is facilitated by using the open source Spatial Temporal Oceanographic Query System (STOQS) software (https://github.com/stoqs/stoqs). The Monterey Bay Aquarium Research Institute (MBARI) originally developed STOQS to help manage and visualize upper water column oceanographic measurements, but the generality of its data model permits effective use for any kind of spatial/temporal measurement data. STOQS consists of a PostgreSQL database and server-side Python/Django software; the client-side is jQuery JavaScript supporting AJAX requests to update a single page web application. The User Interface (UI) is optimized to provide a quick overview of data in spatial and temporal dimensions, as well as in parameter, platform, and data value space. A user may zoom into any feature of interest and select it, initiating a filter operation that updates the UI with an overview of all the data in the new filtered selection. When details are desired, radio buttons and checkboxes are selected to generate a number of different types of visualizations. These include color-filled temporal section and line plots, parameter-parameter plots, 2D map plots, and interactive 3D spatial visualizations. The Extensible 3D (X3D) standard and X3DOM JavaScript library provide the technology for presenting animated 3D data directly within the web browser. Most of the oceanographic measurements from the CCE (e.g. mooring mounted ADCP and CTD data) are easily visualized using established methods. However, unified integration and multiparameter display of several concurrently deployed sensors across a network of platforms is a challenge we hope to solve. Moreover, STOQS also allows display of data from a new instrument - the Benthic Event Detector (BED). The BED records 50Hz samples of orientation and acceleration when it moves. These data are converted to the CF-NetCDF format and then loaded into a STOQS database. Using the Spatial-3D view a user may interact with a virtual playback of BED motions, giving new insight into submarine canyon sediment density flows.

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

PubMed

Müller, H-M; Van Auken, K M; Li, Y; Sternberg, P W

2018-03-09

The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. Textpresso Central URL: http://www.textpresso.org/tpc.

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

PubMed Central

Muller, Jean; Mehlen, André; Vetter, Guillaume; Yatskou, Mikalai; Muller, Arnaud; Chalmel, Frédéric; Poch, Olivier; Friederich, Evelyne; Vallar, Laurent

2007-01-01

Background The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton. Results Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not. Conclusion Our data demonstrate that Actichip is a powerful alternative to commercial high density microarrays for cytoskeleton gene profiling in normal or pathological samples. Actichip is available upon request. PMID:17727702

Mayday - integrative analytics for expression data

PubMed Central

2010-01-01

Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org. PMID:20214778

Swiss Experiment: Design, implemention and use of a cross-disciplinary infrastructure for data intensive science

NASA Astrophysics Data System (ADS)

Dawes, N.; Salehi, A.; Clifton, A.; Bavay, M.; Aberer, K.; Parlange, M. B.; Lehning, M.

2010-12-01

It has long been known that environmental processes are cross-disciplinary, but data has continued to be acquired and held for a single purpose. Swiss Experiment is a rapidly evolving cross-disciplinary, distributed sensor data infrastructure, where tools for the environmental science community stem directly from computer science research. The platform uses the bleeding edge of computer science to acquire, store and distribute data and metadata from all environmental science disciplines at a variety of temporal and spatial resolutions. SwissEx is simultaneously developing new technologies to allow low cost, high spatial and temporal resolution measurements such that small areas can be intensely monitored. This data is then combined with existing widespread, low density measurements in the cross-disciplinary platform to provide well documented datasets, which are of use to multiple research disciplines. We present a flexible, generic infrastructure at an advanced stage of development. The infrastructure makes the most of Web 2.0 technologies for a collaborative working environment and as a user interface for a metadata database. This environment is already closely integrated with GSN, an open-source database middleware developed under Swiss Experiment for acquisition and storage of generic time-series data (2D and 3D). GSN can be queried directly by common data processing packages and makes data available in real-time to models and 3rd party software interfaces via its web service interface. It also provides real-time push or pull data exchange between instances, a user management system which leaves data owners in charge of their data, advanced real-time processing and much more. The SwissEx interface is increasingly gaining users and supporting environmental science in Switzerland. It is also an integral part of environmental education projects ClimAtscope and O3E, where the technologies can provide rapid feedback of results for children of all ages and where the data from their own stations can be compared to national data networks.

Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes.

PubMed

Chandran, Anil Kumar Nalini; Yoo, Yo-Han; Cao, Peijian; Sharma, Rita; Sharma, Manoj; Dardick, Christopher; Ronald, Pamela C; Jung, Ki-Hong

2016-12-01

Protein kinases catalyze the transfer of a phosphate moiety from a phosphate donor to the substrate molecule, thus playing critical roles in cell signaling and metabolism. Although plant genomes contain more than 1000 genes that encode kinases, knowledge is limited about the function of each of these kinases. A major obstacle that hinders progress towards kinase characterization is functional redundancy. To address this challenge, we previously developed the rice kinase database (RKD) that integrated omics-scale data within a phylogenetics context. An updated version of rice kinase database (RKD) that contains metadata derived from NCBI GEO expression datasets has been developed. RKD 2.0 facilitates in-depth transcriptomic analyses of kinase-encoding genes in diverse rice tissues and in response to biotic and abiotic stresses and hormone treatments. We identified 261 kinases specifically expressed in particular tissues, 130 that are significantly up- regulated in response to biotic stress, 296 in response to abiotic stress, and 260 in response to hormones. Based on this update and Pearson correlation coefficient (PCC) analysis, we estimated that 19 out of 26 genes characterized through loss-of-function studies confer dominant functions. These were selected because they either had paralogous members with PCC values of <0.5 or had no paralog. Compared with the previous version of RKD, RKD 2.0 enables more effective estimations of functional redundancy or dominance because it uses comprehensive expression profiles rather than individual profiles. The integrated analysis of RKD with PCC establishes a single platform for researchers to select rice kinases for functional analyses.

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila.

PubMed

Pandey, Ram Vinay; Kofler, Robert; Orozco-terWengel, Pablo; Nolte, Viola; Schlötterer, Christian

2011-03-02

The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses. With the new sequencing technologies it has become feasible to collect sequence information for multiple individuals on a genomic scale. In particular sequencing pooled DNA samples has been shown to provide a cost-effective approach for characterizing variation in natural populations. While a range of software tools have been developed for mapping these reads onto a reference genome and extracting SNPs, linking this information to population genetic estimators and functional information still poses a major challenge to many researchers. We developed PoPoolation DB a user-friendly integrated database. Popoolation DB links variation in natural populations with functional information, allowing a wide range of researchers to take advantage of population genetic data. PoPoolation DB provides the user with population genetic parameters (Watterson's θ or Tajima's π), Tajima's D, SNPs, allele frequencies and indels in regions of interest. The database can be queried by gene name, chromosomal position, or a user-provided query sequence or GTF file. We anticipate that PoPoolation DB will be a highly versatile tool for functional geneticists as well as evolutionary biologists. PoPoolation DB, available at http://www.popoolation.at/pgt, provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.

Episodic Laryngeal Breathing Disorders: Literature Review and Proposal of Preliminary Theoretical Framework.

PubMed

Shembel, Adrianna C; Sandage, Mary J; Verdolini Abbott, Katherine

2017-01-01

The purposes of this literature review were (1) to identify and assess frameworks for clinical characterization of episodic laryngeal breathing disorders (ELBD) and their subtypes, (2) to integrate concepts from these frameworks into a novel theoretical paradigm, and (3) to provide a preliminary algorithm to classify clinical features of ELBD for future study of its clinical manifestations and underlying pathophysiological mechanisms. This is a literature review. Peer-reviewed literature from 1983 to 2015 pertaining to models for ELBD was searched using Pubmed, Ovid, Proquest, Cochrane Database of Systematic Reviews, and Google Scholar. Theoretical models for ELBD were identified, evaluated, and integrated into a novel comprehensive framework. Consensus across three salient models provided a working definition and inclusionary criteria for ELBD within the new framework. Inconsistencies and discrepancies within the models provided an analytic platform for future research. Comparison among three conceptual models-(1) Irritable larynx syndrome, (2) Dichotomous triggers, and (3) Periodic occurrence of laryngeal obstruction-showed that the models uniformly consider ELBD to involve episodic laryngeal obstruction causing dyspnea. The models differed in their description of source of dyspnea, in their inclusion of corollary behaviors, in their inclusion of other laryngeal-based behaviors (eg, cough), and types of triggers. The proposed integrated theoretical framework for ELBD provides a preliminary systematic platform for the identification of key clinical feature patterns indicative of ELBD and associated clinical subgroups. This algorithmic paradigm should evolve with better understanding of this spectrum of disorders and its underlying pathophysiological mechanisms. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Introducing WISDEM:An Integrated System Modeling for Wind Turbines and Plant (Presentation)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dykes, K.; Graf, P.; Scott, G.

2015-01-01

The National Wind Technology Center wind energy systems engineering initiative has developed an analysis platform to leverage its research capabilities toward integrating wind energy engineering and cost models across wind plants. This Wind-Plant Integrated System Design & Engineering Model (WISDEM) platform captures the important interactions between various subsystems to achieve a better National Wind Technology Center wind energy systems engineering initiative has developed an analysis platform to leverage its research capabilities toward integrating wind energy engineering and cost models across wind plants. This Wind-Plant Integrated System Design & Engineering Model (WISDEM) platform captures the important interactions between various subsystems tomore » achieve a better understanding of how to improve system-level performance and achieve system-level cost reductions. This work illustrates a few case studies with WISDEM that focus on the design and analysis of wind turbines and plants at different system levels.« less

Reconstruction of genome-scale human metabolic models using omics data.

PubMed

Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup

2015-08-01

The impact of genome-scale human metabolic models on human systems biology and medical sciences is becoming greater, thanks to increasing volumes of model building platforms and publicly available omics data. The genome-scale human metabolic models started with Recon 1 in 2007, and have since been used to describe metabolic phenotypes of healthy and diseased human tissues and cells, and to predict therapeutic targets. Here we review recent trends in genome-scale human metabolic modeling, including various generic and tissue/cell type-specific human metabolic models developed to date, and methods, databases and platforms used to construct them. For generic human metabolic models, we pay attention to Recon 2 and HMR 2.0 with emphasis on data sources used to construct them. Draft and high-quality tissue/cell type-specific human metabolic models have been generated using these generic human metabolic models. Integration of tissue/cell type-specific omics data with the generic human metabolic models is the key step, and we discuss omics data and their integration methods to achieve this task. The initial version of the tissue/cell type-specific human metabolic models can further be computationally refined through gap filling, reaction directionality assignment and the subcellular localization of metabolic reactions. We review relevant tools for this model refinement procedure as well. Finally, we suggest the direction of further studies on reconstructing an improved human metabolic model.

From Corynebacterium glutamicum to Mycobacterium tuberculosis—towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

PubMed Central

Krawczyk, Justina; Kohl, Thomas A.; Goesmann, Alexander; Kalinowski, Jörn; Baumbach, Jan

2009-01-01

Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de. PMID:19494184

Boutiques: a flexible framework to integrate command-line applications in computing platforms

PubMed Central

Glatard, Tristan; Kiar, Gregory; Aumentado-Armstrong, Tristan; Beck, Natacha; Bellec, Pierre; Bernard, Rémi; Bonnet, Axel; Brown, Shawn T; Camarasu-Pop, Sorina; Cervenansky, Frédéric; Das, Samir; Ferreira da Silva, Rafael; Flandin, Guillaume; Girard, Pascal; Gorgolewski, Krzysztof J; Guttmann, Charles R G; Hayot-Sasson, Valérie; Quirion, Pierre-Olivier; Rioux, Pierre; Rousseau, Marc-Étienne; Evans, Alan C

2018-01-01

Abstract We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science. PMID:29718199

Aluminum nitride integrated photonics platform for the ultraviolet to visible spectrum.

