Experience with ATLAS MySQL PanDA database service

NASA Astrophysics Data System (ADS)

Smirnov, Y.; Wlodek, T.; De, K.; Hover, J.; Ozturk, N.; Smith, J.; Wenaus, T.; Yu, D.

2010-04-01

The PanDA distributed production and analysis system has been in production use for ATLAS data processing and analysis since late 2005 in the US, and globally throughout ATLAS since early 2008. Its core architecture is based on a set of stateless web services served by Apache and backed by a suite of MySQL databases that are the repository for all PanDA information: active and archival job queues, dataset and file catalogs, site configuration information, monitoring information, system control parameters, and so on. This database system is one of the most critical components of PanDA, and has successfully delivered the functional and scaling performance required by PanDA, currently operating at a scale of half a million jobs per week, with much growth still to come. In this paper we describe the design and implementation of the PanDA database system, its architecture of MySQL servers deployed at BNL and CERN, backup strategy and monitoring tools. The system has been developed, thoroughly tested, and brought to production to provide highly reliable, scalable, flexible and available database services for ATLAS Monte Carlo production, reconstruction and physics analysis.

A Distributed Web-based Solution for Ionospheric Model Real-time Management, Monitoring, and Short-term Prediction

NASA Astrophysics Data System (ADS)

Kulchitsky, A.; Maurits, S.; Watkins, B.

2006-12-01

With the widespread availability of the Internet today, many people can monitor various scientific research activities. It is important to accommodate this interest providing on-line access to dynamic and illustrative Web-resources, which could demonstrate different aspects of ongoing research. It is especially important to explain and these research activities for high school and undergraduate students, thereby providing more information for making decisions concerning their future studies. Such Web resources are also important to clarify scientific research for the general public, in order to achieve better awareness of research progress in various fields. Particularly rewarding is dissemination of information about ongoing projects within Universities and research centers to their local communities. The benefits of this type of scientific outreach are mutual, since development of Web-based automatic systems is prerequisite for many research projects targeting real-time monitoring and/or modeling of natural conditions. Continuous operation of such systems provide ongoing research opportunities for the statistically massive validation of the models, as well. We have developed a Web-based system to run the University of Alaska Fairbanks Polar Ionospheric Model in real-time. This model makes use of networking and computational resources at the Arctic Region Supercomputing Center. This system was designed to be portable among various operating systems and computational resources. Its components can be installed across different computers, separating Web servers and computational engines. The core of the system is a Real-Time Management module (RMM) written Python, which facilitates interactions of remote input data transfers, the ionospheric model runs, MySQL database filling, and PHP scripts for the Web-page preparations. The RMM downloads current geophysical inputs as soon as they become available at different on-line depositories. This information is processed to provide inputs for the next ionospheic model time step and then stored in a MySQL database as the first part of the time-specific record. The RMM then performs synchronization of the input times with the current model time, prepares a decision on initialization for the next model time step, and monitors its execution. Then, as soon as the model completes computations for the next time step, RMM visualizes the current model output into various short-term (about 1-2 hours) forecasting products and compares prior results with available ionospheric measurements. The RMM places prepared images into the MySQL database, which can be located on a different computer node, and then proceeds to the next time interval continuing the time-loop. The upper-level interface of this real-time system is the a PHP-based Web site (http://www.arsc.edu/SpaceWeather/new). This site provides general information about the Earth polar and adjacent mid-latitude ionosphere, allows for monitoring of the current developments and short-term forecasts, and facilitates access to the comparisons archive stored in the database.

Development of Web-Based Menu Planning Support System and its Solution Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Kashima, Tomoko; Matsumoto, Shimpei; Ishii, Hiroaki

2009-10-01

Recently lifestyle-related diseases have become an object of public concern, while at the same time people are being more health conscious. As an essential factor for causing the lifestyle-related diseases, we assume that the knowledge circulation on dietary habits is still insufficient. This paper focuses on everyday meals close to our life and proposes a well-balanced menu planning system as a preventive measure of lifestyle-related diseases. The system is developed by using a Web-based frontend and it provides multi-user services and menu information sharing capabilities like social networking services (SNS). The system is implemented on a Web server running Apache (HTTP server software), MySQL (database management system), and PHP (scripting language for dynamic Web pages). For the menu planning, a genetic algorithm is applied by understanding this problem as multidimensional 0-1 integer programming.

Cloud Computing Trace Characterization and Synthetic Workload Generation

DTIC Science & Technology

2013-03-01

measurements [44]. Olio is primarily for learning Web 2.0 technologies, evaluating the three implementations (PHP, Java EE, and RubyOnRails (ROR...Add Event 17 Olio is well documented, but assumes prerequisite knowledge with setup and operation of apache web servers and MySQL databases. Olio...Faban supports numerous servers such as Apache httpd, Sun Java System Web, Portal and Mail Servers, Oracle RDBMS, memcached, and others [18]. Perhaps

Developing Online Communities with LAMP (Linux, Apache, MySQL, PHP) - the IMIA OSNI and CHIRAD Experiences.

PubMed

Murray, Peter J; Oyri, Karl

2005-01-01

Many health informatics organisations do not seem to use, on a practical basis, for the benefit of their activities and interaction with their members, the very technologies that they often promote for use within healthcare environments. In particular, many organisations seem to be slow to take up the benefits of interactive web technologies. This paper presents an introduction to some of the many free/libre and open source (FLOSS) applications currently available and using the LAMP - Linux, Apache, MySQL, PHP architecture - as a way of cheaply deploying reliable, scalable, and secure web applications. The experience of moving to applications using LAMP architecture, in particular that of the Open Source Nursing Informatics (OSNI) Working Group of the Special Interest Group in Nursing Informatics of the International Medical Informatics Association (IMIA-NI), in using PostNuke, a FLOSS Content Management System (CMS) illustrates many of the benefits of such applications. The experiences of the authors in installing and maintaining a large number of websites using FLOSS CMS to develop dynamic, interactive websites that facilitate real engagement with the members of IMIA-NI OSNI, the IMIA Open Source Working Group, and the Centre for Health Informatics Research and Development (CHIRAD), as well as other organisations, is used as the basis for discussing the potential benefits that could be realised by others within the health informatics community.

Survey Software Evaluation

DTIC Science & Technology

2009-01-01

Oracle 9i, 10g  MySQL  MS SQL Server MS SQL Server Operating System Supported Windows 2003 Server  Windows 2000 Server (32 bit...WebStar (Mac OS X)  SunOne Internet Information Services (IIS) Database Server Supported MS SQL Server  MS SQL Server  Oracle 9i, 10g...challenges of Web-based surveys are: 1) identifying the best Commercial Off the Shelf (COTS) Web-based survey packages to serve the particular

Development and implementation of a web-based system to study children with malnutrition.

PubMed

Syed-Mohamad, Sharifah-Mastura

2009-01-01

To develop and implement a collective web-based system to monitor child growth in order to study children with malnutrition. The system was developed using prototyping system development methodology. The implementation was carried out using open-source technologies that include Apache Web Server, PHP scripting, and MySQL database management system. There were four datasets collected by the system: demographic data, measurement data, parent data, and food program data. The system was designed to be used by two groups of users, the clinics and the researchers. The Growth Monitor System was successfully developed and used for the study, "Geoinformation System (GIS) and Remote Sensing in Mapping of Children with Malnutrition." Data collection was implemented in public clinics from two districts in the state of Kelantan, Malaysia. The development of an integrated web-based system, Growth Monitor, for the study of children with malnutrition has been achieved. This system can be expanded to new partners who are involved in the study of children with malnutrition in other parts of Malaysia as well as other countries.

Astronomical databases of Nikolaev Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Y.; Mazhaev, A.

2008-07-01

Several astronomical databases were created at Nikolaev Observatory during the last years. The databases are built by using MySQL search engine and PHP scripts. They are available on NAO web-site http://www.mao.nikolaev.ua.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

Evaluation of the performance of open-source RDBMS and triplestores for storing medical data over a web service.

PubMed

Kilintzis, Vassilis; Beredimas, Nikolaos; Chouvarda, Ioanna

2014-01-01

An integral part of a system that manages medical data is the persistent storage engine. For almost twenty five years Relational Database Management Systems(RDBMS) were considered the obvious decision, yet today new technologies have emerged that require our attention as possible alternatives. Triplestores store information in terms of RDF triples without necessarily binding to a specific predefined structural model. In this paper we present an attempt to compare the performance of Apache JENA-Fuseki and the Virtuoso Universal Server 6 triplestores with that of MySQL 5.6 RDBMS for storing and retrieving medical information that it is communicated as RDF/XML ontology instances over a RESTful web service. The results show that the performance, calculated as average time of storing and retrieving instances, is significantly better using Virtuoso Server while MySQL performed better than Fuseki.

HippDB: a database of readily targeted helical protein-protein interactions.

PubMed

Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

2013-11-01

HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

Towards 100,000 CPU Cycle-Scavenging by Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We examine a web-centric design using standard tools such as web servers, web browsers, PHP, and mySQL. We also consider the applicability of Information Power Grid tools such as the Globus (no relation to the author) Toolkit. We intend to implement this architecture with JavaGenes running on at least two cycle-scavengers: Condor and United Devices. JavaGenes, a genetic algorithm code written in Java, will be used to evolve multi-species reactive molecular force field parameters.

An Auto-management Thesis Program WebMIS Based on Workflow

NASA Astrophysics Data System (ADS)

Chang, Li; Jie, Shi; Weibo, Zhong

An auto-management WebMIS based on workflow for bachelor thesis program is given in this paper. A module used for workflow dispatching is designed and realized using MySQL and J2EE according to the work principle of workflow engine. The module can automatively dispatch the workflow according to the date of system, login information and the work status of the user. The WebMIS changes the management from handwork to computer-work which not only standardizes the thesis program but also keeps the data and documents clean and consistent.

Comprehensive Routing Security Development and Deployment for the Internet

DTIC Science & Technology

2015-02-01

feature enhancement and bug fixes. • MySQL : MySQL is a widely used and popular open source database package. It was chosen for database support in the...RPSTIR depends on several other open source packages. • MySQL : MySQL is used for the the local RPKI database cache. • OpenSSL: OpenSSL is used for...cryptographic libraries for X.509 certificates. • ODBC mySql Connector: ODBC (Open Database Connectivity) is a standard programming interface (API) for

An open source, web based, simple solution for seismic data dissemination and collaborative research

NASA Astrophysics Data System (ADS)

Diviacco, Paolo

2005-06-01

Collaborative research and data dissemination in the field of geophysical exploration need network tools that can access large amounts of data from anywhere using any PC or workstation. Simple solutions based on a combination of Open Source software can be developed to address such requests, exploiting the possibilities offered by the web technologies, and at the same time avoiding the costs and inflexibility of commercial systems. A viable solution consists of MySQL for data storage and retrieval, CWP/SU and GMT for data visualisation and a scripting layer driven by PHP that allows users to access the system via an Apache web server. In the light of the experience building the on-line archive of seismic data of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), we describe the solutions and the methods adopted, with a view to stimulate both the attitude of network collaborative research of other institutions similar to ours, and the development of different applications.

EVpedia: a community web portal for extracellular vesicles research.

PubMed

Kim, Dae-Kyum; Lee, Jaewook; Kim, Sae Rom; Choi, Dong-Sic; Yoon, Yae Jin; Kim, Ji Hyun; Go, Gyeongyun; Nhung, Dinh; Hong, Kahye; Jang, Su Chul; Kim, Si-Hyun; Park, Kyong-Su; Kim, Oh Youn; Park, Hyun Taek; Seo, Ji Hye; Aikawa, Elena; Baj-Krzyworzeka, Monika; van Balkom, Bas W M; Belting, Mattias; Blanc, Lionel; Bond, Vincent; Bongiovanni, Antonella; Borràs, Francesc E; Buée, Luc; Buzás, Edit I; Cheng, Lesley; Clayton, Aled; Cocucci, Emanuele; Dela Cruz, Charles S; Desiderio, Dominic M; Di Vizio, Dolores; Ekström, Karin; Falcon-Perez, Juan M; Gardiner, Chris; Giebel, Bernd; Greening, David W; Gross, Julia Christina; Gupta, Dwijendra; Hendrix, An; Hill, Andrew F; Hill, Michelle M; Nolte-'t Hoen, Esther; Hwang, Do Won; Inal, Jameel; Jagannadham, Medicharla V; Jayachandran, Muthuvel; Jee, Young-Koo; Jørgensen, Malene; Kim, Kwang Pyo; Kim, Yoon-Keun; Kislinger, Thomas; Lässer, Cecilia; Lee, Dong Soo; Lee, Hakmo; van Leeuwen, Johannes; Lener, Thomas; Liu, Ming-Lin; Lötvall, Jan; Marcilla, Antonio; Mathivanan, Suresh; Möller, Andreas; Morhayim, Jess; Mullier, François; Nazarenko, Irina; Nieuwland, Rienk; Nunes, Diana N; Pang, Ken; Park, Jaesung; Patel, Tushar; Pocsfalvi, Gabriella; Del Portillo, Hernando; Putz, Ulrich; Ramirez, Marcel I; Rodrigues, Marcio L; Roh, Tae-Young; Royo, Felix; Sahoo, Susmita; Schiffelers, Raymond; Sharma, Shivani; Siljander, Pia; Simpson, Richard J; Soekmadji, Carolina; Stahl, Philip; Stensballe, Allan; Stępień, Ewa; Tahara, Hidetoshi; Trummer, Arne; Valadi, Hadi; Vella, Laura J; Wai, Sun Nyunt; Witwer, Kenneth; Yáñez-Mó, María; Youn, Hyewon; Zeidler, Reinhard; Gho, Yong Song

2015-03-15

Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. The web site was implemented in PHP, Java, MySQL and Apache, and is freely available at http://evpedia.info. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

Maxima and O-C Diagrams for 489 Mira Stars

NASA Astrophysics Data System (ADS)

Karlsson, T.

2013-11-01

Maxima for 489 Mira stars have been compiled. They were computed with data from AAVSO, AFOEV, VSOLJ, and BAA-VSS and collected from published maxima. The result is presented in a mysql database and on web pages with O-C diagrams, periods and some statistical information for each star.

Database Entity Persistence with Hibernate for the Network Connectivity Analysis Model

DTIC Science & Technology

2014-04-01

time savings in the Java coding development process. Appendices A and B describe address setup procedures for installing the MySQL database...development environment is required: • The open source MySQL Database Management System (DBMS) from Oracle, which is a Java Database Connectivity (JDBC...compliant DBMS • MySQL JDBC Driver library that comes as a plug-in with the Netbeans distribution • The latest Java Development Kit with the latest

Architecture of a spatial data service system for statistical analysis and visualization of regional climate changes

NASA Astrophysics Data System (ADS)

Titov, A. G.; Okladnikov, I. G.; Gordov, E. P.

2017-11-01

The use of large geospatial datasets in climate change studies requires the development of a set of Spatial Data Infrastructure (SDI) elements, including geoprocessing and cartographical visualization web services. This paper presents the architecture of a geospatial OGC web service system as an integral part of a virtual research environment (VRE) general architecture for statistical processing and visualization of meteorological and climatic data. The architecture is a set of interconnected standalone SDI nodes with corresponding data storage systems. Each node runs a specialized software, such as a geoportal, cartographical web services (WMS/WFS), a metadata catalog, and a MySQL database of technical metadata describing geospatial datasets available for the node. It also contains geospatial data processing services (WPS) based on a modular computing backend realizing statistical processing functionality and, thus, providing analysis of large datasets with the results of visualization and export into files of standard formats (XML, binary, etc.). Some cartographical web services have been developed in a system’s prototype to provide capabilities to work with raster and vector geospatial data based on OGC web services. The distributed architecture presented allows easy addition of new nodes, computing and data storage systems, and provides a solid computational infrastructure for regional climate change studies based on modern Web and GIS technologies.