PubMed

Lu, Tsung-Ju; Fanto, Michael; Choi, Hyeongrak; Thomas, Paul; Steidle, Jeffrey; Mouradian, Sara; Kong, Wei; Zhu, Di; Moon, Hyowon; Berggren, Karl; Kim, Jeehwan; Soltani, Mohammad; Preble, Stefan; Englund, Dirk

2018-04-30

We demonstrate a wide-bandgap semiconductor photonics platform based on nanocrystalline aluminum nitride (AlN) on sapphire. This photonics platform guides light at low loss from the ultraviolet (UV) to the visible spectrum. We measure ring resonators with intrinsic quality factor (Q) exceeding 170,000 at 638 nm and Q >20,000 down to 369.5 nm, which shows a promising path for low-loss integrated photonics in UV and visible spectrum. This platform opens up new possibilities in integrated quantum optics with trapped ions or atom-like color centers in solids, as well as classical applications including nonlinear optics and on-chip UV-spectroscopy.

1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway.

PubMed

Bhat, Manoj K; Gadekar, Veerendra P; Jain, Aditya; Paul, Bobby; Rai, Padmalatha S; Satyamoorthy, Kapaettu

2017-01-01

The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded. Hence, we designed the one-carbon metabolism database (1-CMDb) as a platform to interrogate its association with a host of human disorders. DNA sequence and network information of a total of 48 genes were extracted from a literature survey and KEGG pathway that are involved in the one-carbon folate-mediated pathway. The information generated, collected, and compiled for all these genes from the UCSC genome browser included the single nucleotide polymorphisms (SNPs), CpGs, copy number variations (CNVs), and miRNAs, and a comprehensive database was created. Furthermore, a significant correlation analysis was performed for SNPs in the pathway genes. Detailed data of SNPs, CNVs, CpG islands, and miRNAs for 48 folate pathway genes were compiled. The SNPs in CNVs (9670), CpGs (984), and miRNAs (14) were also compiled for all pathway genes. The SIFT score, the prediction and PolyPhen score, as well as the prediction for each of the SNPs were tabulated and represented for folate pathway genes. Also included in the database for folate pathway genes were the links to 124 various phenotypes and disease associations as reported in the literature and from publicly available information. A comprehensive database was generated consisting of genomic elements within and among SNPs, CNVs, CpGs, and miRNAs of one-carbon metabolism pathways to facilitate (a) single source of information and (b) integration into large-genome scale network analysis to be developed in the future by the scientific community. The database can be accessed at http://slsdb.manipal.edu/ocm/. © 2017 S. Karger AG, Basel.

Database for the collection and analysis of clinical data and images of neoplasms of the sinonasal tract.

PubMed

Trimarchi, Matteo; Lund, Valerie J; Nicolai, Piero; Pini, Massimiliano; Senna, Massimo; Howard, David J

2004-04-01

The Neoplasms of the Sinonasal Tract software package (NSNT v 1.0) implements a complete visual database for patients with sinonasal neoplasia, facilitating standardization of data and statistical analysis. The software, which is compatible with the Macintosh and Windows platforms, provides multiuser application with a dedicated server (on Windows NT or 2000 or Macintosh OS 9 or X and a network of clients) together with web access, if required. The system hardware consists of an Apple Power Macintosh G4500 MHz computer with PCI bus, 256 Mb of RAM plus 60 Gb hard disk, or any IBM-compatible computer with a Pentium 2 processor. Image acquisition may be performed with different frame-grabber cards for analog or digital video input of different standards (PAL, SECAM, or NTSC) and levels of quality (VHS, S-VHS, Betacam, Mini DV, DV). The visual database is based on 4th Dimension by 4D Inc, and video compression is made in real-time MPEG format. Six sections have been developed: demographics, symptoms, extent of disease, radiology, treatment, and follow-up. Acquisition of data includes computed tomography and magnetic resonance imaging, histology, and endoscopy images, allowing sequential comparison. Statistical analysis integral to the program provides Kaplan-Meier survival curves. The development of a dedicated, user-friendly database for sinonasal neoplasia facilitates a multicenter network and has obvious clinical and research benefits.

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

PubMed

Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

2016-07-04

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

Integrated WiFi/PDR/Smartphone Using an Unscented Kalman Filter Algorithm for 3D Indoor Localization.

PubMed

Chen, Guoliang; Meng, Xiaolin; Wang, Yunjia; Zhang, Yanzhe; Tian, Peng; Yang, Huachao

2015-09-23

Because of the high calculation cost and poor performance of a traditional planar map when dealing with complicated indoor geographic information, a WiFi fingerprint indoor positioning system cannot be widely employed on a smartphone platform. By making full use of the hardware sensors embedded in the smartphone, this study proposes an integrated approach to a three-dimensional (3D) indoor positioning system. First, an improved K-means clustering method is adopted to reduce the fingerprint database retrieval time and enhance positioning efficiency. Next, with the mobile phone's acceleration sensor, a new step counting method based on auto-correlation analysis is proposed to achieve cell phone inertial navigation positioning. Furthermore, the integration of WiFi positioning with Pedestrian Dead Reckoning (PDR) obtains higher positional accuracy with the help of the Unscented Kalman Filter algorithm. Finally, a hybrid 3D positioning system based on Unity 3D, which can carry out real-time positioning for targets in 3D scenes, is designed for the fluent operation of mobile terminals.

Integrated WiFi/PDR/Smartphone Using an Unscented Kalman Filter Algorithm for 3D Indoor Localization

PubMed Central

Chen, Guoliang; Meng, Xiaolin; Wang, Yunjia; Zhang, Yanzhe; Tian, Peng; Yang, Huachao

2015-01-01

Because of the high calculation cost and poor performance of a traditional planar map when dealing with complicated indoor geographic information, a WiFi fingerprint indoor positioning system cannot be widely employed on a smartphone platform. By making full use of the hardware sensors embedded in the smartphone, this study proposes an integrated approach to a three-dimensional (3D) indoor positioning system. First, an improved K-means clustering method is adopted to reduce the fingerprint database retrieval time and enhance positioning efficiency. Next, with the mobile phone’s acceleration sensor, a new step counting method based on auto-correlation analysis is proposed to achieve cell phone inertial navigation positioning. Furthermore, the integration of WiFi positioning with Pedestrian Dead Reckoning (PDR) obtains higher positional accuracy with the help of the Unscented Kalman Filter algorithm. Finally, a hybrid 3D positioning system based on Unity 3D, which can carry out real-time positioning for targets in 3D scenes, is designed for the fluent operation of mobile terminals. PMID:26404314

A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model

PubMed Central

Castillo, Andreina I; Nelson, Andrew D L; Haug-Baltzell, Asher K; Lyons, Eric

2018-01-01

Abstract Integrated platforms for storage, management, analysis and sharing of large quantities of omics data have become fundamental to comparative genomics. CoGe (https://genomevolution.org/coge/) is an online platform designed to manage and study genomic data, enabling both data- and hypothesis-driven comparative genomics. CoGe’s tools and resources can be used to organize and analyse both publicly available and private genomic data from any species. Here, we demonstrate the capabilities of CoGe through three example workflows using 17 Plasmodium genomes as a model. Plasmodium genomes present unique challenges for comparative genomics due to their rapidly evolving and highly variable genomic AT/GC content. These example workflows are intended to serve as templates to help guide researchers who would like to use CoGe to examine diverse aspects of genome evolution. In the first workflow, trends in genome composition and amino acid usage are explored. In the second, changes in genome structure and the distribution of synonymous (Ks) and non-synonymous (Kn) substitution values are evaluated across species with different levels of evolutionary relatedness. In the third workflow, microsyntenic analyses of multigene families’ genomic organization are conducted using two Plasmodium-specific gene families—serine repeat antigen, and cytoadherence-linked asexual gene—as models. In general, these example workflows show how to achieve quick, reproducible and shareable results using the CoGe platform. We were able to replicate previously published results, as well as leverage CoGe’s tools and resources to gain additional insight into various aspects of Plasmodium genome evolution. Our results highlight the usefulness of the CoGe platform, particularly in understanding complex features of genome evolution. Database URL: https://genomevolution.org/coge/

EFEHR - the European Facilities for Earthquake Hazard and Risk: beyond the web-platform

NASA Astrophysics Data System (ADS)

Danciu, Laurentiu; Wiemer, Stefan; Haslinger, Florian; Kastli, Philipp; Giardini, Domenico

2017-04-01

European Facilities for Earthquake Hazard and Risk (EEFEHR) represents the sustainable community resource for seismic hazard and risk in Europe. The EFEHR web platform is the main gateway to access data, models and tools as well as provide expertise relevant for assessment of seismic hazard and risk. The main services (databases and web-platform) are hosted at ETH Zurich and operated by the Swiss Seismological Service (Schweizerischer Erdbebendienst SED). EFEHR web-portal (www.efehr.org) collects and displays (i) harmonized datasets necessary for hazard and risk modeling, e.g. seismic catalogues, fault compilations, site amplifications, vulnerabilities, inventories; (ii) extensive seismic hazard products, namely hazard curves, uniform hazard spectra and maps for national and regional assessments. (ii) standardized configuration files for re-computing the regional seismic hazard models; (iv) relevant documentation of harmonized datasets, models and web-services. Today, EFEHR distributes full output of the 2013 European Seismic Hazard Model, ESHM13, as developed within the SHARE project (http://www.share-eu.org/); the latest results of the 2014 Earthquake Model of the Middle East (EMME14), derived within the EMME Project (www.emme-gem.org); the 2001 Global Seismic Hazard Assessment Project (GSHAP) results and the 2015 updates of the Swiss Seismic Hazard. New datasets related to either seismic hazard or risk will be incorporated as they become available. We present the currents status of the EFEHR platform, with focus on the challenges, summaries of the up-to-date datasets, user experience and feedback, as well as the roadmap to future technological innovation beyond the web-platform development. We also show the new services foreseen to fully integrate with the seismological core services of European Plate Observing System (EPOS).

The simcyp population based simulator: architecture, implementation, and quality assurance.

PubMed

Jamei, Masoud; Marciniak, Steve; Edwards, Duncan; Wragg, Kris; Feng, Kairui; Barnett, Adrian; Rostami-Hodjegan, Amin

2013-01-01

Developing a user-friendly platform that can handle a vast number of complex physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models both for conventional small molecules and larger biologic drugs is a substantial challenge. Over the last decade the Simcyp Population Based Simulator has gained popularity in major pharmaceutical companies (70% of top 40 - in term of R&D spending). Under the Simcyp Consortium guidance, it has evolved from a simple drug-drug interaction tool to a sophisticated and comprehensive Model Based Drug Development (MBDD) platform that covers a broad range of applications spanning from early drug discovery to late drug development. This article provides an update on the latest architectural and implementation developments within the Simulator. Interconnection between peripheral modules, the dynamic model building process and compound and population data handling are all described. The Simcyp Data Management (SDM) system, which contains the system and drug databases, can help with implementing quality standards by seamless integration and tracking of any changes. This also helps with internal approval procedures, validation and auto-testing of the new implemented models and algorithms, an area of high interest to regulatory bodies.

D Modelling and Visualization Based on the Unity Game Engine - Advantages and Challenges

NASA Astrophysics Data System (ADS)

Buyuksalih, I.; Bayburt, S.; Buyuksalih, G.; Baskaraca, A. P.; Karim, H.; Rahman, A. A.

2017-11-01

3D City modelling is increasingly popular and becoming valuable tools in managing big cities. Urban and energy planning, landscape, noise-sewage modelling, underground mapping and navigation are among the applications/fields which really depend on 3D modelling for their effectiveness operations. Several research areas and implementation projects had been carried out to provide the most reliable 3D data format for sharing and functionalities as well as visualization platform and analysis. For instance, BIMTAS company has recently completed a project to estimate potential solar energy on 3D buildings for the whole Istanbul and now focussing on 3D utility underground mapping for a pilot case study. The research and implementation standard on 3D City Model domain (3D data sharing and visualization schema) is based on CityGML schema version 2.0. However, there are some limitations and issues in implementation phase for large dataset. Most of the limitations were due to the visualization, database integration and analysis platform (Unity3D game engine) as highlighted in this paper.

Ontology based heterogeneous materials database integration and semantic query

NASA Astrophysics Data System (ADS)

Zhao, Shuai; Qian, Quan

2017-10-01

Materials digital data, high throughput experiments and high throughput computations are regarded as three key pillars of materials genome initiatives. With the fast growth of materials data, the integration and sharing of data is very urgent, that has gradually become a hot topic of materials informatics. Due to the lack of semantic description, it is difficult to integrate data deeply in semantic level when adopting the conventional heterogeneous database integration approaches such as federal database or data warehouse. In this paper, a semantic integration method is proposed to create the semantic ontology by extracting the database schema semi-automatically. Other heterogeneous databases are integrated to the ontology by means of relational algebra and the rooted graph. Based on integrated ontology, semantic query can be done using SPARQL. During the experiments, two world famous First Principle Computational databases, OQMD and Materials Project are used as the integration targets, which show the availability and effectiveness of our method.

Field results from a new die-to-database reticle inspection platform

NASA Astrophysics Data System (ADS)

Broadbent, William; Yokoyama, Ichiro; Yu, Paul; Seki, Kazunori; Nomura, Ryohei; Schmalfuss, Heiko; Heumann, Jan; Sier, Jean-Paul

2007-05-01

A new die-to-database high-resolution reticle defect inspection platform, TeraScanHR, has been developed for advanced production use with the 45nm logic node, and extendable for development use with the 32nm node (also the comparable memory nodes). These nodes will use predominantly ArF immersion lithography although EUV may also be used. According to recent surveys, the predominant reticle types for the 45nm node are 6% simple tri-tone and COG. Other advanced reticle types may also be used for these nodes including: dark field alternating, Mask Enhancer, complex tri-tone, high transmission, CPL, etc. Finally, aggressive model based OPC will typically be used which will include many small structures such as jogs, serifs, and SRAF (sub-resolution assist features) with accompanying very small gaps between adjacent structures. The current generation of inspection systems is inadequate to meet these requirements. The architecture and performance of the new TeraScanHR reticle inspection platform is described. This new platform is designed to inspect the aforementioned reticle types in die-to-database and die-to-die modes using both transmitted and reflected illumination. Recent results from field testing at two of the three beta sites are shown (Toppan Printing in Japan and the Advanced Mask Technology Center in Germany). The results include applicable programmed defect test reticles and advanced 45nm product reticles (also comparable memory reticles). The results show high sensitivity and low false detections being achieved. The platform can also be configured for the current 65nm, 90nm, and 130nm nodes.

Integration of Jeddah Historical BIM and 3D GIS for Documentation and Restoration of Historical Monument

NASA Astrophysics Data System (ADS)

Baik, A.; Yaagoubi, R.; Boehm, J.

2015-08-01

This work outlines a new approach for the integration of 3D Building Information Modelling and the 3D Geographic Information System (GIS) to provide semantically rich models, and to get the benefits from both systems to help document and analyse cultural heritage sites. Our proposed framework is based on the Jeddah Historical Building Information Modelling process (JHBIM). This JHBIM consists of a Hijazi Architectural Objects Library (HAOL) that supports higher level of details (LoD) while decreasing the time of modelling. The Hijazi Architectural Objects Library has been modelled based on the Islamic historical manuscripts and Hijazi architectural pattern books. Moreover, the HAOL is implemented using BIM software called Autodesk Revit. However, it is known that this BIM environment still has some limitations with the non-standard architectural objects. Hence, we propose to integrate the developed 3D JHBIM with 3D GIS for more advanced analysis. To do so, the JHBIM database is exported and semantically enriched with non-architectural information that is necessary for restoration and preservation of historical monuments. After that, this database is integrated with the 3D Model in the 3D GIS solution. At the end of this paper, we'll illustrate our proposed framework by applying it to a Historical Building called Nasif Historical House in Jeddah. First of all, this building is scanned by the use of a Terrestrial Laser Scanner (TLS) and Close Range Photogrammetry. Then, the 3D JHBIM based on the HOAL is designed on Revit Platform. Finally, this model is integrated to a 3D GIS solution through Autodesk InfraWorks. The shown analysis presented in this research highlights the importance of such integration especially for operational decisions and sharing the historical knowledge about Jeddah Historical City. Furthermore, one of the historical buildings in Old Jeddah, Nasif Historical House, was chosen as a test case for the project.

Functional integration of automated system databases by means of artificial intelligence

NASA Astrophysics Data System (ADS)

Dubovoi, Volodymyr M.; Nikitenko, Olena D.; Kalimoldayev, Maksat; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

2017-08-01

The paper presents approaches for functional integration of automated system databases by means of artificial intelligence. The peculiarities of turning to account the database in the systems with the usage of a fuzzy implementation of functions were analyzed. Requirements for the normalization of such databases were defined. The question of data equivalence in conditions of uncertainty and collisions in the presence of the databases functional integration is considered and the model to reveal their possible occurrence is devised. The paper also presents evaluation method of standardization of integrated database normalization.

Climate Signals: An On-Line Digital Platform for Mapping Climate Change Impacts in Real Time

NASA Astrophysics Data System (ADS)

Cutting, H.

2016-12-01

Climate Signals is an on-line digital platform for cataloging and mapping the impacts of climate change. The CS platform specifies and details the chains of connections between greenhouse gas emissions and individual climate events. Currently in open-beta release, the platform is designed to to engage and serve the general public, news media, and policy-makers, particularly in real-time during extreme climate events. Climate Signals consists of a curated relational database of events and their links to climate change, a mapping engine, and a gallery of climate change monitors offering real-time data. For each event in the database, an infographic engine provides a custom attribution "tree" that illustrates the connections to climate change. In addition, links to key contextual resources are aggregated and curated for each event. All event records are fully annotated with detailed source citations and corresponding hyper links. The system of attribution used to link events to climate change in real-time is detailed here. This open-beta release is offered for public user testing and engagement. Launched in May 2016, the operation of this platform offers lessons for public engagement in climate change impacts.

Evaluation of Smartphone Inertial Sensor Performance for Cross-Platform Mobile Applications

PubMed Central

Kos, Anton; Tomažič, Sašo; Umek, Anton

2016-01-01

Smartphone sensors are being increasingly used in mobile applications. The performance of sensors varies considerably among different smartphone models and the development of a cross-platform mobile application might be a very complex and demanding task. A publicly accessible resource containing real-life-situation smartphone sensor parameters could be of great help for cross-platform developers. To address this issue we have designed and implemented a pilot participatory sensing application for measuring, gathering, and analyzing smartphone sensor parameters. We start with smartphone accelerometer and gyroscope bias and noise parameters. The application database presently includes sensor parameters of more than 60 different smartphone models of different platforms. It is a modest, but important start, offering information on several statistical parameters of the measured smartphone sensors and insights into their performance. The next step, a large-scale cloud-based version of the application, is already planned. The large database of smartphone sensor parameters may prove particularly useful for cross-platform developers. It may also be interesting for individual participants who would be able to check-up and compare their smartphone sensors against a large number of similar or identical models. PMID:27049391

Knowledge discovery through games and game theory

NASA Astrophysics Data System (ADS)

Smith, James F., III; Rhyne, Robert D.

2001-03-01

A fuzzy logic based expert system has been developed that automatically allocates electronic attack (EA) resources in real-time over many dissimilar platforms. The platforms can be very general, e.g., ships, planes, robots, land based facilities, etc. Potential foes the platforms deal with can also be general. The initial version of the algorithm was optimized using a genetic algorithm employing fitness functions constructed based on expertise. A new approach is being explored that involves embedding the resource manager in a electronic game environment. The game allows a human expert to play against the resource manager in a simulated battlespace with each of the defending platforms being exclusively directed by the fuzzy resource manager and the attacking platforms being controlled by the human expert or operating autonomously under their own logic. This approach automates the data mining problem. The game automatically creates a database reflecting the domain expert's knowledge, it calls a data mining function, a genetic algorithm, for data mining of the database as required. The game allows easy evaluation of the information mined in the second step. The measure of effectiveness (MOE) for re-optimization is discussed. The mined information is extremely valuable as shown through demanding scenarios.

A comprehensive SNP and indel imputability database.

PubMed

Duan, Qing; Liu, Eric Yi; Croteau-Chonka, Damien C; Mohlke, Karen L; Li, Yun

2013-02-15

Genotype imputation has become an indispensible step in genome-wide association studies (GWAS). Imputation accuracy, directly influencing downstream analysis, has shown to be improved using re-sequencing-based reference panels; however, this comes at the cost of high computational burden due to the huge number of potentially imputable markers (tens of millions) discovered through sequencing a large number of individuals. Therefore, there is an increasing need for access to imputation quality information without actually conducting imputation. To facilitate this process, we have established a publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major populations and covering multiple GWAS genotyping platforms. SNP and indel imputability information can be retrieved through a user-friendly interface by providing the ID(s) of the desired variant(s) or by specifying the desired genomic region. The query results can be refined by selecting relevant GWAS genotyping platform(s). This is the first database providing variant imputability information specific to each continental group and to each genotyping platform. In Filipino individuals from the Cebu Longitudinal Health and Nutrition Survey, our database can achieve an area under the receiver-operating characteristic curve of 0.97, 0.91, 0.88 and 0.79 for markers with minor allele frequency >5%, 3-5%, 1-3% and 0.5-1%, respectively. Specifically, by filtering out 48.6% of markers (corresponding to a reduction of up to 48.6% in computational costs for actual imputation) based on the imputability information in our database, we can remove 77%, 58%, 51% and 42% of the poorly imputed markers at the cost of only 0.3%, 0.8%, 1.5% and 4.6% of the well-imputed markers with minor allele frequency >5%, 3-5%, 1-3% and 0.5-1%, respectively. http://www.unc.edu/∼yunmli/imputability.html

Are CD-ROM LANs a Thing of the Past?

ERIC Educational Resources Information Center

Mehta, Apurva

1996-01-01

Remote access to full-text and CD-ROM databases using the Internet has advantages over a CD-ROM local area network. Topics include speed, document delivery, multiple platforms, technical support, licensing, copyright, and access to graphics. Considerations of duplication of information, platform compatibility, print versus digital media, back…

GSP: a web-based platform for designing genome-specific primers in polyploids

USDA-ARS?s Scientific Manuscript database

The primary goal of this research was to develop a web-based platform named GSP for designing genome-specific primers to distinguish subgenome sequences in the polyploid genome background. GSP uses BLAST to extract homeologous sequences of the subgenomes in the existing databases, performed a multip...