New Directions in the NOAO Observing Proposal System

NASA Astrophysics Data System (ADS)

Gasson, David; Bell, Dave

For the past eight years NOAO has been refining its on-line observing proposal system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form, or via the Gemini Phase I Tool. NOAO staff can use the system to do administrative tasks, scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available on-line, including the proposals themselves (in HTML, PDF and PostScript) and technical comments. Grades and TAC comments are entered and edited through web forms, and can be sorted and filtered according to specified criteria. Current developments include a move away from proprietary solutions, toward open standards such as SQL (in the form of the MySQL relational database system), Perl, PHP and XML.

A web-based information system for management and analysis of patient data after refractive eye surgery.

PubMed

Zuberbuhler, Bruno; Galloway, Peter; Reddy, Aravind; Saldana, Manuel; Gale, Richard

2007-12-01

The aim was to develop a software tool for refractive surgeons using a standard user-friendly web-based interface, providing the user with a secure environment to protect large volumes of patient data. The software application was named "Internet-based refractive analysis" (IBRA), and was programmed with the computer languages PHP, HTML and JavaScript, attached to the opensource MySQL database. IBRA facilitated internationally accepted presentation methods including the stability chart, the predictability chart and the safety chart; it was able to perform vector analysis for the course of a single patient or for group data. With the integrated nomogram calculation, treatment could be customised to reduce the postoperative refractive error. Multicenter functions permitted quality-control comparisons between different surgeons and laser units.

Data Processing on Database Management Systems with Fuzzy Query

NASA Astrophysics Data System (ADS)

Şimşek, Irfan; Topuz, Vedat

In this study, a fuzzy query tool (SQLf) for non-fuzzy database management systems was developed. In addition, samples of fuzzy queries were made by using real data with the tool developed in this study. Performance of SQLf was tested with the data about the Marmara University students' food grant. The food grant data were collected in MySQL database by using a form which had been filled on the web. The students filled a form on the web to describe their social and economical conditions for the food grant request. This form consists of questions which have fuzzy and crisp answers. The main purpose of this fuzzy query is to determine the students who deserve the grant. The SQLf easily found the eligible students for the grant through predefined fuzzy values. The fuzzy query tool (SQLf) could be used easily with other database system like ORACLE and SQL server.

TargetCompare: A web interface to compare simultaneous miRNAs targets

PubMed Central

Moreira, Fabiano Cordeiro; Dustan, Bruno; Hamoy, Igor G; Ribeiro-dos-Santos, André M; dos Santos, Ândrea Ribeiro

2014-01-01

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. Availability http://lghm.ufpa.br/targetcompare PMID:25352731

TargetCompare: A web interface to compare simultaneous miRNAs targets.

PubMed

Moreira, Fabiano Cordeiro; Dustan, Bruno; Hamoy, Igor G; Ribeiro-Dos-Santos, André M; Dos Santos, Andrea Ribeiro

2014-01-01

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. http://lghm.ufpa.br/targetcompare.

MaGnET: Malaria Genome Exploration Tool.

PubMed

Sharman, Joanna L; Gerloff, Dietlind L

2013-09-15

The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive 'exploration-style' visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein-protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search). Free online use (Java Web Start) or download (Java application archive and MySQL database; requires local MySQL installation) at http://malariagenomeexplorer.org joanna.sharman@ed.ac.uk or dgerloff@ffame.org Supplementary data are available at Bioinformatics online.

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.

PubMed

Iquebal, M A; Jaiswal, Sarika; Mahato, Ajay Kumar; Jayaswal, Pawan K; Angadi, U B; Kumar, Neeraj; Sharma, Nimisha; Singh, Anand K; Srivastav, Manish; Prakash, Jai; Singh, S K; Khan, Kasim; Mishra, Rupesh K; Rajan, Shailendra; Bajpai, Anju; Sandhya, B S; Nischita, Puttaraju; Ravishankar, K V; Dinesh, M R; Rai, Anil; Kumar, Dinesh; Sharma, Tilak R; Singh, Nagendra K

2017-11-02

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.

Enabling On-Demand Database Computing with MIT SuperCloud Database Management System

DTIC Science & Technology

2015-09-15

arc.liv.ac.uk/trac/SGE) provides these services and is independent of programming language (C, Fortran, Java , Matlab, etc) or parallel programming...a MySQL database to store DNS records. The DNS records are controlled via a simple web service interface that allows records to be created

A web application to support telemedicine services in Brazil.

PubMed

Barbosa, Ana Karina P; de A Novaes, Magdala; de Vasconcelos, Alexandre M L

2003-01-01

This paper describes a system that has been developed to support Telemedicine activities in Brazil, a country that has serious problems in the delivery of health services. The system is a part of the broader Tele-health Project that has been developed to make health services more accessible to the low-income population in the northeast region. The HealthNet system is based upon a pilot area that uses fetal and pediatric cardiology. This article describes both the system's conceptual model, including the tele-diagnosis and second medical opinion services, as well as its architecture and development stages. The system model describes both collaborating tools used asynchronously, such as discussion forums, and synchronous tools, such as videoconference services. Web and free-of-charge tools are utilized for implementation, such as Java and MySQL database. Furthermore, an interface with Electronic Patient Record (EPR) systems using Extended Markup Language (XML) technology is also proposed. Finally, considerations concerning the development and implementation process are presented.

Visualization for genomics: the Microbial Genome Viewer.

PubMed

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Nuclear Data Online Services at Peking University

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

Fan, T.S.; Guo, Z.Y.; Ye, W.G.

2005-05-24

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

VO Access to BASECOL Database

NASA Astrophysics Data System (ADS)

Moreau, N.; Dubernet, M. L.

2006-07-01

Basecol is a combination of a website (using PHP and HTML) and a MySQL database concerning molecular ro-vibrational transitions induced by collisions with atoms or molecules. This database has been created in view of the scientific preparation of the Heterodyne Instrument for the Far-Infrared on board the Herschel Space Observatory (HSO). Basecol offers an access to numerical and bibliographic data through various output methods such as ASCII, HTML or VOTable (which is a first step towards a VO compliant system). A web service using Apache Axis has been developed in order to provide a direct access to data for external applications.

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

Fan, T. S.; Guo, Z. Y.; Ye, W. G.; Liu, W. L.; Liu, T. J.; Liu, C. X.; Chen, J. X.; Tang, G. Y.; Shi, Z. M.; Huang, X. L.; Chen, J. E.

2005-05-01

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

A web-server of cell type discrimination system.

PubMed

Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

A Web-Server of Cell Type Discrimination System

PubMed Central

Zhong, Yan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

Multi-Resolution Playback of Network Trace Files

DTIC Science & Technology

2015-06-01

a com- plete MySQL database, C++ developer tools and the libraries utilized in the development of the system (Boost and Libcrafter), and Wireshark...XE suite has a limit to the allowed size of each database. In order to be scalable, the project had to switch to the MySQL database suite. The...programs that access the database use the MySQL C++ connector, provided by Oracle, and the supplied methods and libraries. 4.4 Flow Generator Chapter 3

An Automated Web Diary System for TeleHomeCare Patient Monitoring

PubMed Central

Ganzinger, Matthias; Demiris, George; Finkelstein, Stanley M.; Speedie, Stuart; Lundgren, Jan Marie

2001-01-01

The TeleHomeCare project monitors home care patients via the Internet. Each patient has a personalized homepage with an electronic diary for collecting the monitoring data with HTML forms. The web pages are generated dynamically using PHP. All data are stored in a MySQL database. Data are checked immediately by the system; if a value exceeds a predefined limit an alarm message is generated and sent automatically to the patient's case manager. Weekly graphical reports (PDF format) are also generated and sent by email to the same destination.

Secure web book to store structural genomics research data.

PubMed

Manjasetty, Babu A; Höppner, Klaus; Mueller, Uwe; Heinemann, Udo

2003-01-01

Recently established collaborative structural genomics programs aim at significantly accelerating the crystal structure analysis of proteins. These large-scale projects require efficient data management systems to ensure seamless collaboration between different groups of scientists working towards the same goal. Within the Berlin-based Protein Structure Factory, the synchrotron X-ray data collection and the subsequent crystal structure analysis tasks are located at BESSY, a third-generation synchrotron source. To organize file-based communication and data transfer at the BESSY site of the Protein Structure Factory, we have developed the web-based BCLIMS, the BESSY Crystallography Laboratory Information Management System. BCLIMS is a relational data management system which is powered by MySQL as the database engine and Apache HTTP as the web server. The database interface routines are written in Python programing language. The software is freely available to academic users. Here we describe the storage, retrieval and manipulation of laboratory information, mainly pertaining to the synchrotron X-ray diffraction experiments and the subsequent protein structure analysis, using BCLIMS.

Web Service Model for Plasma Simulations with Automatic Post Processing and Generation of Visual Diagnostics*

NASA Astrophysics Data System (ADS)

Exby, J.; Busby, R.; Dimitrov, D. A.; Bruhwiler, D.; Cary, J. R.

2003-10-01

We present our design and initial implementation of a web service model for running particle-in-cell (PIC) codes remotely from a web browser interface. PIC codes have grown significantly in complexity and now often require parallel execution on multiprocessor computers, which in turn requires sophisticated post-processing and data analysis. A significant amount of time and effort is required for a physicist to develop all the necessary skills, at the expense of actually doing research. Moreover, parameter studies with a computationally intensive code justify the systematic management of results with an efficient way to communicate them among a group of remotely located collaborators. Our initial implementation uses the OOPIC Pro code [1], Linux, Apache, MySQL, Python, and PHP. The Interactive Data Language is used for visualization. [1] D.L. Bruhwiler et al., Phys. Rev. ST-AB 4, 101302 (2001). * This work is supported by DOE grant # DE-FG02-03ER83857 and by Tech-X Corp. ** Also University of Colorado.

Generic HTML Form Processor: A versatile PHP script to save web-collected data into a MySQL database.

PubMed

Göritz, Anja S; Birnbaum, Michael H

2005-11-01

The customizable PHP script Generic HTML Form Processor is intended to assist researchers and students in quickly setting up surveys and experiments that can be administered via the Web. This script relieves researchers from the burdens of writing new CGI scripts and building databases for each Web study. Generic HTML Form Processor processes any syntactically correct HTML forminput and saves it into a dynamically created open-source database. We describe five modes for usage of the script that allow increasing functionality but require increasing levels of knowledge of PHP and Web servers: The first two modes require no previous knowledge, and the fifth requires PHP programming expertise. Use of Generic HTML Form Processor is free for academic purposes, and its Web address is www.goeritz.net/brmic.

The Emperor’s New Password Manager: Security Analysis of Web-based Password Managers

DTIC Science & Technology

2014-07-07

POST re- quest, LastPass will store h’ as authenticating Alice. Mallory can then use otp’ to log-in to LastPass us- ing otp’. Of course , decrypting the...everywhere. [36] M. Rochkind. Security, forms, and error handling. In Expert PHP and MySQL , pages 191–247. Springer, 2013. [37] D. Silver, S. Jana, E

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

PubMed Central

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry BF; Tipton, Keith F

2007-01-01

Background We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. Description The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at . The data are available for download as SQL and XML files via FTP. Conclusion ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List. PMID:17662133

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

PubMed

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

MaGnET: Malaria Genome Exploration Tool

PubMed Central

Sharman, Joanna L.; Gerloff, Dietlind L.

2013-01-01

Summary: The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein–protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search). Availability and Implementation: Free online use (Java Web Start) or download (Java application archive and MySQL database; requires local MySQL installation) at http://malariagenomeexplorer.org Contact: joanna.sharman@ed.ac.uk or dgerloff@ffame.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23894142

Web-Based Honorarium Confirmation System Prototype

NASA Astrophysics Data System (ADS)

Wisswani, N. W.; Catur Bawa, I. G. N. B.

2018-01-01

Improving services in academic environment can be applied by regulating salary payment process for all employees. As a form of control to maintain financial transparency, employees should have information concerning salary payment process. Currently, notification process of committee honorarium will be accepted by the employees in a manual manner. The salary will be received by the employee bank account and to know its details, they should go to the accounting unit to find out further information. Though there are some employees entering the accounting unit, they still find difficulty to obtain information about detailed honor information that they received in their accounts. This can be caused by many data collected and to be managed. Based on this issue, this research will design a prototype of web-based system for accounting unit system in order to provide detailed financial transaction confirmation to employee bank accounts that have been informed through mobile banking system. This prototype will be developed with Waterfall method through testing on final users after it is developed through PHP program with MySQL as DBMS

[A systematic evaluation of application of the web-based cancer database].

PubMed

Huang, Tingting; Liu, Jialin; Li, Yong; Zhang, Rui

2013-10-01

In order to support the theory and practice of the web-based cancer database development in China, we applied a systematic evaluation to assess the development condition of the web-based cancer databases at home and abroad. We performed computer-based retrieval of the Ovid-MEDLINE, Springerlink, EBSCOhost, Wiley Online Library and CNKI databases, the papers of which were published between Jan. 1995 and Dec. 2011, and retrieved the references of these papers by hand. We selected qualified papers according to the pre-established inclusion and exclusion criteria, and carried out information extraction and analysis of the papers. Eventually, searching the online database, we obtained 1244 papers, and checking the reference lists, we found other 19 articles. Thirty-one articles met the inclusion and exclusion criteria and we extracted the proofs and assessed them. Analyzing these evidences showed that the U.S.A. counted for 26% in the first place. Thirty-nine percent of these web-based cancer databases are comprehensive cancer databases. As for single cancer databases, breast cancer and prostatic cancer are on the top, both counting for 10% respectively. Thirty-two percent of the cancer database are associated with cancer gene information. For the technical applications, MySQL and PHP applied most widely, nearly 23% each.

A web GIS based integrated flood assessment modeling tool for coastal urban watersheds

NASA Astrophysics Data System (ADS)

Kulkarni, A. T.; Mohanty, J.; Eldho, T. I.; Rao, E. P.; Mohan, B. K.

2014-03-01

Urban flooding has become an increasingly important issue in many parts of the world. In this study, an integrated flood assessment model (IFAM) is presented for the coastal urban flood simulation. A web based GIS framework has been adopted to organize the spatial datasets for the study area considered and to run the model within this framework. The integrated flood model consists of a mass balance based 1-D overland flow model, 1-D finite element based channel flow model based on diffusion wave approximation and a quasi 2-D raster flood inundation model based on the continuity equation. The model code is written in MATLAB and the application is integrated within a web GIS server product viz: Web Gram Server™ (WGS), developed at IIT Bombay, using Java, JSP and JQuery technologies. Its user interface is developed using open layers and the attribute data are stored in MySQL open source DBMS. The model is integrated within WGS and is called via Java script. The application has been demonstrated for two coastal urban watersheds of Navi Mumbai, India. Simulated flood extents for extreme rainfall event of 26 July, 2005 in the two urban watersheds of Navi Mumbai city are presented and discussed. The study demonstrates the effectiveness of the flood simulation tool in a web GIS environment to facilitate data access and visualization of GIS datasets and simulation results.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

PubMed Central

Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

2008-01-01

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

PubMed

Choubey, Jyotsna; Choudhari, Jyoti Kant; Patel, Ashish; Verma, Mukesh Kumar

2017-01-01

Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

The development of a web-based assessment system to identify students’ misconception automatically on linear kinematics with a four-tier instrument test

NASA Astrophysics Data System (ADS)

Pujayanto, Pujayanto; Budiharti, Rini; Adhitama, Egy; Nuraini, Niken Rizky Amalia; Vernanda Putri, Hanung

2018-07-01

This research proposes the development of a web-based assessment system to identify students’ misconception. The system, named WAS (web-based assessment system), can identify students’ misconception profile on linear kinematics automatically after the student has finished the test. The test instrument was developed and validated. Items were constructed and arranged from the result of a focus group discussion (FGD), related to previous research. Fifty eight students (female  =  37, male  =  21) were used as samples. They were from different classes with 18 students from the gifted class and another 40 students from the normal class. WAS was designed specifically to support the teacher as an efficient replacement for a paper-based test system. In addition, WAS offers flexible timing functionally, stand-alone subject module, robustness and scalability. The entire WAS program and interface was developed with open source-based technologies such as the XAMP server, MySQL database, Javascript and PHP. It provides results immediately and provides diagrammatic questions as well as scientific symbols. It is feasible to apply this system to many students at once. Thus, it could be integrated in many schools as part of physics courses.