Research and realization of key technology in HILS interactive system

NASA Astrophysics Data System (ADS)

Liu, Che; Lu, Huiming; Wang, Fankai

2018-03-01

This paper designed HILS (Hardware In the Loop Simulation) interactive system based on xPC platform . Through the interface between C++ and MATLAB engine, establish the seamless data connection between Simulink and interactive system, complete data interaction between system and Simulink, realize the function development of model configuration, parameter modification and off line simulation. We establish the data communication between host and target machine through TCP/IP protocol to realize the model download and real-time simulation. Use database to store simulation data, implement real-time simulation monitoring and simulation data management. Realize system function integration by Qt graphic interface library and dynamic link library. At last, take the typical control system as an example to verify the feasibility of HILS interactive system.

Semantic Technologies for Re-Use of Clinical Routine Data.

PubMed

Kreuzthaler, Markus; Martínez-Costa, Catalina; Kaiser, Peter; Schulz, Stefan

2017-01-01

Routine patient data in electronic patient records are only partly structured, and an even smaller segment is coded, mainly for administrative purposes. Large parts are only available as free text. Transforming this content into a structured and semantically explicit form is a prerequisite for querying and information extraction. The core of the system architecture presented in this paper is based on SAP HANA in-memory database technology using the SAP Connected Health platform for data integration as well as for clinical data warehousing. A natural language processing pipeline analyses unstructured content and maps it to a standardized vocabulary within a well-defined information model. The resulting semantically standardized patient profiles are used for a broad range of clinical and research application scenarios.

An open platform for promoting interoperability in solar system sciences

NASA Astrophysics Data System (ADS)

Csillaghy, André; Aboudarham, Jean; Berghmans, David; Jacquey, Christian

2013-04-01

The European coordination project CASSIS is promoting the creation of an integrated data space that will facilitate science across community boundaries in solar system sciences. Many disciplines may need to use the same data set to support scientific research, although the way they are used may depend on the project and on the particular piece of science. Often, access is hindered because of differences in the way the different communities describe, store their data, as well as how they make them accessible. Working towards this goal, we have set up an open collaboration platform, www.explorespace.eu, that can serve as a hub for discovering and developing interoperability resources in the communities involved. The platform is independent of the project and will be maintained well after the end of the funding. As a first step, we have captured the description of services already provided by the community. The openness of the collaboration platform should allow to discuss with all stakeholders ways to make key types of metadata and derived products more complete and coherent and thus more usable across the domain boundaries. Furthermore, software resources and discussions should help facilitating the development of interoperable services. The platform, along with the database of services, address the following questions, which we consider crucial for promoting interoperability: • Current extent of the data space coverage: What part of the common data space is already covered by the existing interoperable services in terms of data access. In other words, what data, from catalogues as well as from raw data, can be reached by an application through standard protocols today? • Needed extension of the data space coverage: What would be needed to extend the data space coverage? In other words, how can the currently accessible data space be extended by adding services? • Missing services: What applications / services are still missing and need to be developed? This is not a trivial question, as the generation of the common data space in itself creates new requirements on overarching applications that might be necessary to provide a unified access to all the services. As an example, one particular aspect discussed in the platform is the design of web services. Applications of today are mainly human centred while interoperability must happen one level below and the back ends (databases) must be generic, i.e. independent from the applications. We intent our effort to provide to developers resources that disentangle user interfaces from data services. Many activities are challenging and we hope they will be discussed on our platform. In particular, the quality of the services, the data space and the needs of interdisciplinary approaches are serious concerns for instruments such as ATST and EST or the ones onboard SDO and, in the future, Solar Orbiter. We believe that our platform might be useful as a kind of guide that would allow groups of not having to reinvent the wheel for each new instrument.

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface.

PubMed

Hoeck, W G

1994-06-01

InfoTrac TFD provides a graphical user interface (GUI) for viewing and manipulating datasets in the Transcription Factor Database, TFD. The interface was developed in Filemaker Pro 2.0 by Claris Corporation, which provides cross platform compatibility between Apple Macintosh computers running System 7.0 and higher and IBM-compatibles running Microsoft Windows 3.0 and higher. TFD ASCII-tables were formatted to fit data into several custom data tables using Add/Strip, a shareware utility and Filemaker Pro's lookup feature. The lookup feature was also put to use to allow TFD data tables to become linked within a flat-file database management system. The 'Navigator', consisting of several pop-up menus listing transcription factor abbreviations, facilitates the search for transcription factor entries. Data are presented onscreen in several layouts, that can be further customized by the user. InfoTrac TFD makes the transcription factor database accessible to a much wider community of scientists by making it available on two popular microcomputer platforms.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

MicroScope: a platform for microbial genome annotation and comparative genomics

PubMed Central

Vallenet, D.; Engelen, S.; Mornico, D.; Cruveiller, S.; Fleury, L.; Lajus, A.; Rouy, Z.; Roche, D.; Salvignol, G.; Scarpelli, C.; Médigue, C.

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope’s rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone. Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc PMID:20157493

MicroScope: a platform for microbial genome annotation and comparative genomics.

PubMed

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone.Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc.

CancerLectinDB: a database of lectins relevant to cancer.

PubMed

Damodaran, Deepa; Jeyakani, Justin; Chauhan, Alok; Kumar, Nirmal; Chandra, Nagasuma R; Surolia, Avadhesha

2008-04-01

The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology. CancerLectinDB can be accessed through http://proline.physics.iisc.ernet.in/cancerdb .

Sharing Health Big Data for Research - A Design by Use Cases: The INSHARE Platform Approach.

PubMed

Bouzillé, Guillaume; Westerlynck, Richard; Defossez, Gautier; Bouslimi, Dalel; Bayat, Sahar; Riou, Christine; Busnel, Yann; Le Guillou, Clara; Cauvin, Jean-Michel; Jacquelinet, Christian; Pladys, Patrick; Oger, Emmanuel; Stindel, Eric; Ingrand, Pierre; Coatrieux, Gouenou; Cuggia, Marc

2017-01-01

Sharing and exploiting Health Big Data (HBD) allow tackling challenges: data protection/governance taking into account legal, ethical, and deontological aspects enables trust, transparent and win-win relationship between researchers, citizens, and data providers. Lack of interoperability: compartmentalized and syntactically/semantica heterogeneous data. INSHARE project using experimental proof of concept explores how recent technologies overcome such issues. Using 6 data providers, platform is designed via 3 steps to: (1) analyze use cases, needs, and requirements; (2) define data sharing governance, secure access to platform; and (3) define platform specifications. Three use cases - from 5 studies and 11 data sources - were analyzed for platform design. Governance derived from SCANNER model was adapted to data sharing. Platform architecture integrates: data repository and hosting, semantic integration services, data processing, aggregate computing, data quality and integrity monitoring, Id linking, multisource query builder, visualization and data export services, data governance, study management service and security including data watermarking.

OpenQuake, a platform for collaborative seismic hazard and risk assessment

NASA Astrophysics Data System (ADS)

Henshaw, Paul; Burton, Christopher; Butler, Lars; Crowley, Helen; Danciu, Laurentiu; Nastasi, Matteo; Monelli, Damiano; Pagani, Marco; Panzeri, Luigi; Simionato, Michele; Silva, Vitor; Vallarelli, Giuseppe; Weatherill, Graeme; Wyss, Ben

2013-04-01

Sharing of data and risk information, best practices, and approaches across the globe is key to assessing risk more effectively. Through global projects, open-source IT development and collaborations with more than 10 regions, leading experts are collaboratively developing unique global datasets, best practice, tools and models for global seismic hazard and risk assessment, within the context of the Global Earthquake Model (GEM). Guided by the needs and experiences of governments, companies and international organisations, all contributions are being integrated into OpenQuake: a web-based platform that - together with other resources - will become accessible in 2014. With OpenQuake, stakeholders worldwide will be able to calculate, visualize and investigate earthquake hazard and risk, capture new data and share findings for joint learning. The platform is envisaged as a collaborative hub for earthquake risk assessment, used at global and local scales, around which an active network of users has formed. OpenQuake will comprise both online and offline tools, many of which can also be used independently. One of the first steps in OpenQuake development was the creation of open-source software for advanced seismic hazard and risk calculations at any scale, the OpenQuake Engine. Although in continuous development, a command-line version of the software is already being test-driven and used by hundreds worldwide; from non-profits in Central Asia, seismologists in sub-Saharan Africa and companies in South Asia to the European seismic hazard harmonization programme (SHARE). In addition, several technical trainings were organized with scientists from different regions of the world (sub-Saharan Africa, Central Asia, Asia-Pacific) to introduce the engine and other OpenQuake tools to the community, something that will continue to happen over the coming years. Other tools that are being developed of direct interest to the hazard community are: • OpenQuake Modeller; fundamental instruments for the creation of seismogenic input models for seismic hazard assessment, a critical input to the OpenQuake Engine. OpenQuake Modeller will consist of a suite of tools (Hazard Modellers Toolkit) for characterizing the seismogenic sources of earthquakes and their models of earthquakes recurrence. An earthquake catalogue homogenization tool, for integration, statistical comparison and user-defined harmonization of multiple catalogues of earthquakes is also included in the OpenQuake modeling tools. • A data capture tool for active faults; a tool that allows geologists to draw (new) fault discoveries on a map in an intuitive GIS-environment and add details on the fault through the tool. This data, once quality checked, can then be integrated with the global active faults database, which will increase in value with every new fault insertion. Building on many ongoing efforts and the knowledge of scientists worldwide, GEM will for the first time integrate state-of-the-art data, models, results and open-source tools into a single platform. The platform will continue to increase in value, in particular for use in local contexts, through contributions from and collaborations with scientists and organisations worldwide. This presentation will showcase the OpenQuake Platform, focusing on the IT solutions that have been adopted as well as the added value that the platform will bring to scientists worldwide.

Geodata Modeling and Query in Geographic Information Systems

NASA Technical Reports Server (NTRS)

Adam, Nabil

1996-01-01

Geographic information systems (GIS) deal with collecting, modeling, man- aging, analyzing, and integrating spatial (locational) and non-spatial (attribute) data required for geographic applications. Examples of spatial data are digital maps, administrative boundaries, road networks, and those of non-spatial data are census counts, land elevations and soil characteristics. GIS shares common areas with a number of other disciplines such as computer- aided design, computer cartography, database management, and remote sensing. None of these disciplines however, can by themselves fully meet the requirements of a GIS application. Examples of such requirements include: the ability to use locational data to produce high quality plots, perform complex operations such as network analysis, enable spatial searching and overlay operations, support spatial analysis and modeling, and provide data management functions such as efficient storage, retrieval, and modification of large datasets; independence, integrity, and security of data; and concurrent access to multiple users. It is on the data management issues that we devote our discussions in this monograph. Traditionally, database management technology have been developed for business applications. Such applications require, among other things, capturing the data requirements of high-level business functions and developing machine- level implementations; supporting multiple views of data and yet providing integration that would minimize redundancy and maintain data integrity and security; providing a high-level language for data definition and manipulation; allowing concurrent access to multiple users; and processing user transactions in an efficient manner. The demands on database management systems have been for speed, reliability, efficiency, cost effectiveness, and user-friendliness. Significant progress have been made in all of these areas over the last two decades to the point that many generalized database platforms are now available for developing data intensive applications that run in real-time. While continuous improvement is still being made at a very fast-paced and competitive rate, new application areas such as computer aided design, image processing, VLSI design, and GIS have been identified by many as the next generation of database applications. These new application areas pose serious challenges to the currently available database technology. At the core of these challenges is the nature of data that is manipulated. In traditional database applications, the database objects do not have any spatial dimension, and as such, can be thought of as point data in a multi-dimensional space. For example, each instance of an entity EMPLOYEE will have a unique value corresponding to every attribute such as employee id, employee name, employee address and so on. Thus, every Employee instance can be thought of as a point in a multi-dimensional space where each dimension is represented by an attribute. Furthermore, all operations on such data are one-dimensional. Thus, users may retrieve all entities satisfying one or more constraints. Examples of such constraints include employees with addresses in a certain area code, or salaries within a certain range. Even though constraints can be specified on multiple attributes (dimensions), the search for such data is essentially orthogonal across these dimensions.