A Web-based database for pathology faculty effort reporting.

PubMed

Dee, Fred R; Haugen, Thomas H; Wynn, Philip A; Leaven, Timothy C; Kemp, John D; Cohen, Michael B

2008-04-01

To ensure appropriate mission-based budgeting and equitable distribution of funds for faculty salaries, our compensation committee developed a pathology-specific effort reporting database. Principles included the following: (1) measurement should be done by web-based databases; (2) most entry should be done by departmental administration or be relational to other databases; (3) data entry categories should be aligned with funding streams; and (4) units of effort should be equal across categories of effort (service, teaching, research). MySQL was used for all data transactions (http://dev.mysql.com/downloads), and scripts were constructed using PERL (http://www.perl.org). Data are accessed with forms that correspond to fields in the database. The committee's work resulted in a novel database using pathology value units (PVUs) as a standard quantitative measure of effort for activities in an academic pathology department. The most common calculation was to estimate the number of hours required for a specific task, divide by 2080 hours (a Medicare year) and then multiply by 100. Other methods included assigning a baseline PVU for program, laboratory, or course directorship with an increment for each student or staff in that unit. With these methods, a faculty member should acquire approximately 100 PVUs. Some outcomes include (1) plotting PVUs versus salary to identify outliers for salary correction, (2) quantifying effort in activities outside the department, (3) documenting salary expenditure for unfunded research, (4) evaluating salary equity by plotting PVUs versus salary by sex, and (5) aggregating data by category of effort for mission-based budgeting and long-term planning.

Analyzing Enron Data: Bitmap Indexing Outperforms MySQL Queries bySeveral Orders of Magnitude

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

Stockinger, Kurt; Rotem, Doron; Shoshani, Arie

2006-01-28

FastBit is an efficient, compressed bitmap indexing technology that was developed in our group. In this report we evaluate the performance of MySQL and FastBit for analyzing the email traffic of the Enron dataset. The first finding shows that materializing the join results of several tables significantly improves the query performance. The second finding shows that FastBit outperforms MySQL by several orders of magnitude.

Real-time Geographic Information System (GIS) for Monitoring the Area of Potential Water Level Using Rule Based System

NASA Astrophysics Data System (ADS)

Anugrah, Wirdah; Suryono; Suseno, Jatmiko Endro

2018-02-01

Management of water resources based on Geographic Information System can provide substantial benefits to water availability settings. Monitoring the potential water level is needed in the development sector, agriculture, energy and others. In this research is developed water resource information system using real-time Geographic Information System concept for monitoring the potential water level of web based area by applying rule based system method. GIS consists of hardware, software, and database. Based on the web-based GIS architecture, this study uses a set of computer that are connected to the network, run on the Apache web server and PHP programming language using MySQL database. The Ultrasound Wireless Sensor System is used as a water level data input. It also includes time and geographic location information. This GIS maps the five sensor locations. GIS is processed through a rule based system to determine the level of potential water level of the area. Water level monitoring information result can be displayed on thematic maps by overlaying more than one layer, and also generating information in the form of tables from the database, as well as graphs are based on the timing of events and the water level values.

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

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

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

Petaminer: Using ROOT for efficient data storage in MySQL database

NASA Astrophysics Data System (ADS)

Cranshaw, J.; Malon, D.; Vaniachine, A.; Fine, V.; Lauret, J.; Hamill, P.

2010-04-01

High Energy and Nuclear Physics (HENP) experiments store Petabytes of event data and Terabytes of calibration data in ROOT files. The Petaminer project is developing a custom MySQL storage engine to enable the MySQL query processor to directly access experimental data stored in ROOT files. Our project is addressing the problem of efficient navigation to PetaBytes of HENP experimental data described with event-level TAG metadata, which is required by data intensive physics communities such as the LHC and RHIC experiments. Physicists need to be able to compose a metadata query and rapidly retrieve the set of matching events, where improved efficiency will facilitate the discovery process by permitting rapid iterations of data evaluation and retrieval. Our custom MySQL storage engine enables the MySQL query processor to directly access TAG data stored in ROOT TTrees. As ROOT TTrees are column-oriented, reading them directly provides improved performance over traditional row-oriented TAG databases. Leveraging the flexible and powerful SQL query language to access data stored in ROOT TTrees, the Petaminer approach enables rich MySQL index-building capabilities for further performance optimization.

A Web-Based Information System for Field Data Management

NASA Astrophysics Data System (ADS)

Weng, Y. H.; Sun, F. S.

2014-12-01

A web-based field data management system has been designed and developed to allow field geologists to store, organize, manage, and share field data online. System requirements were analyzed and clearly defined first regarding what data are to be stored, who the potential users are, and what system functions are needed in order to deliver the right data in the right way to the right user. A 3-tiered architecture was adopted to create this secure, scalable system that consists of a web browser at the front end while a database at the back end and a functional logic server in the middle. Specifically, HTML, CSS, and JavaScript were used to implement the user interface in the front-end tier, the Apache web server runs PHP scripts, and MySQL to server is used for the back-end database. The system accepts various types of field information, including image, audio, video, numeric, and text. It allows users to select data and populate them on either Google Earth or Google Maps for the examination of the spatial relations. It also makes the sharing of field data easy by converting them into XML format that is both human-readable and machine-readable, and thus ready for reuse.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

A new information architecture, website and services for the CMS experiment

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

Taylor, Lucas; Rusack, Eleanor; Zemleris, Vidmantas

2012-01-01

The age and size of the CMS collaboration at the LHC means it now has many hundreds of inhomogeneous web sites and services, and hundreds of thousands of documents. We describe a major initiative to create a single coherent CMS internal and public web site. This uses the Drupal web Content Management System (now supported by CERN/IT) on top of a standard LAMP stack (Linux, Apache, MySQL, and php/perl). The new navigation, content and search services are coherently integrated with numerous existing CERN services (CDS, EDMS, Indico, phonebook, Twiki) as well as many CMS internal Web services. We describe themore » information architecture, the system design, implementation and monitoring, the document and content database, security aspects, and our deployment strategy, which ensured continual smooth operation of all systems at all times.« less

A new Information Architecture, Website and Services for the CMS Experiment

NASA Astrophysics Data System (ADS)

Taylor, Lucas; Rusack, Eleanor; Zemleris, Vidmantas

2012-12-01

The age and size of the CMS collaboration at the LHC means it now has many hundreds of inhomogeneous web sites and services, and hundreds of thousands of documents. We describe a major initiative to create a single coherent CMS internal and public web site. This uses the Drupal web Content Management System (now supported by CERN/IT) on top of a standard LAMP stack (Linux, Apache, MySQL, and php/perl). The new navigation, content and search services are coherently integrated with numerous existing CERN services (CDS, EDMS, Indico, phonebook, Twiki) as well as many CMS internal Web services. We describe the information architecture; the system design, implementation and monitoring; the document and content database; security aspects; and our deployment strategy, which ensured continual smooth operation of all systems at all times.

STINGRAY: system for integrated genomic resources and analysis.

PubMed

Wagner, Glauber; Jardim, Rodrigo; Tschoeke, Diogo A; Loureiro, Daniel R; Ocaña, Kary A C S; Ribeiro, Antonio C B; Emmel, Vanessa E; Probst, Christian M; Pitaluga, André N; Grisard, Edmundo C; Cavalcanti, Maria C; Campos, Maria L M; Mattoso, Marta; Dávila, Alberto M R

2014-03-07

The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

STINGRAY: system for integrated genomic resources and analysis

PubMed Central

2014-01-01

Background The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/. PMID:24606808

Hardware Assisted Stealthy Diversity (CHECKMATE)

DTIC Science & Technology

2013-09-01

applicable across multiple architectures. Figure 29 shows an example an attack against an interpreted environment with a Java executable. CHECKMATE can...Architectures ARM PPCx86 Java VM Java VMJava VM Java Executable Attack APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED 33 a user executes “/usr/bin/wget...Server 1 - Administration Server 2 – Database ( mySQL ) Server 3 – Web server (Mongoose) Server 4 – File server (SSH) Server 5 – Email server

A Visual Galaxy Classification Interface and its Classroom Application

NASA Astrophysics Data System (ADS)

Kautsch, Stefan J.; Phung, Chau; VanHilst, Michael; Castro, Victor H

2014-06-01

Galaxy morphology is an important topic in modern astronomy to understand questions concerning the evolution and formation of galaxies and their dark matter content. In order to engage students in exploring galaxy morphology, we developed a web-based, graphical interface that allows students to visually classify galaxy images according to various morphological types. The website is designed with HTML5, JavaScript, PHP, and a MySQL database. The classification interface provides hands-on research experience and training for students and interested clients, and allows them to contribute to studies of galaxy morphology. We present the first results of a pilot study and compare the visually classified types using our interface with that from automated classification routines.

Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications.

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

Integration of gel-based proteome data with pProRep.

PubMed

Laukens, Kris; Matthiesen, Rune; Lemière, Filip; Esmans, Eddy; Onckelen, Harry Van; Jensen, Ole Nørregaard; Witters, Erwin

2006-11-15

pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.

IntegratedMap: a Web interface for integrating genetic map data.

PubMed

Yang, Hongyu; Wang, Hongyu; Gingle, Alan R

2005-05-01

IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources. IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

Student’s Entrepreneur Model Development in Creative Industry through Utilization of Web Development Software and Educational Game

NASA Astrophysics Data System (ADS)

Hasan, B.; Hasbullah, H.; Elvyanti, S.; Purnama, W.

2018-02-01

The creative industry is the utilization of creativity, skill and talent of individuals to create wealth and jobs by generating and exploiting creativity power of individual. In the field of design, utilization of information technology can spur creative industry, development of creative industry design will accommodate a lot of creative energy that can pour their ideas and creativity without limitations. Open Source software is a trend in the field of information technology has developed since the 1990s. Examples of applications developed by the Open Source approach is the Apache web services, Linux and Android Operating System, the MySQL database. This community service activities based entrepreneurship aims to: 1). give an idea about the profile of the UPI student’s knowledge of entrepreneurship about the business based creative industries in software by using web software development and educational game 2) create a model for fostering entrepreneurship based on the creative industries in software by leveraging web development and educational games, 3) conduct training and guidance on UPI students who want to develop business in the field of creative industries engaged in the software industry . PKM-based entrepreneurship activity was attended by about 35 students DPTE FPTK UPI had entrepreneurial high interest and competence in information technology. Outcome generated from PKM entrepreneurship is the emergence of entrepreneurs from the students who are interested in the creative industry in the field of software which is able to open up business opportunities for themselves and others. Another outcome of this entrepreneurship PKM activity is the publication of articles or scientific publications in journals of national/international indexed.

The CMS dataset bookkeeping service

NASA Astrophysics Data System (ADS)

Afaq, A.; Dolgert, A.; Guo, Y.; Jones, C.; Kosyakov, S.; Kuznetsov, V.; Lueking, L.; Riley, D.; Sekhri, V.

2008-07-01

The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires processing and analysis activities at various service levels and the DBS system provides support for localized processing or private analysis, as well as global access for CMS users at large. Catalog entries can be moved among the various service levels with a simple set of migration tools, thus forming a loose federation of databases. DBS is available to CMS users via a Python API, Command Line, and a Discovery web page interfaces. The system is built as a multi-tier web application with Java servlets running under Tomcat, with connections via JDBC to Oracle or MySQL database backends. Clients connect to the service through HTTP or HTTPS with authentication provided by GRID certificates and authorization through VOMS. DBS is an integral part of the overall CMS Data Management and Workflow Management systems.

Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

PubMed

Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio

2015-03-01

In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.

NOAO observing proposal processing system

NASA Astrophysics Data System (ADS)

Bell, David J.; Gasson, David; Hartman, Mia

2002-12-01

Since going electronic in 1994, NOAO has continued to refine and enhance its observing proposal handling system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form or via Gemini's downloadable Phase-I Tool. NOAO staff can use online interfaces for administrative tasks, technical reviews, telescope scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available online. The system, now known as ANDES, is designed as a thin-client architecture (web pages are now used for almost all database functions) built using open source tools (FreeBSD, Apache, MySQL, Perl, PHP) to process descriptively-marked (LaTeX, XML) proposal documents.

PathScore: a web tool for identifying altered pathways in cancer data.

PubMed

Gaffney, Stephen G; Townsend, Jeffrey P

2016-12-01

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects. Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license. stephen.gaffney@yale.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Reuse of the Cloud Analytics and Collaboration Environment within Tactical Applications (TacApps): A Feasibility Analysis

DTIC Science & Technology

2016-03-01

Representational state transfer  Java messaging service  Java application programming interface (API)  Internet relay chat (IRC)/extensible messaging and...JBoss application server or an Apache Tomcat servlet container instance. The relational database management system can be either PostgreSQL or MySQL ... Java library called direct web remoting. This library has been part of the core CACE architecture for quite some time; however, there have not been

Piloting a Collaborative Web-Based System for Testing ICD-11.

PubMed

Donada, Marc; Kostanjsek, Nenad; Della Mea, Vincenzo; Celik, Can; Jakob, Robert

2017-01-01

The 11^th revision of the International Classification of Diseases (ICD-11), for the first time in ICD history, deployed web-based collaboration of experts and ICT tools. To ensure that ICD-11 is working well, it needs to be systematically field tested in different settings, across the world. This will be done by means of a number of experiments. In order to support its implementation, a web-based system (ICDfit) has been designed and developed. The present paper illustrates the current prototype of the system and its technical testing. the system has been designed according to WHO requirements, and implemented using PHP and MySQL. Then, a preliminary technical test has been designed and run in January 2016, involving 8 users. They had to carry out double coding, that is, coding case summaries with both ICD-10 and ICD-11, and answering quick questions on the coding difficulty. the 8 users coded 632 cases each, spending an average of 163 seconds per case. While we found an issue in the mechanism used to record coding times, no further issues were found. the proposed system seems to be technically adequate for supporting future ICD-11 testing.

Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

Efficient hemodynamic event detection utilizing relational databases and wavelet analysis

NASA Technical Reports Server (NTRS)

Saeed, M.; Mark, R. G.

2001-01-01

Development of a temporal query framework for time-oriented medical databases has hitherto been a challenging problem. We describe a novel method for the detection of hemodynamic events in multiparameter trends utilizing wavelet coefficients in a MySQL relational database. Storage of the wavelet coefficients allowed for a compact representation of the trends, and provided robust descriptors for the dynamics of the parameter time series. A data model was developed to allow for simplified queries along several dimensions and time scales. Of particular importance, the data model and wavelet framework allowed for queries to be processed with minimal table-join operations. A web-based search engine was developed to allow for user-defined queries. Typical queries required between 0.01 and 0.02 seconds, with at least two orders of magnitude improvement in speed over conventional queries. This powerful and innovative structure will facilitate research on large-scale time-oriented medical databases.

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

PubMed

Hallin, Peter F; Ussery, David W

2004-12-12

Currently, new bacterial genomes are being published on a monthly basis. With the growing amount of genome sequence data, there is a demand for a flexible and easy-to-maintain structure for storing sequence data and results from bioinformatic analysis. More than 150 sequenced bacterial genomes are now available, and comparisons of properties for taxonomically similar organisms are not readily available to many biologists. In addition to the most basic information, such as AT content, chromosome length, tRNA count and rRNA count, a large number of more complex calculations are needed to perform detailed comparative genomics. DNA structural calculations like curvature and stacking energy, DNA compositions like base skews, oligo skews and repeats at the local and global level are just a few of the analysis that are presented on the CBS Genome Atlas Web page. Complex analysis, changing methods and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues. A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/suppl/bioinfdatabase.

An Analysis Platform for Mobile Ad Hoc Network (MANET) Scenario Execution Log Data

DTIC Science & Technology

2016-01-01

these technologies. 4.1 Backend Technologies • Java 1.8 • my-sql-connector- java -5.0.8.jar • Tomcat • VirtualBox • Kali MANET Virtual Machine 4.2...Frontend Technologies • LAMPP 4.3 Database • MySQL Server 5. Database The SEDAP database settings and structure are described in this section...contains all the backend java functionality including the web services, should be placed in the webapps directory inside the Tomcat installation

Ensemble: a web-based system for psychology survey and experiment management.

PubMed

Tomic, Stefan T; Janata, Petr

2007-08-01

We provide a description of Ensemble, a suite of Web-integrated modules for managing and analyzing data associated with psychology experiments in a small research lab. The system delivers interfaces via a Web browser for creating and presenting simple surveys without the need to author Web pages and with little or no programming effort. The surveys may be extended by selecting and presenting auditory and/or visual stimuli with MATLAB and Flash to enable a wide range of psychophysical and cognitive experiments which do not require the recording of precise reaction times. Additionally, one is provided with the ability to administer and present experiments remotely. The software technologies employed by the various modules of Ensemble are MySQL, PHP, MATLAB, and Flash. The code for Ensemble is open source and available to the public, so that its functions can be readily extended by users. We describe the architecture of the system, the functionality of each module, and provide basic examples of the interfaces.

Improved Information Retrieval Performance on SQL Database Using Data Adapter

NASA Astrophysics Data System (ADS)

Husni, M.; Djanali, S.; Ciptaningtyas, H. T.; Wicaksana, I. G. N. A.

2018-02-01

The NoSQL databases, short for Not Only SQL, are increasingly being used as the number of big data applications increases. Most systems still use relational databases (RDBs), but as the number of data increases each year, the system handles big data with NoSQL databases to analyze and access data more quickly. NoSQL emerged as a result of the exponential growth of the internet and the development of web applications. The query syntax in the NoSQL database differs from the SQL database, therefore requiring code changes in the application. Data adapter allow applications to not change their SQL query syntax. Data adapters provide methods that can synchronize SQL databases with NotSQL databases. In addition, the data adapter provides an interface which is application can access to run SQL queries. Hence, this research applied data adapter system to synchronize data between MySQL database and Apache HBase using direct access query approach, where system allows application to accept query while synchronization process in progress. From the test performed using data adapter, the results obtained that the data adapter can synchronize between SQL databases, MySQL, and NoSQL database, Apache HBase. This system spends the percentage of memory resources in the range of 40% to 60%, and the percentage of processor moving from 10% to 90%. In addition, from this system also obtained the performance of database NoSQL better than SQL database.

OxfordGrid: a web interface for pairwise comparative map views.

PubMed

Yang, Hongyu; Gingle, Alan R

2005-12-01

OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

The Creative task Creator: a tool for the generation of customized, Web-based creativity tasks.

PubMed

Pretz, Jean E; Link, John A

2008-11-01

This article presents a Web-based tool for the creation of divergent-thinking and open-ended creativity tasks. A Java program generates HTML forms with PHP scripting that run an Alternate Uses Task and/or open-ended response items. Researchers may specify their own instructions, objects, and time limits, or use default settings. Participants can also be prompted to select their best responses to the Alternate Uses Task (Silvia et al., 2008). Minimal programming knowledge is required. The program runs on any server, and responses are recorded in a standard MySQL database. Responses can be scored using the consensual assessment technique (Amabile, 1996) or Torrance's (1998) traditional scoring method. Adoption of this Web-based tool should facilitate creativity research across cultures and access to eminent creators. The Creative Task Creator may be downloaded from the Psychonomic Society's Archive of Norms, Stimuli, and Data, www.psychonomic.org/archive.

ESTminer: a Web interface for mining EST contig and cluster databases.

PubMed

Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

2005-03-01

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

Barg, M. I.; Stobie, E. B.; Ferro, A. J.; O'Neil, E. J.

In the spring of 2000, at the request of the ADASS Program Organizing Committee (POC), we began organizing information from previous ADASS conferences in an effort to create a centralized database. The beginnings of this database originated from data (invited speakers, participants, papers, etc.) extracted from HyperText Markup Language (HTML) documents from past ADASS host sites. Unfortunately, not all HTML documents are well formed and parsing them proved to be an iterative process. It was evident at the beginning that if these Web documents were organized in a standardized way, such as XML (Extensible Markup Language), the processing of this information across the Web could be automated, more efficient, and less error prone. This paper will briefly review the many programming tools available for processing XML, including Java, Perl and Python, and will explore the mapping of relational data from our MySQL database to XML.

The Ensembl Web Site: Mechanics of a Genome Browser

PubMed Central

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V.

2004-01-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species. PMID:15123591

The Ensembl Web site: mechanics of a genome browser.

PubMed

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V

2004-05-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

New tools and methods for direct programmatic access to the dbSNP relational database.

PubMed

Saccone, Scott F; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A; Rice, John P

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

YODA++: A proposal for a semi-automatic space mission control

NASA Astrophysics Data System (ADS)

Casolino, M.; de Pascale, M. P.; Nagni, M.; Picozza, P.

YODA++ is a proposal for a semi-automated data handling and analysis system for the PAMELA space experiment. The core of the routines have been developed to process a stream of raw data downlinked from the Resurs DK1 satellite (housing PAMELA) to the ground station in Moscow. Raw data consist of scientific data and are complemented by housekeeping information. Housekeeping information will be analyzed within a short time from download (1 h) in order to monitor the status of the experiment and to foreseen the mission acquisition planning. A prototype for the data visualization will run on an APACHE TOMCAT web application server, providing an off-line analysis tool using a browser and part of code for the system maintenance. Data retrieving development is in production phase, while a GUI interface for human friendly monitoring is on preliminary phase as well as a JavaServerPages/JavaServerFaces (JSP/JSF) web application facility. On a longer timescale (1 3 h from download) scientific data are analyzed. The data storage core will be a mix of CERNs ROOT files structure and MySQL as a relational database. YODA++ is currently being used in the integration and testing on ground of PAMELA data.

Playing the Metadata Game: Technologies and Strategies Used by Climate Diagnostics Center for Cataloging and Distributing Climate Data.

NASA Astrophysics Data System (ADS)

Schweitzer, R. H.

2001-05-01

The Climate Diagnostics Center maintains a collection of gridded climate data primarily for use by local researchers. Because this data is available on fast digital storage and because it has been converted to netCDF using a standard metadata convention (called COARDS), we recognize that this data collection is also useful to the community at large. At CDC we try to use technology and metadata standards to reduce our costs associated with making these data available to the public. The World Wide Web has been an excellent technology platform for meeting that goal. Specifically we have developed Web-based user interfaces that allow users to search, plot and download subsets from the data collection. We have also been exploring use of the Pacific Marine Environment Laboratory's Live Access Server (LAS) as an engine for this task. This would result in further savings by allowing us to concentrate on customizing the LAS where needed, rather that developing and maintaining our own system. One such customization currently under development is the use of Java Servlets and JavaServer pages in conjunction with a metadata database to produce a hierarchical user interface to LAS. In addition to these Web-based user interfaces all of our data are available via the Distributed Oceanographic Data System (DODS). This allows other sites using LAS and individuals using DODS-enabled clients to use our data as if it were a local file. All of these technology systems are driven by metadata. When we began to create netCDF files, we collaborated with several other agencies to develop a netCDF convention (COARDS) for metadata. At CDC we have extended that convention to incorporate additional metadata elements to make the netCDF files as self-describing as possible. Part of the local metadata is a set of controlled names for the variable, level in the atmosphere and ocean, statistic and data set for each netCDF file. To allow searching and easy reorganization of these metadata, we loaded the metadata from the netCDF files into a mySQL database. The combination of the mySQL database and the controlled names makes it possible to automate the construction of user interfaces and standard format metadata descriptions, like Federal Geographic Data Committee (FGDC) and Directory Interchange Format (DIF). These standard descriptions also include an association between our controlled names and standard keywords such as those developed by the Global Change Master Directory (GCMD). This talk will give an overview of each of these technology and metadata standards as it applies to work at the Climate Diagnostics Center. The talk will also discuss the pros and cons of each approach and discuss areas for future development.

ExplorEnz: the primary source of the IUBMB enzyme list

PubMed Central

McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

2009-01-01

ExplorEnz is the MySQL database that is used for the curation and dissemination of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature. A simple web-based query interface is provided, along with an advanced search engine for more complex Boolean queries. The WWW front-end is accessible at http://www.enzyme-database.org, from where downloads of the database as SQL and XML are also available. An associated form-based curatorial application has been developed to facilitate the curation of enzyme data as well as the internal and public review processes that occur before an enzyme entry is made official. Suggestions for new enzyme entries, or modifications to existing ones, can be made using the forms provided at http://www.enzyme-database.org/forms.php. PMID:18776214

The CMS dataset bookkeeping service

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

Afaq, Anzar,; /Fermilab; Dolgert, Andrew

2007-10-01

The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires processing and analysis activities at various service levels and the DBS system provides support for localized processing or private analysis, as well as global access for CMS users at large. Catalog entries can be moved among the various service levels with a simple set of migration tools, thus forming a loose federation of databases. DBS ismore » available to CMS users via a Python API, Command Line, and a Discovery web page interfaces. The system is built as a multi-tier web application with Java servlets running under Tomcat, with connections via JDBC to Oracle or MySQL database backends. Clients connect to the service through HTTP or HTTPS with authentication provided by GRID certificates and authorization through VOMS. DBS is an integral part of the overall CMS Data Management and Workflow Management systems.« less

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.

Warehouses information system design and development

NASA Astrophysics Data System (ADS)

Darajatun, R. A.; Sukanta

2017-12-01

Materials/goods handling industry is fundamental for companies to ensure the smooth running of their warehouses. Efficiency and organization within every aspect of the business is essential in order to gain a competitive advantage. The purpose of this research is design and development of Kanban of inventory storage and delivery system. Application aims to facilitate inventory stock checks to be more efficient and effective. Users easily input finished goods from production department, warehouse, customer, and also suppliers. Master data designed as complete as possible to be prepared applications used in a variety of process logistic warehouse variations. The author uses Java programming language to develop the application, which is used for building Java Web applications, while the database used is MySQL. System development methodology that I use is the Waterfall methodology. Waterfall methodology has several stages of the Analysis, System Design, Implementation, Integration, Operation and Maintenance. In the process of collecting data the author uses the method of observation, interviews, and literature.

DHLAS: A web-based information system for statistical genetic analysis of HLA population data.

PubMed

Thriskos, P; Zintzaras, E; Germenis, A

2007-03-01

DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.

Tracking delays in report availability caused by incorrect exam status with Web-based issue tracking: a quality initiative.

PubMed

Awan, Omer Abdulrehman; van Wagenberg, Frans; Daly, Mark; Safdar, Nabile; Nagy, Paul

2011-04-01

Many radiology information systems (RIS) cannot accept a final report from a dictation reporting system before the exam has been completed in the RIS by a technologist. A radiologist can still render a report in a reporting system once images are available, but the RIS and ancillary systems may not get the results because of the study's uncompleted status. This delay in completing the study caused an alarming number of delayed reports and was undetected by conventional RIS reporting techniques. We developed a Web-based reporting tool to monitor uncompleted exams and automatically page section supervisors when a report was being delayed by its incomplete status in the RIS. Institutional Review Board exemption was obtained. At four imaging centers, a Python script was developed to poll the dictation system every 10 min for exams in five different modalities that were signed by the radiologist but could not be sent to the RIS. This script logged the exams into an existing Web-based tracking tool using PHP and a MySQL database. The script also text-paged the modality supervisor. The script logged the time at which the report was finally sent, and statistics were aggregated onto a separate Web-based reporting tool. Over a 1-year period, the average number of uncompleted exams per month and time to problem resolution decreased at every imaging center and in almost every imaging modality. Automated feedback provides a vital link in improving technologist performance and patient care without assigning a human resource to manage report queues.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

PubMed

Thibodeau, Asa; Márquez, Eladio J; Luo, Oscar; Ruan, Yijun; Menghi, Francesca; Shin, Dong-Guk; Stitzel, Michael L; Vera-Licona, Paola; Ucar, Duygu

2016-06-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

Developing an automated database for monitoring ultrasound- and computed tomography-guided procedure complications and diagnostic yield.

PubMed

Itri, Jason N; Jones, Lisa P; Kim, Woojin; Boonn, William W; Kolansky, Ana S; Hilton, Susan; Zafar, Hanna M

2014-04-01

Monitoring complications and diagnostic yield for image-guided procedures is an important component of maintaining high quality patient care promoted by professional societies in radiology and accreditation organizations such as the American College of Radiology (ACR) and Joint Commission. These outcome metrics can be used as part of a comprehensive quality assurance/quality improvement program to reduce variation in clinical practice, provide opportunities to engage in practice quality improvement, and contribute to developing national benchmarks and standards. The purpose of this article is to describe the development and successful implementation of an automated web-based software application to monitor procedural outcomes for US- and CT-guided procedures in an academic radiology department. The open source tools PHP: Hypertext Preprocessor (PHP) and MySQL were used to extract relevant procedural information from the Radiology Information System (RIS), auto-populate the procedure log database, and develop a user interface that generates real-time reports of complication rates and diagnostic yield by site and by operator. Utilizing structured radiology report templates resulted in significantly improved accuracy of information auto-populated from radiology reports, as well as greater compliance with manual data entry. An automated web-based procedure log database is an effective tool to reliably track complication rates and diagnostic yield for US- and CT-guided procedures performed in a radiology department.

Development, Technical, and User Evaluation of a Web Mobile Application for Self-Control of Diabetes.

PubMed

Garcia-Zapirain, Begoña; de la Torre Díez, Isabel; Sainz de Abajo, Beatriz; López-Coronado, Miguel

2016-09-01

The main objective of this research was to develop and evaluate a Web-based mobile application (app) known as "Diario Diabetes" on both a technical and user level, by means of which individuals with diabetes may monitor their illness easily at any time and in any place using any device that has Internet access. The technologies used to develop the app were HTML, CSS, JavaScript, PHP, and MySQL, all of which are an open source. Once the app was developed, it was evaluated on a technical level (by measuring loading times) and on a user level, through a survey. Different loading times for the application were measured, with it being noted that under no circumstances does this exceed 2 s. Usability was evaluated by 150 users who initially used the application. A majority (71%) of users used a PC to access the app, 83% considered the app's design to be attractive, 67% considered the tasks to be very useful, and 67% found it very easy to use. Although applications exist for controlling diabetes both at mobile virtual shops or on a research level, our app may help to improve the administration of these types of patients and they are the ones who will ultimately opt for one or the other. According to the results obtained, we can state that all users would recommend the app's use to other users.