Photonic Integrated Circuits

NASA Technical Reports Server (NTRS)

Krainak, Michael; Merritt, Scott

2016-01-01

Integrated photonics generally is the integration of multiple lithographically defined photonic and electronic components and devices (e.g. lasers, detectors, waveguides passive structures, modulators, electronic control and optical interconnects) on a single platform with nanometer-scale feature sizes. The development of photonic integrated circuits permits size, weight, power and cost reductions for spacecraft microprocessors, optical communication, processor buses, advanced data processing, and integrated optic science instrument optical systems, subsystems and components. This is particularly critical for small spacecraft platforms. We will give an overview of some NASA applications for integrated photonics.

Integrated testing system FiTest for diagnosis of PCBA

NASA Astrophysics Data System (ADS)

Bogdan, Arkadiusz; Lesniak, Adam

2016-12-01

This article presents the innovative integrated testing system FiTest for automatic, quick inspection of printed circuit board assemblies (PCBA) manufactured in Surface Mount Technology (SMT). Integration of Automatic Optical Inspection (AOI), In-Circuit Tests (ICT) and Functional Circuit Tests (FCT) resulted in universal hardware platform for testing variety of electronic circuits. The platform provides increased test coverage, decreased level of false calls and optimization of test duration. The platform is equipped with powerful algorithms performing tests in a stable and repetitive way and providing effective management of diagnosis.

High-performance silicon photonics technology for telecommunications applications.

PubMed

Yamada, Koji; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Hiraki, Tatsurou; Takeda, Kotaro; Fukuda, Hiroshi; Ishikawa, Yasuhiko; Wada, Kazumi; Yamamoto, Tsuyoshi

2014-04-01

By way of a brief review of Si photonics technology, we show that significant improvements in device performance are necessary for practical telecommunications applications. In order to improve device performance in Si photonics, we have developed a Si-Ge-silica monolithic integration platform, on which compact Si-Ge-based modulators/detectors and silica-based high-performance wavelength filters are monolithically integrated. The platform features low-temperature silica film deposition, which cannot damage Si-Ge-based active devices. Using this platform, we have developed various integrated photonic devices for broadband telecommunications applications.

High-performance silicon photonics technology for telecommunications applications

PubMed Central

Yamada, Koji; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Hiraki, Tatsurou; Takeda, Kotaro; Fukuda, Hiroshi; Ishikawa, Yasuhiko; Wada, Kazumi; Yamamoto, Tsuyoshi

2014-01-01

By way of a brief review of Si photonics technology, we show that significant improvements in device performance are necessary for practical telecommunications applications. In order to improve device performance in Si photonics, we have developed a Si-Ge-silica monolithic integration platform, on which compact Si-Ge–based modulators/detectors and silica-based high-performance wavelength filters are monolithically integrated. The platform features low-temperature silica film deposition, which cannot damage Si-Ge–based active devices. Using this platform, we have developed various integrated photonic devices for broadband telecommunications applications. PMID:27877659

High-performance silicon photonics technology for telecommunications applications

NASA Astrophysics Data System (ADS)

Yamada, Koji; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Hiraki, Tatsurou; Takeda, Kotaro; Fukuda, Hiroshi; Ishikawa, Yasuhiko; Wada, Kazumi; Yamamoto, Tsuyoshi

2014-04-01

By way of a brief review of Si photonics technology, we show that significant improvements in device performance are necessary for practical telecommunications applications. In order to improve device performance in Si photonics, we have developed a Si-Ge-silica monolithic integration platform, on which compact Si-Ge-based modulators/detectors and silica-based high-performance wavelength filters are monolithically integrated. The platform features low-temperature silica film deposition, which cannot damage Si-Ge-based active devices. Using this platform, we have developed various integrated photonic devices for broadband telecommunications applications.

SorghumFDB: sorghum functional genomics database with multidimensional network analysis.

PubMed

Tian, Tian; You, Qi; Zhang, Liwei; Yi, Xin; Yan, Hengyu; Xu, Wenying; Su, Zhen

2016-01-01

Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C4 grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein-protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants.Database URL: http://structuralbiology.cau.edu.cn/sorghum/index.html. © The Author(s) 2016. Published by Oxford University Press.

ASD: a comprehensive database of allosteric proteins and modulators

PubMed Central

Huang, Zhimin; Zhu, Liang; Cao, Yan; Wu, Geng; Liu, Xinyi; Chen, Yingyi; Wang, Qi; Shi, Ting; Zhao, Yaxue; Wang, Yuefei; Li, Weihua; Li, Yixue; Chen, Haifeng; Chen, Guoqiang; Zhang, Jian

2011-01-01

Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloSteric Database (ASD), the first online database that provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Currently, ASD contains 336 allosteric proteins from 101 species and 8095 modulators in three categories (activators, inhibitors and regulators). Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area. Integrating the information of allosteric proteins in ASD should allow for the identification of specific allosteric sites of a given subtype among proteins of the same family that can potentially serve as ideal targets for experimental validation. In addition, modulators curated in ASD can be used to investigate potent allosteric targets for the query compound, and also help chemists to implement structure modifications for novel allosteric drug design. Therefore, ASD could be a platform and a starting point for biologists and medicinal chemists for furthering allosteric research. ASD is freely available at http://mdl.shsmu.edu.cn/ASD/. PMID:21051350

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

PubMed Central

Overbeek, Ross; Olson, Robert; Pusch, Gordon D.; Olsen, Gary J.; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang; Stevens, Rick

2014-01-01

In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources. PMID:24293654

PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing.

PubMed

Wang, Yanli; Cheng, Tiejun; Bryant, Stephen H

2017-07-01

High-throughput screening (HTS) is now routinely conducted for drug discovery by both pharmaceutical companies and screening centers at academic institutions and universities. Rapid advance in assay development, robot automation, and computer technology has led to the generation of terabytes of data in screening laboratories. Despite the technology development toward HTS productivity, fewer efforts were devoted to HTS data integration and sharing. As a result, the huge amount of HTS data was rarely made available to the public. To fill this gap, the PubChem BioAssay database ( https://www.ncbi.nlm.nih.gov/pcassay/ ) was set up in 2004 to provide open access to the screening results tested on chemicals and RNAi reagents. With more than 10 years' development and contributions from the community, PubChem has now become the largest public repository for chemical structures and biological data, which provides an information platform to worldwide researchers supporting drug development, medicinal chemistry study, and chemical biology research. This work presents a review of the HTS data content in the PubChem BioAssay database and the progress of data deposition to stimulate knowledge discovery and data sharing. It also provides a description of the database's data standard and basic utilities facilitating information access and use for new users.

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

PubMed

Overbeek, Ross; Olson, Robert; Pusch, Gordon D; Olsen, Gary J; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang; Stevens, Rick

2014-01-01

In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

PubMed Central

Nagpure, Naresh Sahebrao; Rashid, Iliyas; Pathak, Ajey Kumar; Singh, Mahender; Singh, Shri Prakash; Sarkar, Uttam Kumar

2012-01-01

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. Availability The database is available for free at http://mail.nbfgr.res.in/fbis/ PMID:22715304

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

PubMed

Huan, Tianxiao; Sivachenko, Andrey Y; Harrison, Scott H; Chen, Jake Y

2008-08-12

New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network. The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.

Health Technology-Enabled Interventions for Adherence Support and Retention in Care Among US HIV-Infected Adolescents and Young Adults: An Integrative Review.

PubMed

Navarra, Ann-Margaret Dunn; Gwadz, Marya Viorst; Whittemore, Robin; Bakken, Suzanne R; Cleland, Charles M; Burleson, Winslow; Jacobs, Susan Kaplan; Melkus, Gail D'Eramo

2017-11-01

The objective of this integrative review was to describe current US trends for health technology-enabled adherence interventions among behaviorally HIV-infected youth (ages 13-29 years), and present the feasibility and efficacy of identified interventions. A comprehensive search was executed across five electronic databases (January 2005-March 2016). Of the 1911 identified studies, nine met the inclusion criteria of quantitative or mixed methods design, technology-enabled adherence and or retention intervention for US HIV-infected youth. The majority were small pilots. Intervention dose varied between studies applying similar technology platforms with more than half not informed by a theoretical framework. Retention in care was not a reported outcome, and operationalization of adherence was heterogeneous across studies. Despite these limitations, synthesized findings from this review demonstrate feasibility of computer-based interventions, and initial efficacy of SMS texting for adherence support among HIV-infected youth. Moving forward, there is a pressing need for the expansion of this evidence base.

Virtual Network Configuration Management System for Data Center Operations and Management

NASA Astrophysics Data System (ADS)

Okita, Hideki; Yoshizawa, Masahiro; Uehara, Keitaro; Mizuno, Kazuhiko; Tarui, Toshiaki; Naono, Ken

Virtualization technologies are widely deployed in data centers to improve system utilization. However, they increase the workload for operators, who have to manage the structure of virtual networks in data centers. A virtual-network management system which automates the integration of the configurations of the virtual networks is provided. The proposed system collects the configurations from server virtualization platforms and VLAN-supported switches, and integrates these configurations according to a newly developed XML-based management information model for virtual-network configurations. Preliminary evaluations show that the proposed system helps operators by reducing the time to acquire the configurations from devices and correct the inconsistency of operators' configuration management database by about 40 percent. Further, they also show that the proposed system has excellent scalability; the system takes less than 20 minutes to acquire the virtual-network configurations from a large scale network that includes 300 virtual machines. These results imply that the proposed system is effective for improving the configuration management process for virtual networks in data centers.

Newborn screening healthcare information system based on service-oriented architecture.

PubMed

Hsieh, Sung-Huai; Hsieh, Sheau-Ling; Chien, Yin-Hsiu; Weng, Yung-Ching; Hsu, Kai-Ping; Chen, Chi-Huang; Tu, Chien-Ming; Wang, Zhenyu; Lai, Feipei

2010-08-01

In this paper, we established a newborn screening system under the HL7/Web Services frameworks. We rebuilt the NTUH Newborn Screening Laboratory's original standalone architecture, having various heterogeneous systems operating individually, and restructured it into a Service-Oriented Architecture (SOA), distributed platform for further integrity and enhancements of sample collections, testing, diagnoses, evaluations, treatments or follow-up services, screening database management, as well as collaboration, communication among hospitals; decision supports and improving screening accuracy over the Taiwan neonatal systems are also addressed. In addition, the new system not only integrates the newborn screening procedures among phlebotomy clinics, referral hospitals, as well as the newborn screening center in Taiwan, but also introduces new models of screening procedures for the associated, medical practitioners. Furthermore, it reduces the burden of manual operations, especially the reporting services, those were heavily dependent upon previously. The new system can accelerate the whole procedures effectively and efficiently. It improves the accuracy and the reliability of the screening by ensuring the quality control during the processing as well.

Lectindb: a plant lectin database.

PubMed

Chandra, Nagasuma R; Kumar, Nirmal; Jeyakani, Justin; Singh, Desh Deepak; Gowda, Sharan B; Prathima, M N

2006-10-01

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.

PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

PubMed Central

Plikus, Maksim V; Zhang, Zina; Chuong, Cheng-Ming

2006-01-01

Background Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. Results PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. Conclusion We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute) thesaurus and MGD (Mouse Genome Database) mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed. PMID:17014720

Robust PBPK/PD-Based Model Predictive Control of Blood Glucose.

PubMed

Schaller, Stephan; Lippert, Jorg; Schaupp, Lukas; Pieber, Thomas R; Schuppert, Andreas; Eissing, Thomas

2016-07-01

Automated glucose control (AGC) has not yet reached the point where it can be applied clinically [3]. Challenges are accuracy of subcutaneous (SC) glucose sensors, physiological lag times, and both inter- and intraindividual variability. To address above issues, we developed a novel scheme for MPC that can be applied to AGC. An individualizable generic whole-body physiology-based pharmacokinetic and dynamics (PBPK/PD) model of the glucose, insulin, and glucagon metabolism has been used as the predictive kernel. The high level of mechanistic detail represented by the model takes full advantage of the potential of MPC and may make long-term prediction possible as it captures at least some relevant sources of variability [4]. Robustness against uncertainties was increased by a control cascade relying on proportional-integrative derivative-based offset control. The performance of this AGC scheme was evaluated in silico and retrospectively using data from clinical trials. This analysis revealed that our approach handles sensor noise with a MARD of 10%-14%, and model uncertainties and disturbances. The results suggest that PBPK/PD models are well suited for MPC in a glucose control setting, and that their predictive power in combination with the integrated database-driven (a priori individualizable) model framework will help overcome current challenges in the development of AGC systems. This study provides a new, generic, and robust mechanistic approach to AGC using a PBPK platform with extensive a priori (database) knowledge for individualization.

Privacy protection and public goods: building a genetic database for health research in Newfoundland and Labrador

PubMed Central

Pullman, Daryl; Perrot-Daley, Astrid; Hodgkinson, Kathy; Street, Catherine; Rahman, Proton

2013-01-01

Objective To provide a legal and ethical analysis of some of the implementation challenges faced by the Population Therapeutics Research Group (PTRG) at Memorial University (Canada), in using genealogical information offered by individuals for its genetics research database. Materials and methods This paper describes the unique historical and genetic characteristics of the Newfoundland and Labrador founder population, which gave rise to the opportunity for PTRG to build the Newfoundland Genealogy Database containing digitized records of all pre-confederation (1949) census records of the Newfoundland founder population. In addition to building the database, PTRG has developed the Heritability Analytics Infrastructure, a data management structure that stores genotype, phenotype, and pedigree information in a single database, and custom linkage software (KINNECT) to perform pedigree linkages on the genealogy database. Discussion A newly adopted legal regimen in Newfoundland and Labrador is discussed. It incorporates health privacy legislation with a unique research ethics statute governing the composition and activities of research ethics boards and, for the first time in Canada, elevating the status of national research ethics guidelines into law. The discussion looks at this integration of legal and ethical principles which provides a flexible and seamless framework for balancing the privacy rights and welfare interests of individuals, families, and larger societies in the creation and use of research data infrastructures as public goods. Conclusion The complementary legal and ethical frameworks that now coexist in Newfoundland and Labrador provide the legislative authority, ethical legitimacy, and practical flexibility needed to find a workable balance between privacy interests and public goods. Such an approach may also be instructive for other jurisdictions as they seek to construct and use biobanks and related research platforms for genetic research. PMID:22859644

Privacy protection and public goods: building a genetic database for health research in Newfoundland and Labrador.

PubMed

Kosseim, Patricia; Pullman, Daryl; Perrot-Daley, Astrid; Hodgkinson, Kathy; Street, Catherine; Rahman, Proton

2013-01-01

To provide a legal and ethical analysis of some of the implementation challenges faced by the Population Therapeutics Research Group (PTRG) at Memorial University (Canada), in using genealogical information offered by individuals for its genetics research database. This paper describes the unique historical and genetic characteristics of the Newfoundland and Labrador founder population, which gave rise to the opportunity for PTRG to build the Newfoundland Genealogy Database containing digitized records of all pre-confederation (1949) census records of the Newfoundland founder population. In addition to building the database, PTRG has developed the Heritability Analytics Infrastructure, a data management structure that stores genotype, phenotype, and pedigree information in a single database, and custom linkage software (KINNECT) to perform pedigree linkages on the genealogy database. A newly adopted legal regimen in Newfoundland and Labrador is discussed. It incorporates health privacy legislation with a unique research ethics statute governing the composition and activities of research ethics boards and, for the first time in Canada, elevating the status of national research ethics guidelines into law. The discussion looks at this integration of legal and ethical principles which provides a flexible and seamless framework for balancing the privacy rights and welfare interests of individuals, families, and larger societies in the creation and use of research data infrastructures as public goods. The complementary legal and ethical frameworks that now coexist in Newfoundland and Labrador provide the legislative authority, ethical legitimacy, and practical flexibility needed to find a workable balance between privacy interests and public goods. Such an approach may also be instructive for other jurisdictions as they seek to construct and use biobanks and related research platforms for genetic research.

Development of a System Model for Non-Invasive Quantification of Bilirubin in Jaundice Patients

NASA Astrophysics Data System (ADS)

Alla, Suresh K.

Neonatal jaundice is a medical condition which occurs in newborns as a result of an imbalance between the production and elimination of bilirubin. Excess bilirubin in the blood stream diffuses into the surrounding tissue leading to a yellowing of the skin. An optical system integrated with a signal processing system is used as a platform to noninvasively quantify bilirubin concentration through the measurement of diffuse skin reflectance. Initial studies have lead to the generation of a clinical analytical model for neonatal jaundice which generates spectral reflectance data for jaundiced skin with varying levels of bilirubin concentration in the tissue. The spectral database built using the clinical analytical model is then used as a test database to validate the signal processing system in real time. This evaluation forms the basis for understanding the translation of this research to human trials. The clinical analytical model and signal processing system have been successful validated on three spectral databases. First spectral database is constructed using a porcine model as a surrogate for neonatal skin tissue. Samples of pig skin were soaked in bilirubin solutions of varying concentrations to simulate jaundice skin conditions. The resulting skins samples were analyzed with our skin reflectance systems producing bilirubin concentration values that show a high correlation (R2 = 0.94) to concentration of the bilirubin solution that each porcine tissue sample is soaked in. The second spectral database is the spectral measurements collected on human volunteers to quantify the different chromophores and other physical properties of the tissue such a Hematocrit, Hemoglobin etc. The third spectral database is the spectral data collected at different time periods from the moment a bruise is induced.

Proteomic platform for the identification of proteins in olive (Olea europaea) pulp.

PubMed

Capriotti, Anna Laura; Cavaliere, Chiara; Foglia, Patrizia; Piovesana, Susy; Samperi, Roberto; Stampachiacchiere, Serena; Laganà, Aldo

2013-10-24

The nutritional and cancer-protective properties of the oil extracted mechanically from the ripe fruits of Olea europaea trees are attracting constantly more attention worldwide. The preparation of high-quality protein samples from plant tissues for proteomic analysis poses many challenging problems. In this study we employed a proteomic platform based on two different extraction methods, SDS and CHAPS based protocols, followed by two precipitation protocols, TCA/acetone and MeOH precipitation, in order to increase the final number of identified proteins. The use of advanced MS techniques in combination with the Swissprot and NCBI Viridiplantae databases and TAIR10 Arabidopsis database allowed us to identify 1265 proteins, of which 22 belong to O. europaea. The application of this proteomic platform for protein extraction and identification will be useful also for other proteomic studies on recalcitrant plant/fruit tissues. Copyright © 2013. Published by Elsevier B.V.

The Melbourne East Monash General Practice Database (MAGNET): Using data from computerised medical records to create a platform for primary care and health services research.

PubMed

Mazza, Danielle; Pearce, Christopher; Turner, Lyle Robert; De Leon-Santiago, Maria; McLeod, Adam; Ferriggi, Jason; Shearer, Marianne

2016-07-04

The Melbourne East MonAsh GeNeral PracticE DaTabase (MAGNET) research platform was launched in 2013 to provide a unique data source for primary care and health services research in Australia.  MAGNET contains information from the computerised records of 50 participating general practices and includes data from the computerised medical records of more than 1,100,000 patients.  The data extracted is patient-level episodic information and includes a variety of fields related to patient demographics and historical clinical information, along with the characteristics of the participating general practices.  While there are limitations to the data that is currently available, the MAGNET research platform continues to investigate other avenues for improving the breadth and quality of data, with the aim of providing a more comprehensive picture of primary care in Australia.

An automated benchmarking platform for MHC class II binding prediction methods.

PubMed

Andreatta, Massimo; Trolle, Thomas; Yan, Zhen; Greenbaum, Jason A; Peters, Bjoern; Nielsen, Morten

2018-05-01

Computational methods for the prediction of peptide-MHC binding have become an integral and essential component for candidate selection in experimental T cell epitope discovery studies. The sheer amount of published prediction methods-and often discordant reports on their performance-poses a considerable quandary to the experimentalist who needs to choose the best tool for their research. With the goal to provide an unbiased, transparent evaluation of the state-of-the-art in the field, we created an automated platform to benchmark peptide-MHC class II binding prediction tools. The platform evaluates the absolute and relative predictive performance of all participating tools on data newly entered into the Immune Epitope Database (IEDB) before they are made public, thereby providing a frequent, unbiased assessment of available prediction tools. The benchmark runs on a weekly basis, is fully automated, and displays up-to-date results on a publicly accessible website. The initial benchmark described here included six commonly used prediction servers, but other tools are encouraged to join with a simple sign-up procedure. Performance evaluation on 59 data sets composed of over 10 000 binding affinity measurements suggested that NetMHCIIpan is currently the most accurate tool, followed by NN-align and the IEDB consensus method. Weekly reports on the participating methods can be found online at: http://tools.iedb.org/auto_bench/mhcii/weekly/. mniel@bioinformatics.dtu.dk. Supplementary data are available at Bioinformatics online.