FluDetWeb: an interactive web-based system for the early detection of the onset of influenza epidemics.

PubMed

Conesa, David; López-Quílez, Antonio; Martínez-Beneito, Miguel Angel; Miralles, María Teresa; Verdejo, Francisco

2009-07-29

The early identification of influenza outbreaks has became a priority in public health practice. A large variety of statistical algorithms for the automated monitoring of influenza surveillance have been proposed, but most of them require not only a lot of computational effort but also operation of sometimes not-so-friendly software. In this paper, we introduce FluDetWeb, an implementation of a prospective influenza surveillance methodology based on a client-server architecture with a thin (web-based) client application design. Users can introduce and edit their own data consisting of a series of weekly influenza incidence rates. The system returns the probability of being in an epidemic phase (via e-mail if desired). When the probability is greater than 0.5, it also returns the probability of an increase in the incidence rate during the following week. The system also provides two complementary graphs. This system has been implemented using statistical free-software (R and WinBUGS), a web server environment for Java code (Tomcat) and a software module created by us (Rdp) responsible for managing internal tasks; the software package MySQL has been used to construct the database management system. The implementation is available on-line from: http://www.geeitema.org/meviepi/fludetweb/. The ease of use of FluDetWeb and its on-line availability can make it a valuable tool for public health practitioners who want to obtain information about the probability that their system is in an epidemic phase. Moreover, the architecture described can also be useful for developers of systems based on computationally intensive methods.

FluDetWeb: an interactive web-based system for the early detection of the onset of influenza epidemics

PubMed Central

2009-01-01

Background The early identification of influenza outbreaks has became a priority in public health practice. A large variety of statistical algorithms for the automated monitoring of influenza surveillance have been proposed, but most of them require not only a lot of computational effort but also operation of sometimes not-so-friendly software. Results In this paper, we introduce FluDetWeb, an implementation of a prospective influenza surveillance methodology based on a client-server architecture with a thin (web-based) client application design. Users can introduce and edit their own data consisting of a series of weekly influenza incidence rates. The system returns the probability of being in an epidemic phase (via e-mail if desired). When the probability is greater than 0.5, it also returns the probability of an increase in the incidence rate during the following week. The system also provides two complementary graphs. This system has been implemented using statistical free-software (ℝ and WinBUGS), a web server environment for Java code (Tomcat) and a software module created by us (Rdp) responsible for managing internal tasks; the software package MySQL has been used to construct the database management system. The implementation is available on-line from: http://www.geeitema.org/meviepi/fludetweb/. Conclusion The ease of use of FluDetWeb and its on-line availability can make it a valuable tool for public health practitioners who want to obtain information about the probability that their system is in an epidemic phase. Moreover, the architecture described can also be useful for developers of systems based on computationally intensive methods. PMID:19640304

Content Documents Management

NASA Technical Reports Server (NTRS)

Muniz, R.; Hochstadt, J.; Boelke J.; Dalton, A.

2011-01-01

The Content Documents are created and managed under the System Software group with. Launch Control System (LCS) project. The System Software product group is lead by NASA Engineering Control and Data Systems branch (NEC3) at Kennedy Space Center. The team is working on creating Operating System Images (OSI) for different platforms (i.e. AIX, Linux, Solaris and Windows). Before the OSI can be created, the team must create a Content Document which provides the information of a workstation or server, with the list of all the software that is to be installed on it and also the set where the hardware belongs. This can be for example in the LDS, the ADS or the FR-l. The objective of this project is to create a User Interface Web application that can manage the information of the Content Documents, with all the correct validations and filters for administrator purposes. For this project we used one of the most excellent tools in agile development applications called Ruby on Rails. This tool helps pragmatic programmers develop Web applications with Rails framework and Ruby programming language. It is very amazing to see how a student can learn about OOP features with the Ruby language, manage the user interface with HTML and CSS, create associations and queries with gems, manage databases and run a server with MYSQL, run shell commands with command prompt and create Web frameworks with Rails. All of this in a real world project and in just fifteen weeks!

SU-E-T-220: A Web-Based Research System for Outcome Analysis of NSCLC Treated with SABR.

PubMed

Le, A; Yang, Y; Michalski, D; Heron, D; Huq, M

2012-06-01

To establish a web-based software system, an electronic patient record (ePR), to consolidate and evaluate clinical data, dose delivery and treatment outcomes for non small cell lung cancer (NSCLC) patients treated with hypofractionated stereotactic ablative radiation therapy (SABR) across institutions. The new trend of information technology in medical imaging and informatics is towards the development of an electronic patient record (ePR), in which all health and medical information of each patient are organized under the patient's name and identification number. The system has been developed using the Wamp Server, a package of Apache web server, PHP and MySQL database to facilitate patient data input and management, and evaluation of patient clinical data and dose delivery across institution using web technology. The data of each patient to be recorded in the database include pre-treatment clinical data, treatment plan in DICOM-RT format and follow-up data. The pre-treatment data include demographics data, pathology condition, cancer staging. The follow-up data include the survival status, local tumor control condition and toxicity. The clinical data are entered to the system through the web page while the treatment plan data will be imported from the treatment planning system (TPS) using DICOM communication. The collection of data of NSCLC patients treated with SABR stored in the ePR is always accessible and can be retrieved and processed in the future. The core of the ePR is the database which integrates all patient data in one location. The web-based DICOM RT ePR system utilizes the current state-of-the-art medical informatics approach to investigate the combination and consolidation of patient data and outcome results. This will allow clinically-driven data mining for dose distributions and resulting treatment outcome in connection with biological modeling of the treatment parameters to quantify the efficacy of SABR in treating NSCLC patients. © 2012 American Association of Physicists in Medicine.

Information Flow Integrity for Systems of Independently-Developed Components

DTIC Science & Technology

2015-06-22

We also examined three programs (Apache, MySQL , and PHP) in detail to evaluate the efficacy of using the provided package test suites to generate...method are just as effective as hooks that were manually placed over the course of years while greatly reducing the burden on programmers. ”Leveraging...to validate optimizations of real-world, mature applications: the Apache software suite, the Mozilla Suite, and the MySQL database. ”Validating Library

The Shared Decision Making Frontier: a Feasibility and Usability Study for Managing Non-Critical Chronic Illness by Combining Behavioural & Decision Theory with Online Technology.

PubMed

Russell, Amina; Van Woensel, William; Abidi, Samina Raza

2015-01-01

The objective of this study is to determine if shared decisions for managing non-critical chronic illness, made through an online biomedical technology intervention, us feasible and usable. The technology intervention incorporates behavioural and decision theories to increase patient engagement, and ultimately long term adherence to health behaviour change. We devised the iheart web intervention as a "proof of concept" in five phases. The implementation incorporates the Vaadin web application framework, Drools, EclipseLink and a MySQL database. Two-thirds of the study participants favoured the technology intervention, based on Likert-scale questions from a post-study questionnaire. Qualitative analysis of think aloud feedback, video screen captures and open-ended questions from the post-study questionnaire uncovered six main areas or themes for improvement. We conclude that online shared decisions for managing a non-critical chronic illness are feasible and usable through the iheart web intervention.

FLEX: A Modular Software Architecture for Flight License Exam

NASA Astrophysics Data System (ADS)

Arsan, Taner; Saka, Hamit Emre; Sahin, Ceyhun

This paper is about the design and implementation of an examination system based on World Wide Web. It is called FLEX-Flight License Exam Software. We designed and implemented flexible and modular software architecture. The implemented system has basic specifications such as appending questions in system, building exams with these appended questions and making students to take these exams. There are three different types of users with different authorizations. These are system administrator, operators and students. System administrator operates and maintains the system, and also audits the system integrity. The system administrator can not be able to change the result of exams and can not take an exam. Operator module includes instructors. Operators have some privileges such as preparing exams, entering questions, changing the existing questions and etc. Students can log on the system and can be accessed to exams by a certain URL. The other characteristic of our system is that operators and system administrator are not able to delete questions due to the security problems. Exam questions can be inserted on their topics and lectures in the database. Thus; operators and system administrator can easily choose questions. When all these are taken into consideration, FLEX software provides opportunities to many students to take exams at the same time in safe, reliable and user friendly conditions. It is also reliable examination system for the authorized aviation administration companies. Web development platform - LAMP; Linux, Apache web server, MySQL, Object-oriented scripting Language - PHP are used for developing the system and page structures are developed by Content Management System - CMS.

New tools and methods for direct programmatic access to the dbSNP relational database

PubMed Central

Saccone, Scott F.; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A.; Rice, John P.

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale. PMID:21037260

Development of Human Face Literature Database Using Text Mining Approach: Phase I.

PubMed

Kaur, Paramjit; Krishan, Kewal; Sharma, Suresh K

2018-06-01

The face is an important part of the human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. The amount of experiments being performed and the number of research papers being published under the domain of human face have surged in the past few decades. Several scientific disciplines, which are conducting research on human face include: Medical Science, Anthropology, Information Technology (Biometrics, Robotics, and Artificial Intelligence, etc.), Psychology, Forensic Science, Neuroscience, etc. This alarms the need of collecting and managing the data concerning human face so that the public and free access of it can be provided to the scientific community. This can be attained by developing databases and tools on human face using bioinformatics approach. The current research emphasizes on creating a database concerning literature data of human face. The database can be accessed on the basis of specific keywords, journal name, date of publication, author's name, etc. The collected research papers will be stored in the form of a database. Hence, the database will be beneficial to the research community as the comprehensive information dedicated to the human face could be found at one place. The information related to facial morphologic features, facial disorders, facial asymmetry, facial abnormalities, and many other parameters can be extracted from this database. The front end has been developed using Hyper Text Mark-up Language and Cascading Style Sheets. The back end has been developed using hypertext preprocessor (PHP). The JAVA Script has used as scripting language. MySQL (Structured Query Language) is used for database development as it is most widely used Relational Database Management System. XAMPP (X (cross platform), Apache, MySQL, PHP, Perl) open source web application software has been used as the server.The database is still under the developmental phase and discusses the initial steps of its creation. The current paper throws light on the work done till date.

Blind Seer: A Scalable Private DBMS

DTIC Science & Technology

2014-05-01

searchable index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower...than MySQL , although some queries are costlier). We support a rich query set, including searching on arbitrary boolean formulas on keywords and ranges...index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower than MySQL

A Quality-Control-Oriented Database for a Mesoscale Meteorological Observation Network

NASA Astrophysics Data System (ADS)

Lussana, C.; Ranci, M.; Uboldi, F.

2012-04-01

In the operational context of a local weather service, data accessibility and quality related issues must be managed by taking into account a wide set of user needs. This work describes the structure and the operational choices made for the operational implementation of a database system storing data from highly automated observing stations, metadata and information on data quality. Lombardy's environmental protection agency, ARPA Lombardia, manages a highly automated mesoscale meteorological network. A Quality Assurance System (QAS) ensures that reliable observational information is collected and disseminated to the users. The weather unit in ARPA Lombardia, at the same time an important QAS component and an intensive data user, has developed a database specifically aimed to: 1) providing quick access to data for operational activities and 2) ensuring data quality for real-time applications, by means of an Automatic Data Quality Control (ADQC) procedure. Quantities stored in the archive include hourly aggregated observations of: precipitation amount, temperature, wind, relative humidity, pressure, global and net solar radiation. The ADQC performs several independent tests on raw data and compares their results in a decision-making procedure. An important ADQC component is the Spatial Consistency Test based on Optimal Interpolation. Interpolated and Cross-Validation analysis values are also stored in the database, providing further information to human operators and useful estimates in case of missing data. The technical solution adopted is based on a LAMP (Linux, Apache, MySQL and Php) system, constituting an open source environment suitable for both development and operational practice. The ADQC procedure itself is performed by R scripts directly interacting with the MySQL database. Users and network managers can access the database by using a set of web-based Php applications.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

PubMed Central

Thibodeau, Asa; Márquez, Eladio J.; Luo, Oscar; Ruan, Yijun; Shin, Dong-Guk; Stitzel, Michael L.; Ucar, Duygu

2016-01-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/. PMID:27336171

The database design of LAMOST based on MYSQL/LINUX

NASA Astrophysics Data System (ADS)

Li, Hui-Xian, Sang, Jian; Wang, Sha; Luo, A.-Li

2006-03-01

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) will be set up in the coming years. A fully automated software system for reducing and analyzing the spectra has to be developed with the telescope. This database system is an important part of the software system. The requirements for the database of the LAMOST, the design of the LAMOST database system based on MYSQL/LINUX and performance tests of this system are described in this paper.

Recent advancements on the development of web-based applications for the implementation of seismic analysis and surveillance systems

NASA Astrophysics Data System (ADS)

Friberg, P. A.; Luis, R. S.; Quintiliani, M.; Lisowski, S.; Hunter, S.

2014-12-01

Recently, a novel set of modules has been included in the Open Source Earthworm seismic data processing system, supporting the use of web applications. These include the Mole sub-system, for storing relevant event data in a MySQL database (see M. Quintiliani and S. Pintore, SRL, 2013), and an embedded webserver, Moleserv, for serving such data to web clients in QuakeML format. These modules have enabled, for the first time using Earthworm, the use of web applications for seismic data processing. These can greatly simplify the operation and maintenance of seismic data processing centers by having one or more servers providing the relevant data as well as the data processing applications themselves to client machines running arbitrary operating systems.Web applications with secure online web access allow operators to work anywhere, without the often cumbersome and bandwidth hungry use of secure shell or virtual private networks. Furthermore, web applications can seamlessly access third party data repositories to acquire additional information, such as maps. Finally, the usage of HTML email brought the possibility of specialized web applications, to be used in email clients. This is the case of EWHTMLEmail, which produces event notification emails that are in fact simple web applications for plotting relevant seismic data.Providing web services as part of Earthworm has enabled a number of other tools as well. One is ISTI's EZ Earthworm, a web based command and control system for an otherwise command line driven system; another is a waveform web service. The waveform web service serves Earthworm data to additional web clients for plotting, picking, and other web-based processing tools. The current Earthworm waveform web service hosts an advanced plotting capability for providing views of event-based waveforms from a Mole database served by Moleserve.The current trend towards the usage of cloud services supported by web applications is driving improvements in JavaScript, css and HTML, as well as faster and more efficient web browsers, including mobile. It is foreseeable that in the near future, web applications are as powerful and efficient as native applications. Hence the work described here has been the first step towards bringing the Open Source Earthworm seismic data processing system to this new paradigm.

ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

PubMed

Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

2017-01-01

Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of Graph Database for the Integration of Heterogeneous Biological Data.

PubMed

Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

2017-03-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

Use of Graph Database for the Integration of Heterogeneous Biological Data

PubMed Central

Yoon, Byoung-Ha; Kim, Seon-Kyu

2017-01-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data. PMID:28416946

SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

PubMed

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R.

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

PubMed Central

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G.; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. PMID:24066126

Phynx: an open source software solution supporting data management and web-based patient-level data review for drug safety studies in the general practice research database and other health care databases.