Reviewing Clinical Effectiveness of Active Training Strategies of Platform-Based Ankle Rehabilitation Robots

PubMed Central

2018-01-01

Objective This review aims to provide a systematical investigation of clinical effectiveness of active training strategies applied in platform-based ankle robots. Method English-language studies published from Jan 1980 to Aug 2017 were searched from four databases using key words of “Ankle∗” AND “Robot∗” AND “Effect∗ OR Improv∗ OR Increas∗.” Following an initial screening, three rounds of discrimination were successively conducted based on the title, the abstract, and the full paper. Result A total of 21 studies were selected with 311 patients involved; of them, 13 studies applied a single group while another eight studies used different groups for comparison to verify the therapeutic effect. Virtual-reality (VR) game training was applied in 19 studies, while two studies used proprioceptive neuromuscular facilitation (PNF) training. Conclusion Active training techniques delivered by platform ankle rehabilitation robots have been demonstrated with great potential for clinical applications. Training strategies are mostly combined with one another by considering rehabilitation schemes and motion ability of ankle joints. VR game environment has been commonly used with active ankle training. Bioelectrical signals integrated with VR game training can implement intelligent identification of movement intention and assessment. These further provide the foundation for advanced interactive training strategies that can lead to enhanced training safety and confidence for patients and better treatment efficacy. PMID:29675142

An approach to drought data web-dissemination

NASA Astrophysics Data System (ADS)

Angeluccetti, Irene; Perez, Francesca; Balbo, Simone; Cámaro, Walther; Boccardo, Piero

2017-04-01

Drought data dissemination has always been a challenge for the scientific community. Firstly, a variety of widely known datasets is currently being used to describe different aspects of this same phenomenon. Secondly, new indexes are constantly being produced by scientists trying to better capture drought events. The present work aims at presenting how the drought monitoring communication issue was addressed by the ITHACA team. The ITHACA drought monitoring system makes use of two indicators: the Standardized Precipitation Index (SPI) and the Seasonal Small Integral Deviation (SSID). The first one is obtained considering the 3-months cumulating interval of the rainfall derived from the TRMM dataset; the second one is the percent deviation from the historical average value of the integral of the NDVI function describing the vegetation season. The SPI and the SSID are 30 and 5 km gridded respectively. The whole time-series of these two indicators (since year 2000 onwards), covering the whole Africa, are published by a WebGIS platform (http://drought.ithacaweb.org). On the one hand, although the SPI has been used for decades in different contexts and little explanation is due when presenting this indicator to an audience with a scientific background, the WebGIS platform shows a guide for its correct interpretation. On the other hand, being the SSID not commonly used in the field of vegetation analysis, the guide shown on the WebGIS platform is essential for the visitor to understand the data. Recently a new index has been created in order to synthesize, for a non-expert audience, the information provided by the indicators. It is aggregated per second order administrative levels and is calculated as follows: (i) a meteorological drought warning is issued when negative SPI and no vegetative season is detected (a blue palette is used); (ii) a warning value is assigned if SSID, SPI, or both, are negative (amber to brown palette is used) i.e., where the vegetative season is ongoing and the SSID is negative, a negative SPI value entails an agricultural drought warning, while a positive SPI implies a vegetation stress warning; (iv) a meteorological drought warning is issued when negative SPI during the vegetation season is detected but vegetation stress effects are not (i.e. positive SSID). The latest available Drought Warning Index is also published on the mentioned WebGIS platform. The index is stored in a database table: a single value is calculated for each administrative level. A table view on the database contains fields describing the geometry of the administrative level polygons and the respective index; this table view is published as a WMS service, by associating the symbology previously described. The WMS service is then captured in order to generate a live map with a series of basic WebGIS functionalities. The integrated index is undoubtedly useful for a non-expert user to understand immediately if a particular region is subject to a drought stress. However, the simplification introduces uncertainty as it implies several assumptions that couldn't be verified at a continental scale.

Design and control of multifunctional sorting and training platform based on PLC control

NASA Astrophysics Data System (ADS)

Wan, Hongqiang; Ge, Shuai; Han, Peiying; Li, Fancong; Zhang, Simiao

2018-05-01

Electromechanical integration, as a multi-disciplinary subject, has been paid much attention by universities and is widely used in the automation production of enterprises. Aiming at the problem of the lack of control among enterprises and the lack of training among colleges and universities, this paper presents a design of multifunctional sorting training platform based on PLC control. Firstly, the structure of the platform is determined and three-dimensional modeling is done. Then design the platform's aerodynamic control and electrical control. Finally, realize the platform sorting function through PLC programming and configuration software development. The training platform can be used to design the practical training experiment, which has a strong advance and pertinence in the electromechanical integration teaching. At the same time, the platform makes full use of modular thinking to make the sorting modules more flexible. Compared with the traditional training platform, its teaching effect is more significant.

Integrated protein analysis platform based on column switch recycling size exclusion chromatography, microenzymatic reactor and microRPLC-ESI-MS/MS.

PubMed

Yuan, Huiming; Zhou, Yuan; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

2009-10-30

An integrated platform with the combination of proteins and peptides separation was established via the unit of on-line proteins digestion, by which proteins were in sequence separated by column switch recycling size exclusion chromatography (csrSEC), on-line digested by an immobilized trypsin microreactor, trapped and desalted by two parallel C8 precolumns, separated by microRPLC with the linear gradient of organic modifier concentration, and identified by ESI-MS/MS. A 6-protein mixture, with Mr ranging from 10 kDa to 80 kDa, was used to evaluate the performance of the integrated platform, and all proteins were identified with sequence coverage over 5.67%. Our experimental results demonstrate that such an integrated platform is of advantages such as good time compatibility, high peak capacity, and facile automation, which might be a promising approach for proteome study.

Distribution Grid Integration Unit Cost Database | Solar Research | NREL

Science.gov Websites

Unit Cost Database Distribution Grid Integration Unit Cost Database NREL's Distribution Grid Integration Unit Cost Database contains unit cost information for different components that may be used to associated with PV. It includes information from the California utility unit cost guides on traditional

Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa.

PubMed

Nag, Ambarish; Karpinets, Tatiana V; Chang, Christopher H; Bar-Peled, Maor

2012-01-01

Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s). Database URL: The curated Populus PGDB is available in the BESC public portal at http://cricket.ornl.gov/cgi-bin/beocyc_home.cgi and the nucleotide-sugar biosynthetic pathways can be directly accessed at http://cricket.ornl.gov:1555/PTR/new-image?object=SUGAR-NUCLEOTIDES.

Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa

PubMed Central

Nag, Ambarish; Karpinets, Tatiana V.; Chang, Christopher H.; Bar-Peled, Maor

2012-01-01

Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s). Database URL: The curated Populus PGDB is available in the BESC public portal at http://cricket.ornl.gov/cgi-bin/beocyc_home.cgi and the nucleotide-sugar biosynthetic pathways can be directly accessed at http://cricket.ornl.gov:1555/PTR/new-image?object=SUGAR-NUCLEOTIDES. PMID:22465851

A Web-Based Earth-Systems Knowledge Portal and Collaboration Platform

NASA Astrophysics Data System (ADS)

D'Agnese, F. A.; Turner, A. K.

2010-12-01

In support of complex water-resource sustainability projects in the Great Basin region of the United States, Earth Knowledge, Inc. has developed several web-based data management and analysis platforms that have been used by its scientists, clients, and public to facilitate information exchanges, collaborations, and decision making. These platforms support accurate water-resource decision-making by combining second-generation internet (Web 2.0) technologies with traditional 2D GIS and web-based 2D and 3D mapping systems such as Google Maps, and Google Earth. Most data management and analysis systems use traditional software systems to address the data needs and usage behavior of the scientific community. In contrast, these platforms employ more accessible open-source and “off-the-shelf” consumer-oriented, hosted web-services. They exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize earth, engineering, and social science datasets. Thus, they respond to the information needs and web-interface expectations of both subject-matter experts and the public. Because the platforms continue to gather and store all the contributions of their broad-spectrum of users, each new assessment leverages the data, information, and expertise derived from previous investigations. In the last year, Earth Knowledge completed a conceptual system design and feasibility study for a platform, which has a Knowledge Portal providing access to users wishing to retrieve information or knowledge developed by the science enterprise and a Collaboration Environment Module, a framework that links the user-access functions to a Technical Core supporting technical and scientific analyses including Data Management, Analysis and Modeling, and Decision Management, and to essential system administrative functions within an Administrative Module. The over-riding technical challenge is the design and development of a single technical platform that is accessed through a flexible series of knowledge portal and collaboration environment styles reflecting the information needs and user expectations of a diverse community of users. Recent investigations have defined the information needs and expectations of the major end-users and also have reviewed and assessed a wide variety of modern web-based technologies. Combining these efforts produced design specifications and recommendations for the selection and integration of web- and client-based tools. When fully developed, the resulting platform will: -Support new, advanced information systems and decision environments that take full advantage of multiple data sources and platforms; -Provide a distribution network tailored to the timely delivery of products to a broad range of users that are needed to support applications in disaster management, resource management, energy, and urban sustainability; -Establish new integrated multiple-user requirements and knowledge databases that support researchers and promote infusion of successful technologies into existing processes; and -Develop new decision support strategies and presentation methodologies for applied earth science applications to reduce risk, cost, and time.

Discovering Knowledge from AIS Database for Application in VTS

NASA Astrophysics Data System (ADS)

Tsou, Ming-Cheng

The widespread use of the Automatic Identification System (AIS) has had a significant impact on maritime technology. AIS enables the Vessel Traffic Service (VTS) not only to offer commonly known functions such as identification, tracking and monitoring of vessels, but also to provide rich real-time information that is useful for marine traffic investigation, statistical analysis and theoretical research. However, due to the rapid accumulation of AIS observation data, the VTS platform is often unable quickly and effectively to absorb and analyze it. Traditional observation and analysis methods are becoming less suitable for the modern AIS generation of VTS. In view of this, we applied the same data mining technique used for business intelligence discovery (in Customer Relation Management (CRM) business marketing) to the analysis of AIS observation data. This recasts the marine traffic problem as a business-marketing problem and integrates technologies such as Geographic Information Systems (GIS), database management systems, data warehousing and data mining to facilitate the discovery of hidden and valuable information in a huge amount of observation data. Consequently, this provides the marine traffic managers with a useful strategic planning resource.

Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd

Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved frommore » 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.« less

STEP-TRAMM - A modeling interface for simulating localized rainfall induced shallow landslides and debris flow runout pathways

NASA Astrophysics Data System (ADS)

von Ruette, Jonas; Lehmann, Peter; Fan, Linfeng; Bickel, Samuel; Or, Dani

2017-04-01

Landslides and subsequent debris-flows initiated by rainfall represent a ubiquitous natural hazard in steep mountainous regions. We integrated a landslide hydro-mechanical triggering model and associated debris flow runout pathways with a graphical user interface (GUI) to represent these natural hazards in a wide range of catchments over the globe. The STEP-TRAMM GUI provides process-based locations and sizes of landslides patterns using digital elevation models (DEM) from SRTM database (30 m resolution) linked with soil maps from global database SoilGrids (250 m resolution) and satellite based information on rainfall statistics for the selected region. In a preprocessing step STEP-TRAMM models soil depth distribution and complements soil information that jointly capture key hydrological and mechanical properties relevant to local soil failure representation. In the presentation we will discuss feature of this publicly available platform and compare landslide and debris flow patterns for different regions considering representative intense rainfall events. Model outcomes will be compared for different spatial and temporal resolutions to test applicability of web-based information on elevation and rainfall for hazard assessment.

Searching bioremediation patents through Cooperative Patent Classification (CPC).

PubMed

Prasad, Rajendra

2016-03-01

Patent classification systems have traditionally evolved independently at each patent jurisdiction to classify patents handled by their examiners to be able to search previous patents while dealing with new patent applications. As patent databases maintained by them went online for free access to public as also for global search of prior art by examiners, the need arose for a common platform and uniform structure of patent databases. The diversity of different classification, however, posed problems of integrating and searching relevant patents across patent jurisdictions. To address this problem of comparability of data from different sources and searching patents, WIPO in the recent past developed what is known as International Patent Classification (IPC) system which most countries readily adopted to code their patents with IPC codes along with their own codes. The Cooperative Patent Classification (CPC) is the latest patent classification system based on IPC/European Classification (ECLA) system, developed by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO) which is likely to become a global standard. This paper discusses this new classification system with reference to patents on bioremediation.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

DataBase on Demand

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, R.; Gomez, D.; Coterillo Coz, I.; Wojcik, D.