PubMed

Egbring, Marco; Kullak-Ublick, Gerd A; Russmann, Stefan

2010-01-01

To develop a software solution that supports management and clinical review of patient data from electronic medical records databases or claims databases for pharmacoepidemiological drug safety studies. We used open source software to build a data management system and an internet application with a Flex client on a Java application server with a MySQL database backend. The application is hosted on Amazon Elastic Compute Cloud. This solution named Phynx supports data management, Web-based display of electronic patient information, and interactive review of patient-level information in the individual clinical context. This system was applied to a dataset from the UK General Practice Research Database (GPRD). Our solution can be setup and customized with limited programming resources, and there is almost no extra cost for software. Access times are short, the displayed information is structured in chronological order and visually attractive, and selected information such as drug exposure can be blinded. External experts can review patient profiles and save evaluations and comments via a common Web browser. Phynx provides a flexible and economical solution for patient-level review of electronic medical information from databases considering the individual clinical context. It can therefore make an important contribution to an efficient validation of outcome assessment in drug safety database studies.

EpiHosp: A web-based visualization tool enabling the exploratory analysis of complications of implantable medical devices from a nationwide hospital database.

PubMed

Ficheur, Grégoire; Ferreira Careira, Lionel; Beuscart, Régis; Chazard, Emmanuel

2015-01-01

Administrative data can be used for the surveillance of the outcomes of implantable medical devices (IMDs). The objective of this work is to build a web-based tool allowing for an exploratory analysis of time-dependent events that may occur after the implementation of an IMD. This tool should enable a pharmacoepidemiologist to explore on the fly the relationship between a given IMD and a potential outcome. This tool mine the French nationwide database of inpatient stays from 2008 to 2013. The data are preprocessed in order to optimize the queries. A web tool is developed in PHP, MySQL and Javascript. The user selects one or a group of IMD from a tree, and can filter the results using years and hospital names. Four result pages describe the selected inpatient stays: (1) temporal and demographic description, (2) a description of the geographical location of the hospital, (3) a description of the geographical place of residence of the patient and (4) a table showing the rehospitalization reasons by decreasing order of frequency. Then, the user can select one readmission reason and display dynamically the probability of readmission by mean of a Kaplan-Meier curve with confidence intervals. This tool enables to dynamically monitor the occurrence of time-dependent complications of IMD.

Research and design on system of asset management based on RFID

NASA Astrophysics Data System (ADS)

Guan, Peng; Du, HuaiChang; Jing, Hua; Zhang, MengYue; Zhang, Meng; Xu, GuiXian

2011-10-01

By analyzing the problems in the current assets management, this thesis proposing RFID technology will be applied to asset management in order to improve the management level of automation and information. This paper designed the equipment identification based on 433MHz RFID tag and reader which was deeply studied on the basis of RFID tag and card reader circuits, and this paper also illustrates the system of asset management. The RS232 converts Ethernet is a innovative technology to transfer data to PC monitor software, and implement system of asset management based on WEB techniques (PHP and MySQL).

Implementation of electronic logbook for trainees of general surgery in Thailand.

PubMed

Aphinives, Potchavit

2013-01-01

All trainees are required to keep a record of their surgical skill and experiences throughout the trainingperiod in a logbook format. Paper-based logbook has several limitations. Therefore, an electronic logbook was introduced to replace the paper-based logbook. An electronic logbook program was developed in November 2005. This program was designed as web-based application based upon PHP scripts beneath Apache web server and MySQL database implementation. Only simpliJfied and essential data, such as hospital number diagnosis, surgical procedure, and pathological findings, etc. are recorded. The electronic logbook databases between Academic year 2006 and 2011 were analyzed. The annual recordedsurgical procedures gradually increasedfrom 41,214 procedures in 2006 to 66,643 procedures in 2011. Around one-third of all records were not verified by attending staffs, i.e. 27.59% (2006), 31.69% (2007), 18.06% (2008), 28.42% (2009), 30.18% (2010), and 31.41% (2011). On the Education year 2011, the three most common procedural groups included colon, rectum & anus group, appendix group, and vascular group, respectively. Advantages of the electronic logbook included more efficient data access, increased ability to monitor trainees and trainers, and analysis of procedural varieties among the training institutes.

LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach.

PubMed

Fokkema, Ivo F A C; den Dunnen, Johan T; Taschner, Peter E M

2005-08-01

The completion of the human genome project has initiated, as well as provided the basis for, the collection and study of all sequence variation between individuals. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). We have developed the Leiden Open (source) Variation Database (LOVD) software approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of DNA sequence variations. With minimal effort, the LOVD platform is extendable with clinical data. The open set-up should both facilitate and promote functional extension with scripts written by the community. The LOVD software is freely available from the Leiden Muscular Dystrophy pages (www.DMD.nl/LOVD/). To promote the use of LOVD, we currently offer curators the possibility to set up an LSDB on our Leiden server. (c) 2005 Wiley-Liss, Inc.

Development of smartphone application that aids stroke screening and identifying nearby acute stroke care hospitals.

PubMed

Nam, Hyo Suk; Heo, JoonNyung; Kim, Jinkwon; Kim, Young Dae; Song, Tae Jin; Park, Eunjeong; Heo, Ji Hoe

2014-01-01

The benefits of thrombolytic treatment are time-dependent. We developed a smartphone application that aids stroke patient self-screening and hospital selection, and may also decrease hospital arrival time. The application was developed for iPhone and Android smartphones. Map data for the application were adopted from the open map. For hospital registration, a web page (http://stroke119.org) was developed using PHP and MySQL. The Stroke 119 application includes a stroke screening tool and real-time information on nearby hospitals that provide thrombolytic treatment. It also provides information on stroke symptoms, thrombolytic treatment, and prescribed actions when stroke is suspected. The stroke screening tool was adopted from the Cincinnati Prehospital Stroke Scale and is displayed in a cartoon format. If the user taps a cartoon image that represents abnormal findings, a pop-up window shows that the user may be having a stroke, informs the user what to do, and directs the user to call emergency services. Information on nearby hospitals is provided in map and list views, incorporating proximity to the user's location using a Global Positioning System (a built-in function of smartphones). Users can search for a hospital according to specialty and treatment levels. We also developed a web page for hospitals to register in the system. Neurology training hospitals and hospitals that provide acute stroke care in Korea were invited to register. Seventy-seven hospitals had completed registration. This application may be useful for reducing hospital arrival times for thrombolytic candidates.

Data base management system for lymphatic filariasis--a neglected tropical disease.

PubMed

Upadhyayula, Suryanaryana Murty; Mutheneni, Srinivasa Rao; Kadiri, Madhusudhan Rao; Kumaraswamy, Sriram; Nelaturu, Sarat Chandra Babu

2012-01-01

Researchers working in the area of Public Health are being confronted with large volumes of data on various aspects of entomology and epidemiology. To obtain the relevant information out of these data requires particular database management system. In this paper, we have described about the usages of our developed database on lymphatic filariasis. This database application is developed using Model View Controller (MVC) architecture, with MySQL as database and a web based interface. We have collected and incorporated the data on filariasis in the database from Karimnagar, Chittoor, East and West Godavari districts of Andhra Pradesh, India. The importance of this database is to store the collected data, retrieve the information and produce various combinational reports on filarial aspects which in turn will help the public health officials to understand the burden of disease in a particular locality. This information is likely to have an imperative role on decision making for effective control of filarial disease and integrated vector management operations.

The database of the Nikolaev Astronomical Observatory as a unit of an international virtual observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Yu.; Pinigin, G.; Shulga, A.

2005-06-01

Results of the development and organization of the digital database of the Nikolaev Astronomical Observatory (NAO) are presented. At present, three telescopes are connected to the local area network of NAO. All the data obtained, and results of data processing are entered into the common database of NAO. The daily average volume of new astronomical information obtained from the CCD instruments ranges from 300 MB up to 2 GB, depending on the purposes and conditions of observations. The overwhelming majority of the data are stored in the FITS format. Development and further improvement of storage standards, procedures of data handling and data processing are being carried out. It is planned to create an astronomical web portal with the possibility to have interactive access to databases and telescopes. In the future, this resource may become a part of an international virtual observatory. There are the prototypes of search tools with the use of PHP and MySQL. Efforts for getting more links to the Internet are being made.

BGDB: a database of bivalent genes.

PubMed

Li, Qingyan; Lian, Shuabin; Dai, Zhiming; Xiang, Qian; Dai, Xianhua

2013-01-01

Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/

BEARS: a multi-mission anomaly response system

NASA Astrophysics Data System (ADS)

Roberts, Bryce A.

2009-05-01

The Mission Operations Group at UC Berkeley's Space Sciences Laboratory operates a highly automated ground station and presently a fleet of seven satellites, each with its own associated command and control console. However, the requirement for prompt anomaly detection and resolution is shared commonly between the ground segment and all spacecraft. The efficient, low-cost operation and "lights-out" staffing of the Mission Operations Group requires that controllers and engineers be notified of spacecraft and ground system problems around the clock. The Berkeley Emergency Anomaly and Response System (BEARS) is an in-house developed web- and paging-based software system that meets this need. BEARS was developed as a replacement for an existing emergency reporting software system that was too closedsource, platform-specific, expensive, and antiquated to expand or maintain. To avoid these limitations, the new system design leverages cross-platform, open-source software products such as MySQL, PHP, and Qt. Anomaly notifications and responses make use of the two-way paging capabilities of modern smart phones.

A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE

PubMed Central

Jayakodi, Murukarthick; selvan, Sreedevi Ghokhilamani; Natesan, Senthil; Muthurajan, Raveendran; Duraisamy, Raghu; Ramineni, Jana Jeevan; Rathinasamy, Sakthi Ambothi; Karuppusamy, Nageswari; Lakshmanan, Pugalenthi; Chokkappan, Mohan

2011-01-01

The goal of our research is to establish a unique portal to bring out the potential outcome of the research in the Casssava crop. The Biogen base for cassava clearly brings out the variations of different traits of the germplasms, maintained at the Tapioca and Castor Research Station, Tamil Nadu Agricultural University. Phenotypic and genotypic variations of the accessions are clearly depicted, for the users to browse and interpret the variations using the microsatellite markers. Database (BIOGEN BASE ‐ CASSAVA) is designed using PHP and MySQL and is equipped with extensive search options. It is more user-friendly and made publicly available, to improve the research and development of cassava by making a wealth of genetics and genomics data available through open, common, and worldwide forum for all individuals interested in the field. Availability The database is available for free at http://www.tnaugenomics.com/biogenbase/casava.php PMID:21904428

A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE.

PubMed

Jayakodi, Murukarthick; Selvan, Sreedevi Ghokhilamani; Natesan, Senthil; Muthurajan, Raveendran; Duraisamy, Raghu; Ramineni, Jana Jeevan; Rathinasamy, Sakthi Ambothi; Karuppusamy, Nageswari; Lakshmanan, Pugalenthi; Chokkappan, Mohan

2011-01-01

The goal of our research is to establish a unique portal to bring out the potential outcome of the research in the Casssava crop. The Biogen base for cassava clearly brings out the variations of different traits of the germplasms, maintained at the Tapioca and Castor Research Station, Tamil Nadu Agricultural University. Phenotypic and genotypic variations of the accessions are clearly depicted, for the users to browse and interpret the variations using the microsatellite markers. Database (BIOGEN BASE - CASSAVA) is designed using PHP and MySQL and is equipped with extensive search options. It is more user-friendly and made publicly available, to improve the research and development of cassava by making a wealth of genetics and genomics data available through open, common, and worldwide forum for all individuals interested in the field. The database is available for free at http://www.tnaugenomics.com/biogenbase/casava.php.

De-MA: a web Database for electron Microprobe Analyses to assist EMP lab manager and users

NASA Astrophysics Data System (ADS)

Allaz, J. M.

2012-12-01

Lab managers and users of electron microprobe (EMP) facilities require comprehensive, yet flexible documentation structures, as well as an efficient scheduling mechanism. A single on-line database system for managing reservations, and providing information on standards, quantitative and qualitative setups (element mapping, etc.), and X-ray data has been developed for this purpose. This system is particularly useful in multi-user facilities where experience ranges from beginners to the highly experienced. New users and occasional facility users will find these tools extremely useful in developing and maintaining high quality, reproducible, and efficient analyses. This user-friendly database is available through the web, and uses MySQL as a database and PHP/HTML as script language (dynamic website). The database includes several tables for standards information, X-ray lines, X-ray element mapping, PHA, element setups, and agenda. It is configurable for up to five different EMPs in a single lab, each of them having up to five spectrometers and as many diffraction crystals as required. The installation should be done on a web server supporting PHP/MySQL, although installation on a personal computer is possible using third-party freeware to create a local Apache server, and to enable PHP/MySQL. Since it is web-based, any user outside the EMP lab can access this database anytime through any web browser and on any operating system. The access can be secured using a general password protection (e.g. htaccess). The web interface consists of 6 main menus. (1) "Standards" lists standards defined in the database, and displays detailed information on each (e.g. material type, name, reference, comments, and analyses). Images such as EDS spectra or BSE can be associated with a standard. (2) "Analyses" lists typical setups to use for quantitative analyses, allows calculation of mineral composition based on a mineral formula, or calculation of mineral formula based on a fixed amount of oxygen, or of cation (using an analysis in element or oxide weight-%); this latter includes re-calculation of H2O/CO2 based on stoichiometry, and oxygen correction for F and Cl. Another option offers a list of any available standards and possible peak or background interferences for a series of elements. (3) "X-ray maps" lists the different setups recommended for element mapping using WDS, and a map calculator to facilitate maps setups and to estimate the total mapping time. (4) "X-ray data" lists all x-ray lines for a specific element (K, L, M, absorption edges, and satellite peaks) in term of energy, wavelength and peak position. A check for possible interferences on peak or background is also possible. Theoretical x-ray peak positions for each crystal are calculated based on the 2d spacing of each crystal and the wavelength of each line. (5) "Agenda" menu displays the reservation dates for each month and for each EMP lab defined. It also offers a reservation request option, this request being sent by email to the EMP manager for approval. (6) Finally, "Admin" is password restricted, and contains all necessary options to manage the database through user-friendly forms. The installation of this database is made easy and knowledge of HTML, PHP, or MySQL is unnecessary to install, configure, manage, or use it. A working database is accessible at http://cub.geoloweb.ch.

Urgent Virtual Machine Eviction with Enlightened Post-Copy

DTIC Science & Technology

2015-12-01

memory is in use, almost all of which is by Memcached. MySQL : The VMs run MySQL 5.6, and the clients execute OLTPBenchmark [3] using the Twitter...workload with scale factor of 960. The VMs are each allocated 16 cores and 30 GB of memory, and MySQL is configured with a 16 GB buffer pool in memory. The...operation mix for 5 minutes as a warm-up. At the time of migration, MySQL uses approximately 17 GB of memory, and almost all of the 30 GB memory is

UCbase 2.0: ultraconserved sequences database (2014 update)

PubMed Central

Lomonaco, Vincenzo; Martoglia, Riccardo; Mandreoli, Federica; Anderlucci, Laura; Emmett, Warren; Bicciato, Silvio; Taccioli, Cristian

2014-01-01

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it PMID:24951797

Automated ocean color product validation for the Southern California Bight

NASA Astrophysics Data System (ADS)

Davis, Curtiss O.; Tufillaro, Nicholas; Jones, Burt; Arnone, Robert

2012-06-01

Automated match ups allow us to maintain and improve the products of current satellite ocean color sensors (MODIS, MERIS), and new sensors (VIIRS). As part of the VIIRS mission preparation, we have created a web based automated match up tool that provides access to searchable fields for date, site, and products, and creates match-ups between satellite (MODIS, MERIS, VIIRS), and in-situ measurements (HyperPRO and SeaPRISM). The back end of the system is a 'mySQL' database, and the front end is a `php' web portal with pull down menus for searchable fields. Based on selections, graphics are generated showing match-ups and statistics, and ascii files are created for downloads for the matchup data. Examples are shown for matching the satellite data with the data from Platform Eureka SeaPRISM off L.A. Harbor in the Southern California Bight.