2012-12-01

At CERN a number of key database applications are running on user-managed MySQL database services. The database on demand project was born out of an idea to provide the CERN user community with an environment to develop and run database services outside of the actual centralised Oracle based database services. The Database on Demand (DBoD) empowers the user to perform certain actions that had been traditionally done by database administrators, DBA's, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently open community version of MySQL and single instance Oracle database server. This article describes a technology approach to face this challenge, a service level agreement, the SLA that the project provides, and an evolution of possible scenarios.

The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.

PubMed

Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

2015-01-01

There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set. CVSP web site is located at http://cvsp.chemspider.com/. A platform for the validation and standardization of chemical structure representations of various formats has been developed and made available to the community to assist and encourage the processing of chemical structure files to produce more homogeneous compound representations for exchange and interchange between online databases. While the CVSP platform is designed with flexibility inherent to the rules that can be used for processing the data we have produced a recommended rule set based on our own experiences with the large data sets such as DrugBank, ChEMBL, and data sets from ChemSpider.

Enhancing Mobility: Integrating New Services into Your Library's Mobile Platform to Increase Traffic

ERIC Educational Resources Information Center

Felts, John W., Jr.

2014-01-01

Kimbel Library launched its mobile environment and ran it in full production for several months yet usage patterns were quite low and flat. The library only saw a substantial increase in usage when new, value-added services were integrated into this platform. Upon implementing and integrating discovery services, chat and SMS capabilities, and…

Sensors integration for smartphone navigation: performances and future challenges

NASA Astrophysics Data System (ADS)

Aicardi, I.; Dabove, P.; Lingua, A.; Piras, M.

2014-08-01

Nowadays the modern smartphones include several sensors which are usually adopted in geomatic application, as digital camera, GNSS (Global Navigation Satellite System) receivers, inertial platform, RFID and Wi-Fi systems. In this paper the authors would like to testing the performances of internal sensors (Inertial Measurement Unit, IMU) of three modern smartphones (Samsung GalaxyS4, Samsung GalaxyS5 and iPhone4) compared to external mass-market IMU platform in order to verify their accuracy levels, in terms of positioning. Moreover, the Image Based Navigation (IBN) approach is also investigated: this approach can be very useful in hard-urban environment or for indoor positioning, as alternative to GNSS positioning. IBN allows to obtain a sub-metrical accuracy, but a special database of georeferenced images (Image DataBase, IDB) is needed, moreover it is necessary to use dedicated algorithm to resizing the images which are collected by smartphone, in order to share it with the server where is stored the IDB. Moreover, it is necessary to characterize smartphone camera lens in terms of focal length and lens distortions. The authors have developed an innovative method with respect to those available today, which has been tested in a covered area, adopting a special support where all sensors under testing have been installed. Geomatic instrument have been used to define the reference trajectory, with purpose to compare this one, with the path obtained with IBN solution. First results leads to have an horizontal and vertical accuracies better than 60 cm, respect to the reference trajectories. IBN method, sensors, test and result will be described in the paper.

The Canadian Preterm Birth Network: a study protocol for improving outcomes for preterm infants and their families

PubMed Central

Shah, Prakesh S.; McDonald, Sarah D.; Barrett, Jon; Synnes, Anne; Robson, Kate; Foster, Jonathan; Pasquier, Jean-Charles; Joseph, K.S.; Piedboeuf, Bruno; Lacaze-Masmonteil, Thierry; O'Brien, Karel; Shivananda, Sandesh; Chaillet, Nils; Pechlivanoglou, Petros

2018-01-01

Background: Preterm birth (birth before 37 wk of gestation) occurs in about 8% of pregnancies in Canada and is associated with high mortality and morbidity rates that substantially affect infants, their families and the health care system. Our overall goal is to create a transdisciplinary platform, the Canadian Preterm Birth Network (CPTBN), where investigators, stakeholders and families will work together to improve childhood outcomes of preterm neonates. Methods: Our national cohort will include 24 maternal-fetal/obstetrical units, 31 neonatal intensive care units and 26 neonatal follow-up programs across Canada with planned linkages to provincial health information systems. Three broad clusters of projects will be undertaken. Cluster 1 will focus on quality-improvement efforts that use the Evidence-based Practice for Improving Quality method to evaluate information from the CPTBN database and review the current literature, then identify potentially better health care practices and implement identified strategies. Cluster 2 will assess the impact of current practices and practice changes in maternal, perinatal and neonatal care on maternal, neonatal and neurodevelopmental outcomes. Cluster 3 will evaluate the effect of preterm birth on babies, their families and the health care system by integrating CPTBN data, parent feedback, and national and provincial database information in order to identify areas where more parental support is needed, and also generate robust estimates of resource use, cost and cost-effectiveness around preterm neonatal care. Interpretation: These collaborative efforts will create a flexible, transdisciplinary, evaluable and informative research and quality-improvement platform that supports programs, projects and partnerships focused on improving outcomes of preterm neonates. PMID:29348260

Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop.

PubMed

Chang, Chia-Jung; Osoegawa, Kazutoyo; Milius, Robert P; Maiers, Martin; Xiao, Wenzhong; Fernandez-Viňa, Marcelo; Mack, Steven J

2018-02-01

For over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage. The 17th IHIW adopted a centralized approach to these issues, and we developed the tools, services and systems to create an effective system for capturing and managing these NGS data. We worked with NGS platform and software developers to define a set of distinct but equivalent NGS typing reports that record NGS data in a uniform fashion. The 17th IHIW database applied our standards, tools and services to collect, validate and store those structured, multi-platform data in an automated fashion. We have created community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database, with the goal of creating a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications. Copyright © 2017 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

High Level of Integration in Integrated Disease Management Leads to Higher Usage in the e-Vita Study: Self-Management of Chronic Obstructive Pulmonary Disease With Web-Based Platforms in a Parallel Cohort Design

PubMed Central

Verdijk, Noortje A; Kasteleyn, Marise J; Harmans, Lara M; Talboom, Irvin JSH; Numans, Mattijs E; Chavannes, Niels H

2017-01-01

Background Worldwide, nearly 3 million people die of chronic obstructive pulmonary disease (COPD) every year. Integrated disease management (IDM) improves disease-specific quality of life and exercise capacity for people with COPD, but can also reduce hospital admissions and hospital days. Self-management of COPD through eHealth interventions has shown to be an effective method to improve the quality and efficiency of IDM in several settings, but it remains unknown which factors influence usage of eHealth and change in behavior of patients. Objective Our study, e-Vita COPD, compares different levels of integration of Web-based self-management platforms in IDM in three primary care settings. The main aim of this study is to analyze the factors that successfully promote the use of a self-management platform for COPD patients. Methods The e-Vita COPD study compares three different approaches to incorporating eHealth via Web-based self-management platforms into IDM of COPD using a parallel cohort design. Three groups integrated the platforms to different levels. In groups 1 (high integration) and 2 (medium integration), randomization was performed to two levels of personal assistance for patients (high and low assistance); in group 3 there was no integration into disease management (none integration). Every visit to the e-Vita and Zorgdraad COPD Web platforms was tracked objectively by collecting log data (sessions and services). At the first log-in, patients completed a baseline questionnaire. Baseline characteristics were automatically extracted from the log files including age, gender, education level, scores on the Clinical COPD Questionnaire (CCQ), dyspnea scale (MRC), and quality of life questionnaire (EQ5D). To predict the use of the platforms, multiple linear regression analyses for the different independent variables were performed: integration in IDM (high, medium, none), personal assistance for the participants (high vs low), educational level, and self-efficacy level (General Self-Efficacy Scale [GSES]). All analyses were adjusted for age and gender. Results Of the 702 invited COPD patients, 215 (30.6%) registered to a platform. Of the 82 patients in group 1 (high integration IDM), 36 were in group 1A (personal assistance) and 46 in group 1B (low assistance). Of the 96 patients in group 2 (medium integration IDM), 44 were in group 2A (telephone assistance) and 52 in group 2B (low assistance). A total of 37 patients participated in group 3 (no integration IDM). In all, 107 users (49.8%) visited the platform at least once in the 15-month period. The mean number of sessions differed between the three groups (group 1: mean 10.5, SD 1.3; group 2: mean 8.8, SD 1.4; group 3: mean 3.7, SD 1.8; P=.01). The mean number of sessions differed between the high-assistance and low-assistance groups in groups 1 and 2 (high: mean 11.8, SD 1.3; low: mean 6.7, SD 1.4; F1,80=6.55, P=.01). High-assistance participants used more services (mean 45.4, SD 6.2) than low-assistance participants (mean 21.2, SD 6.8; F1,80=6.82, P=.01). No association was found between educational level and usage and between GSES and usage. Conclusions Use of a self-management platform is higher when participants receive adequate personal assistance about how to use the platform. Blended care, where digital health and usual care are integrated, will likely lead to increased use of the online program. Future research should provide additional insights into the preferences of different patient groups. Trial Registration Nederlands Trial Register NTR4098; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=4098 (Archived by WebCite at http://www.webcitation.org/6qO1hqiJ1) PMID:28566268

Integrating heterogeneous databases in clustered medic care environments using object-oriented technology

NASA Astrophysics Data System (ADS)

Thakore, Arun K.; Sauer, Frank

1994-05-01

The organization of modern medical care environments into disease-related clusters, such as a cancer center, a diabetes clinic, etc., has the side-effect of introducing multiple heterogeneous databases, often containing similar information, within the same organization. This heterogeneity fosters incompatibility and prevents the effective sharing of data amongst applications at different sites. Although integration of heterogeneous databases is now feasible, in the medical arena this is often an ad hoc process, not founded on proven database technology or formal methods. In this paper we illustrate the use of a high-level object- oriented semantic association method to model information found in different databases into an integrated conceptual global model that integrates the databases. We provide examples from the medical domain to illustrate an integration approach resulting in a consistent global view, without attacking the autonomy of the underlying databases.

The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era.

PubMed

Polvi, Anne; Linturi, Henna; Varilo, Teppo; Anttonen, Anna-Kaisa; Byrne, Myles; Fokkema, Ivo F A C; Almusa, Henrikki; Metzidis, Anthony; Avela, Kristiina; Aula, Pertti; Kestilä, Marjo; Muilu, Juha

2013-11-01

The Finnish Disease Heritage Database (FinDis) (http://findis.org) was originally published in 2004 as a centralized information resource for rare monogenic diseases enriched in the Finnish population. The FinDis database originally contained 405 causative variants for 30 diseases. At the time, the FinDis database was a comprehensive collection of data, but since 1994, a large amount of new information has emerged, making the necessity to update the database evident. We collected information and updated the database to contain genes and causative variants for 35 diseases, including six more genes and more than 1,400 additional disease-causing variants. Information for causative variants for each gene is collected under the LOVD 3.0 platform, enabling easy updating. The FinDis portal provides a centralized resource and user interface to link information on each disease and gene with variant data in the LOVD 3.0 platform. The software written to achieve this has been open-sourced and made available on GitHub (http://github.com/findis-db), allowing biomedical institutions in other countries to present their national data in a similar way, and to both contribute to, and benefit from, standardized variation data. The updated FinDis portal provides a unique resource to assist patient diagnosis, research, and the development of new cures. © 2013 WILEY PERIODICALS, INC.