A user-friendly, dynamic web environment for remote data browsing and analysis of multiparametric geophysical data within the MULTIMO project

NASA Astrophysics Data System (ADS)

Carniel, Roberto; Di Cecca, Mauro; Jaquet, Olivier

2006-05-01

In the framework of the EU-funded project "Multi-disciplinary monitoring, modelling and forecasting of volcanic hazard" (MULTIMO), multiparametric data have been recorded at the MULTIMO station in Montserrat. Moreover, several other long time series, recorded at Montserrat and at other volcanoes, have been acquired in order to test stochastic and deterministic methodologies under development. Creating a general framework to handle data efficiently is a considerable task even for homogeneous data. In the case of heterogeneous data, this becomes a major issue. A need for a consistent way of browsing such a heterogeneous dataset in a user-friendly way therefore arose. Additionally, a framework for applying the calculation of the developed dynamical parameters on the data series was also needed in order to easily keep these parameters under control, e.g. for monitoring, research or forecasting purposes. The solution which we present is completely based on Open Source software, including Linux operating system, MySql database management system, Apache web server, Zope application server, Scilab math engine, Plone content management framework, Unified Modelling Language. From the user point of view the main advantage is the possibility of browsing through datasets recorded on different volcanoes, with different instruments, with different sampling frequencies, stored in different formats, all via a consistent, user- friendly interface that transparently runs queries to the database, gets the data from the main storage units, generates the graphs and produces dynamically generated web pages to interact with the user. The involvement of third parties for continuing the development in the Open Source philosophy and/or extending the application fields is now sought.

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.

Development of a data mining and imaging informatics display tool for a multiple sclerosis e-folder system

NASA Astrophysics Data System (ADS)

Liu, Margaret; Loo, Jerry; Ma, Kevin; Liu, Brent

2011-03-01

Multiple sclerosis (MS) is a debilitating autoimmune disease of the central nervous system that damages axonal pathways through inflammation and demyelination. In order to address the need for a centralized application to manage and study MS patients, the MS e-Folder - a web-based, disease-specific electronic medical record system - was developed. The e-Folder has a PHP and MySQL based graphical user interface (GUI) that can serve as both a tool for clinician decision support and a data mining tool for researchers. This web-based GUI gives the e-Folder a user friendly interface that can be securely accessed through the internet and requires minimal software installation on the client side. The e-Folder GUI displays and queries patient medical records--including demographic data, social history, past medical history, and past MS history. In addition, DICOM format imaging data, and computer aided detection (CAD) results from a lesion load algorithm are also displayed. The GUI interface is dynamic and allows manipulation of the DICOM images, such as zoom, pan, and scrolling, and the ability to rotate 3D images. Given the complexity of clinical management and the need to bolster research in MS, the MS e-Folder system will improve patient care and provide MS researchers with a function-rich patient data hub.

KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain

PubMed Central

2013-01-01

Background Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there are so many diverse methods and methodologies available, that for biomedical researchers who are inexperienced in the use of even relatively popular knowledge discovery methods, it can be very difficult to select the most appropriate method for their particular research problem. Results A web application, called KNODWAT (KNOwledge Discovery With Advanced Techniques) has been developed, using Java on Spring framework 3.1. and following a user-centered approach. The software runs on Java 1.6 and above and requires a web server such as Apache Tomcat and a database server such as the MySQL Server. For frontend functionality and styling, Twitter Bootstrap was used as well as jQuery for interactive user interface operations. Conclusions The framework presented is user-centric, highly extensible and flexible. Since it enables methods for testing using existing data to assess suitability and performance, it is especially suitable for inexperienced biomedical researchers, new to the field of knowledge discovery and data mining. For testing purposes two algorithms, CART and C4.5 were implemented using the WEKA data mining framework. PMID:23763826

KNODWAT: a scientific framework application for testing knowledge discovery methods for the biomedical domain.

PubMed

Holzinger, Andreas; Zupan, Mario

2013-06-13

Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there are so many diverse methods and methodologies available, that for biomedical researchers who are inexperienced in the use of even relatively popular knowledge discovery methods, it can be very difficult to select the most appropriate method for their particular research problem. A web application, called KNODWAT (KNOwledge Discovery With Advanced Techniques) has been developed, using Java on Spring framework 3.1. and following a user-centered approach. The software runs on Java 1.6 and above and requires a web server such as Apache Tomcat and a database server such as the MySQL Server. For frontend functionality and styling, Twitter Bootstrap was used as well as jQuery for interactive user interface operations. The framework presented is user-centric, highly extensible and flexible. Since it enables methods for testing using existing data to assess suitability and performance, it is especially suitable for inexperienced biomedical researchers, new to the field of knowledge discovery and data mining. For testing purposes two algorithms, CART and C4.5 were implemented using the WEKA data mining framework.

BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems.

PubMed

Barbosa, Luiz Carlos Bertucci; Garrido, Saulo Santesso; Marchetto, Reinaldo

2015-03-01

Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems. The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems. The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available. The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uft.edu.br/btoxdb. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of an open source tool for indexing and searching enterprise radiology and pathology reports

NASA Astrophysics Data System (ADS)

Kim, Woojin; Boonn, William

2010-03-01

Data mining of existing radiology and pathology reports within an enterprise health system can be used for clinical decision support, research, education, as well as operational analyses. In our health system, the database of radiology and pathology reports exceeds 13 million entries combined. We are building a web-based tool to allow search and data analysis of these combined databases using freely available and open source tools. This presentation will compare performance of an open source full-text indexing tool to MySQL's full-text indexing and searching and describe implementation procedures to incorporate these capabilities into a radiology-pathology search engine.

ESAP plus: a web-based server for EST-SSR marker development.

PubMed

Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

2016-12-22

Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface. ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ .

Maintaining Multimedia Data in a Geospatial Database

DTIC Science & Technology

2012-09-01

at PostgreSQL and MySQL as spatial databases was offered. Given their results, as each database produced result sets from zero to 100,000, it was...excelled given multiple conditions. A different look at PostgreSQL and MySQL as spatial databases was offered. Given their results, as each database... MySQL ................................................................................................14  B.  BENCHMARKING DATA RETRIEVED FROM TABLE

Romanian Complex Data Center for Dense Seismic network

NASA Astrophysics Data System (ADS)

Neagoe, Cristian; Ionescu, Constantin; Marius Manea, Liviu

2010-05-01

Since 2002 the National Institute for Earth Physics (NIEP) developed its own real-time digital seismic network: consisting of 96 seismic stations of which 35 are broadband sensors and 24 stations equipped with short period sensors and two arrays earthquakes that transmit data in real time at the National Data Center (NDC) and Eforie Nord (EFOR) Seismic Observatory. EFOR is the back-up for the NDC and also a monitoring center for Black Sea tsunamis. Seismic stations are equipped with Quanterra Q330 and K2 digitizers, broadband seismometers (STS2, CMG40T, CMG 3ESP, CMG3T) and acceleration sensors Episensor Kinemetrics (+ / - 2G). SeedLink who is a part of Seiscomp2.5 and Antelope are software packages used for acquisition in real time (RT) and for data exchange. Communication of digital seismic stations to the National Data Center in Bucharest and Seismic Observatory Eforie Nord is assured by 5 providers (GPRS, VPN, satellite radio and Internet communication). For acquisition and data processing at the two centers of reception and processing is used AntelopeTM 4.11 running on 2 workstations: one for real-time and other for offline processing and also a Seiscomp 3 server that works as back-up for Antelope 4.11 Both acquisition and analysis of seismic data systems produced information about local and global parameters of earthquakes, in addition Antelope is used for manual processing (association events, the calculation of magnitude, creating a database, sending seismic bulletins, calculation of PGA and PGV , etc.), generating ShakeMap products and interacts with global data centers. In order to make all this information easily available across the Web and also lay the grounds for a more modular and flexible development environment the National Data Center developed tools to enable centralizing of data from software such as Antelope which is using a dedicated database system ( Datascope, a database system based on text files ) to a more general-purpose database, MySQL which acts like a hub between the different acquisition and analysis systems used in the data center while also providing better connectivity at no expense in security. Mirroring certain data to MySQL also allows the National Data Center to easily share information to the public via the new application which is being developed and also mix in data collected from the public (e.g. information about the damages observed after an earthquake which intern is being used to produce macroseismic intensity indices which are then stored in the database and also made available via the web application). For internal usage there is also a web application which using data stored in the database displays earthquake information like location, magnitude and depth in semi-real-time thus aiding the personnel on duty. Another usage for the collected data is to create and maintain contact lists to which the datacenter sends notifications (SMS and emails) based on the parameters of the earthquake. For future development, amongst others the Data Center plans to develop the means to crosscheck the generated data between the different acquisition and analysis systems (e.g. comparing data generated by Antelope with data generated by Seiscomp).

Using a web-based system for the continuous distance education in cytopathology.

PubMed

Stergiou, Nikolaos; Georgoulakis, Giannis; Margari, Niki; Aninos, Dionisios; Stamataki, Melina; Stergiou, Efi; Pouliakis, Abraam; Karakitsos, Petros

2009-12-01

The evolution of information technologies and telecommunications has made the World Wide Web a low cost and easily accessible tool for the dissemination of information and knowledge. Continuous Medical Education (CME) sites dedicated in cytopathology field are rather poor, they do not succeed in following the constant changes and lack the ability of providing cytopathologists with a dynamic learning environment, adaptable to the development of cytopathology. Learning methods including skills such as decision making, reasoning and problem solving are critical in the development of such a learning environment. The objectives of this study are (1) to demonstrate on the basis of a web-based training system the successful application of traditional learning theories and methods and (2) to effectively evaluate users' perception towards the educational program, using a combination of observers, theories and methods. Trainees are given the opportunity to browse through the educational material, collaborate in synchronous and asynchronous mode, practice their skills through problems and tasks and test their knowledge using the self-evaluation tool. On the other hand, the trainers are responsible for editing learning material, attending students' progress and organizing the problem-based and task-based scenarios. The implementation of the web-based training system is based on the three-tier architecture and uses an Apache Tomcat web server and a MySQL database server. By December 2008, CytoTrainer's learning environment contains two courses in cytopathology: Gynaecological Cytology and Thyroid Cytology offering about 2000 digital images and 20 case sessions. Our evaluation method is a combination of both qualitative and quantitative approaches to explore how the various parts of the system and students' attitudes work together. Trainees approved of the course's content, methodology and learning activities. The triangulation of evaluation methods revealed that the training program is suitable for the continuous distance education in cytopathology and that it has improved the trainees' skills in diagnostic cytopathology. The web-based training system can be successfully involved in the continuous distance education in cytopathology. It provides the opportunity to access learning material from any place at any time and supports the acquisition of diagnostic knowledge.

A simple versatile solution for collecting multidimensional clinical data based on the CakePHP web application framework.

PubMed

Biermann, Martin

2014-04-01

Clinical trials aiming for regulatory approval of a therapeutic agent must be conducted according to Good Clinical Practice (GCP). Clinical Data Management Systems (CDMS) are specialized software solutions geared toward GCP-trials. They are however less suited for data management in small non-GCP research projects. For use in researcher-initiated non-GCP studies, we developed a client-server database application based on the public domain CakePHP framework. The underlying MySQL database uses a simple data model based on only five data tables. The graphical user interface can be run in any web browser inside the hospital network. Data are validated upon entry. Data contained in external database systems can be imported interactively. Data are automatically anonymized on import, and the key lists identifying the subjects being logged to a restricted part of the database. Data analysis is performed by separate statistics and analysis software connecting to the database via a generic Open Database Connectivity (ODBC) interface. Since its first pilot implementation in 2011, the solution has been applied to seven different clinical research projects covering different clinical problems in different organ systems such as cancer of the thyroid and the prostate glands. This paper shows how the adoption of a generic web application framework is a feasible, flexible, low-cost, and user-friendly way of managing multidimensional research data in researcher-initiated non-GCP clinical projects. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

PubMed Central

Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

2005-01-01

Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at . PMID:15910681

The ALICE Electronic Logbook

NASA Astrophysics Data System (ADS)

Altini, V.; Carena, F.; Carena, W.; Chapeland, S.; Chibante Barroso, V.; Costa, F.; Divià, R.; Fuchs, U.; Makhlyueva, I.; Roukoutakis, F.; Schossmaier, K.; Soòs, C.; Vande Vyvre, P.; Von Haller, B.; ALICE Collaboration

2010-04-01

All major experiments need tools that provide a way to keep a record of the events and activities, both during commissioning and operations. In ALICE (A Large Ion Collider Experiment) at CERN, this task is performed by the Alice Electronic Logbook (eLogbook), a custom-made application developed and maintained by the Data-Acquisition group (DAQ). Started as a statistics repository, the eLogbook has evolved to become not only a fully functional electronic logbook, but also a massive information repository used to store the conditions and statistics of the several online systems. It's currently used by more than 600 users in 30 different countries and it plays an important role in the daily ALICE collaboration activities. This paper will describe the LAMP (Linux, Apache, MySQL and PHP) based architecture of the eLogbook, the database schema and the relevance of the information stored in the eLogbook to the different ALICE actors, not only for near real time procedures but also for long term data-mining and analysis. It will also present the web interface, including the different used technologies, the implemented security measures and the current main features. Finally it will present the roadmap for the future, including a migration to the web 2.0 paradigm, the handling of the database ever-increasing data volume and the deployment of data-mining tools.

Methods to Secure Databases Against Vulnerabilities

DTIC Science & Technology

2015-12-01

for several languages such as C, C++, PHP, Java and Python [16]. MySQL will work well with very large databases. The documentation references...using Eclipse and connected to each database management system using Python and Java drivers provided by MySQL , MongoDB, and Datastax (for Cassandra...tiers in Python and Java . Problem MySQL MongoDB Cassandra 1. Injection a. Tautologies Vulnerable Vulnerable Not Vulnerable b. Illegal query

Internet-based peer support for Ménière's disease: a summary of web-based data collection, impact evaluation, and user evaluation.

PubMed

Pyykkő, Ilmari; Manchaiah, Vinaya; Levo, Hilla; Kentala, Erna; Juhola, Martti

2017-07-01

This paper presents a summary of web-based data collection, impact evaluation, and user evaluations of an Internet-based peer support program for Ménière's disease (MD). The program is written in html-form. The data are stored in a MySQL database and uses machine learning in the diagnosis of MD. The program works interactively with the user and assesses the participant's disorder profile in various dimensions (i.e., symptoms, impact, personal traits, and positive attitude). The inference engine uses a database to compare the impact with 50 referents, and provides regular feedback to the user. Data were analysed using descriptive statistics and regression analysis. The impact evaluation was based on 740 cases and the user evaluation on a sample of 75 cases of MD respectively. The web-based system was useful in data collection and impact evaluation of people with MD. Among those with a recent onset of MD, 78% rated the program as useful or very useful, whereas those with chronic MD rated the program 55%. We suggest that a web-based data collection and impact evaluation for peer support can be helpful while formulating the rehabilitation goals of building the self-confidence needed for coping and increasing social participation.

A targeted e-learning program for surgical trainees to enhance patient safety in preventing surgical infection.

PubMed

McHugh, Seamus Mark; Corrigan, Mark; Dimitrov, Borislav; Cowman, Seamus; Tierney, Sean; Humphreys, Hilary; Hill, Arnold

2010-01-01

Surgical site infection accounts for 20% of all health care-associated infections (HCAIs); however, a program incorporating the education of surgeons has yet to be established across the specialty. An audit of surgical practice in infection prevention was carried out in Beaumont Hospital from July to November 2009. An educational Web site was developed targeting deficiencies highlighted in the audit. Interactive clinical cases were constructed using PHP coding, an HTML-embedded language, and then linked to a MySQL relational database. PowerPoint tutorials were produced as online Flash audiovisual movies. An online repository of streaming videos demonstrating best practice was made available, and weekly podcasts were made available on the iTunes© store for free download. Usage of the e-learning program was assessed quantitatively over 6 weeks in May and June 2010 using the commercial company Hitslink. During the 5-month audit, deficiencies in practice were highlighted, including the timing of surgical prophylaxis (33% noncompliance) and intravascular catheter care in surgical patients (38% noncompliance regarding necessity). Over the 6-week assessment of the educational material, the SurgInfection.com Web pages were accessed more than 8000 times; 77.9% of the visitors were from Ireland. The most commonly accessed modality was the repository with interactive clinical cases, accounting for 3463 (43%) of the Web site visits. The average user spent 57 minutes per visit, with 30% of them visiting the Web site multiple times. Interactive virtual cases mirroring real-life clinical scenarios are likely to be successful as an e-learning modality. User-friendly interfaces and 24-hour accessibility will increases uptake by surgical trainees.

A New Data Management System for Biological and Chemical Oceanography

NASA Astrophysics Data System (ADS)

Groman, R. C.; Chandler, C.; Allison, D.; Glover, D. M.; Wiebe, P. H.

2007-12-01

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was created to serve PIs principally funded by NSF to conduct marine chemical and ecological research. The new office is dedicated to providing open access to data and information developed in the course of scientific research on short and intermediate time-frames. The data management system developed in support of U.S. JGOFS and U.S. GLOBEC programs is being modified to support the larger scope of the BCO-DMO effort, which includes ultimately providing a way to exchange data with other data systems. The open access system is based on a philosophy of data stewardship, support for existing and evolving data standards, and use of public domain software. The DMO staff work closely with originating PIs to manage data gathered as part of their individual programs. In the new BCO-DMO data system, project and data set metadata records designed to support re-use of the data are stored in a relational database (MySQL) and the data are stored in or made accessible by the JGOFS/GLOBEC object- oriented, relational, data management system. Data access will be provided via any standard Web browser client user interface through a GIS application (Open Source, OGC-compliant MapServer), a directory listing from the data holdings catalog, or a custom search engine that facilitates data discovery. In an effort to maximize data system interoperability, data will also be available via Web Services; and data set descriptions will be generated to comply with a variety of metadata content standards. The office is located at the Woods Hole Oceanographic Institution and web access is via http://www.bco-dmo.org.

Prototype of web-based database of surface wave investigation results for site classification

NASA Astrophysics Data System (ADS)

Hayashi, K.; Cakir, R.; Martin, A. J.; Craig, M. S.; Lorenzo, J. M.

2016-12-01

As active and passive surface wave methods are getting popular for evaluating site response of earthquake ground motion, demand on the development of database for investigation results is also increasing. Seismic ground motion not only depends on 1D velocity structure but also on 2D and 3D structures so that spatial information of S-wave velocity must be considered in ground motion prediction. The database can support to construct 2D and 3D underground models. Inversion of surface wave processing is essentially non-unique so that other information must be combined into the processing. The database of existed geophysical, geological and geotechnical investigation results can provide indispensable information to improve the accuracy and reliability of investigations. Most investigations, however, are carried out by individual organizations and investigation results are rarely stored in the unified and organized database. To study and discuss appropriate database and digital standard format for the surface wave investigations, we developed a prototype of web-based database to store observed data and processing results of surface wave investigations that we have performed at more than 400 sites in U.S. and Japan. The database was constructed on a web server using MySQL and PHP so that users can access to the database through the internet from anywhere with any device. All data is registered in the database with location and users can search geophysical data through Google Map. The database stores dispersion curves, horizontal to vertical spectral ratio and S-wave velocity profiles at each site that was saved in XML files as digital data so that user can review and reuse them. The database also stores a published 3D deep basin and crustal structure and user can refer it during the processing of surface wave data.

Graphics interfaces and numerical simulations: Mexican Virtual Solar Observatory

NASA Astrophysics Data System (ADS)

Hernández, L.; González, A.; Salas, G.; Santillán, A.

2007-08-01

Preliminary results associated to the computational development and creation of the Mexican Virtual Solar Observatory (MVSO) are presented. Basically, the MVSO prototype consists of two parts: the first, related to observations that have been made during the past ten years at the Solar Observation Station (EOS) and at the Carl Sagan Observatory (OCS) of the Universidad de Sonora in Mexico. The second part is associated to the creation and manipulation of a database produced by numerical simulations related to solar phenomena, we are using the MHD ZEUS-3D code. The development of this prototype was made using mysql, apache, java and VSO 1.2. based GNU and `open source philosophy'. A graphic user interface (GUI) was created in order to make web-based, remote numerical simulations. For this purpose, Mono was used, because it is provides the necessary software to develop and run .NET client and server applications on Linux. Although this project is still under development, we hope to have access, by means of this portal, to other virtual solar observatories and to be able to count on a database created through numerical simulations or, given the case, perform simulations associated to solar phenomena.

Application of crowdsourced hail data and damage information for hail risk assessment in the province of Styria, Austria

NASA Astrophysics Data System (ADS)

Tani, Satyanarayana; Rechberger, Andreas; Süsser Rechberger, Barbara; Teschl, Reinhard; Paulitsch, Helmut

2017-04-01

Hail storm damage is a major concern to the farmers in the province of Styria, Austria. Each year severe hail storms are causing damages to crops, resulting in losses of millions of euros. High spatial and timely ground truth information of the hail event and crop damage measurements are essential for better hail risk assessment. Usually, hail pad networks and visual damage surveys are used to collect the hail data and corresponding damage information. However, these hail pad networks are expensive and need laborious maintenance. The traditional crop damage assessment approaches are very labour-intensive and time-consuming. The advancements in information and communication technology (ICT) and the power of citizen based crowdsourcing data, will help to overcome these problems and ultimately provide a platform for data collection. A user-friendly and bilingual web interface was developed to collect hail data and crop damage information in the province of Styria, Austria. The dynamic web interface was developed using HTML5, JavaScript, and PHP7 combined with a MySQL database back-end. OpenStreetMap was integrated into the web interface and tile server optimised for an easy identification of geolocation information. The user needs an internet connection to transfer the data through smartphone or computer. Crowdsourced data will be quality tested and evaluated with 3D single polarisation C-band weather radar data to remove potential false reports. Further, the relationship between the reported hail events and radar-based hail detection algorithms (Waldvogel and Auer) and derived hail signature information intended for crop hail risk assessment will be investigated. The details about the web interface tool, application and verification methods to collect, analyse, and integrate different data sets are given. Further, the high spatial risk assessment information is communicated to support risk management policy.

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

PubMed

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

HTT-DB: horizontally transferred transposable elements database.

PubMed

Dotto, Bruno Reis; Carvalho, Evelise Leis; Silva, Alexandre Freitas; Duarte Silva, Luiz Fernando; Pinto, Paulo Marcos; Ortiz, Mauro Freitas; Wallau, Gabriel Luz

2015-09-01

Horizontal transfer of transposable (HTT) elements among eukaryotes was discovered in the mid-1980s. As then, >300 new cases have been described. New findings about HTT are revealing the evolutionary impact of this phenomenon on host genomes. In order to provide an up to date, interactive and expandable database for such events, we developed the HTT-DB database. HTT-DB allows easy access to most of HTT cases reported along with rich information about each case. Moreover, it allows the user to generate tables and graphs based on searches using Transposable elements and/or host species classification and export them in several formats. This database is freely available on the web at http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase. HTT-DB was developed based on Java and MySQL with all major browsers supported. Tools and software packages used are free for personal or non-profit projects. bdotto82@gmail.com or gabriel.wallau@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

PubMed Central

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

BGDB: a database of bivalent genes

PubMed Central

Li, Qingyan; Lian, Shuabin; Dai, Zhiming; Xiang, Qian; Dai, Xianhua

2013-01-01

Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/ PMID:23894186

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

Consistent data recording across a health system and web-enablement allow service quality comparisons: online data for commissioning dermatology services.

PubMed

Dmitrieva, Olga; Michalakidis, Georgios; Mason, Aaron; Jones, Simon; Chan, Tom; de Lusignan, Simon

2012-01-01

A new distributed model of health care management is being introduced in England. Family practitioners have new responsibilities for the management of health care budgets and commissioning of services. There are national datasets available about health care providers and the geographical areas they serve. These data could be better used to assist the family practitioner turned health service commissioners. Unfortunately these data are not in a form that is readily usable by these fledgling family commissioning groups. We therefore Web enabled all the national hospital dermatology treatment data in England combining it with locality data to provide a smart commissioning tool for local communities. We used open-source software including the Ruby on Rails Web framework and MySQL. The system has a Web front-end, which uses hypertext markup language cascading style sheets (HTML/CSS) and JavaScript to deliver and present data provided by the database. A combination of advanced caching and schema structures allows for faster data retrieval on every execution. The system provides an intuitive environment for data analysis and processing across a large health system dataset. Web-enablement has enabled data about in patients, day cases and outpatients to be readily grouped, viewed, and linked to other data. The combination of web-enablement, consistent data collection from all providers; readily available locality data; and a registration based primary system enables the creation of data, which can be used to commission dermatology services in small areas. Standardized datasets collected across large health enterprises when web enabled can readily benchmark local services and inform commissioning decisions.

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers.

PubMed

Cao, Han; Ng, Marcus C K; Jusoh, Siti Azma; Tai, Hio Kuan; Siu, Shirley W I

2017-09-01

[Formula: see text]-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM . Website is implemented in PHP, MySQL and Apache, with all major browsers supported.

IoT real time data acquisition using MQTT protocol

NASA Astrophysics Data System (ADS)

Atmoko, R. A.; Riantini, R.; Hasin, M. K.

2017-05-01

The Internet of Things (IoT) provides ease to monitor and to gain sensor data through the Internet [1]. The need of high quality data is increasing to the extent that data monitoring and acquisition system in real time is required, such as smart city or telediagnostic in medical areas [2]. Therefore, an appropriate communication protocol is required to resolve these problems. Lately, researchers have developed a lot of communication protocols for IoT, of which each has advantages and disadvantages. This study proposes the utilization of MQTT as a communication protocol, which is one of data communication protocols for IoT. This study used temperature and humidity sensors because the physical parameters are often needed as parameters of environment condition [3]. Data acquisition was done in real-time and stored in MySQL database. This study is also completed by interface web-based and mobile for online monitoring. This result of this study is the enhancement of data quality and reliability using MQTT protocol.

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

NASA Astrophysics Data System (ADS)

Cao, Han; Ng, Marcus C. K.; Jusoh, Siti Azma; Tai, Hio Kuan; Siu, Shirley W. I.

2017-09-01

α-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.

UCbase 2.0: ultraconserved sequences database (2014 update).

PubMed

Lomonaco, Vincenzo; Martoglia, Riccardo; Mandreoli, Federica; Anderlucci, Laura; Emmett, Warren; Bicciato, Silvio; Taccioli, Cristian

2014-01-01

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it. © The Author(s) 2014. Published by Oxford University Press.

A Web-based telemedicine system for diabetic retinopathy screening using digital fundus photography.

PubMed

Wei, Jack C; Valentino, Daniel J; Bell, Douglas S; Baker, Richard S

2006-02-01

The purpose was to design and implement a Web-based telemedicine system for diabetic retinopathy screening using digital fundus cameras and to make the software publicly available through Open Source release. The process of retinal imaging and case reviewing was modeled to optimize workflow and implement use of computer system. The Web-based system was built on Java Servlet and Java Server Pages (JSP) technologies. Apache Tomcat was chosen as the JSP engine, while MySQL was used as the main database and Laboratory of Neuro Imaging (LONI) Image Storage Architecture, from the LONI-UCLA, as the platform for image storage. For security, all data transmissions were carried over encrypted Internet connections such as Secure Socket Layer (SSL) and HyperText Transfer Protocol over SSL (HTTPS). User logins were required and access to patient data was logged for auditing. The system was deployed at Hubert H. Humphrey Comprehensive Health Center and Martin Luther King/Drew Medical Center of Los Angeles County Department of Health Services. Within 4 months, 1500 images of more than 650 patients were taken at Humphrey's Eye Clinic and successfully transferred to King/Drew's Department of Ophthalmology. This study demonstrates an effective architecture for remote diabetic retinopathy screening.

Web mapping system for complex processing and visualization of environmental geospatial datasets

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny; Okladnikov, Igor

2016-04-01

Environmental geospatial datasets (meteorological observations, modeling and reanalysis results, etc.) are used in numerous research applications. Due to a number of objective reasons such as inherent heterogeneity of environmental datasets, big dataset volume, complexity of data models used, syntactic and semantic differences that complicate creation and use of unified terminology, the development of environmental geodata access, processing and visualization services as well as client applications turns out to be quite a sophisticated task. According to general INSPIRE requirements to data visualization geoportal web applications have to provide such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. It should be noted that modern web mapping systems as integrated geoportal applications are developed based on the SOA and might be considered as complexes of interconnected software tools for working with geospatial data. In the report a complex web mapping system including GIS web client and corresponding OGC services for working with geospatial (NetCDF, PostGIS) dataset archive is presented. There are three basic tiers of the GIS web client in it: 1. Tier of geospatial metadata retrieved from central MySQL repository and represented in JSON format 2. Tier of JavaScript objects implementing methods handling: --- NetCDF metadata --- Task XML object for configuring user calculations, input and output formats --- OGC WMS/WFS cartographical services 3. Graphical user interface (GUI) tier representing JavaScript objects realizing web application business logic Metadata tier consists of a number of JSON objects containing technical information describing geospatial datasets (such as spatio-temporal resolution, meteorological parameters, valid processing methods, etc). The middleware tier of JavaScript objects implementing methods for handling geospatial metadata, task XML object, and WMS/WFS cartographical services interconnects metadata and GUI tiers. The methods include such procedures as JSON metadata downloading and update, launching and tracking of the calculation task running on the remote servers as well as working with WMS/WFS cartographical services including: obtaining the list of available layers, visualizing layers on the map, exporting layers in graphical (PNG, JPG, GeoTIFF), vector (KML, GML, Shape) and digital (NetCDF) formats. Graphical user interface tier is based on the bundle of JavaScript libraries (OpenLayers, GeoExt and ExtJS) and represents a set of software components implementing web mapping application business logic (complex menus, toolbars, wizards, event handlers, etc.). GUI provides two basic capabilities for the end user: configuring the task XML object functionality and cartographical information visualizing. The web interface developed is similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Web mapping system developed has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical form. The work is supported by SB RAS Basic Program Projects VIII.80.2.1 and IV.38.1.7.

Spectrum Savings from High Performance Recording and Playback Onboard the Test Article

DTIC Science & Technology

2013-02-20

execute within a Windows 7 environment, and data is recorded on SSDs. The underlying database is implemented using MySQL . Figure 1 illustrates the... MySQL database. This is effectively the time at which the recorded data are available for retransmission. CPU and Memory utilization were collected...17.7% MySQL avg. 3.9% EQDR Total avg. 21.6% Table 1 CPU Utilization with260 Mbits/sec Load The difference between the total System CPU (27.8

Flexible Decision Support in Device-Saturated Environments

DTIC Science & Technology

2003-10-01

also output tuples to a remote MySQL or Postgres database. 3.3 GUI The GUI allows the user to pose queries using SQL and to display query...DatabaseConnection.java – handles connections to an external database (such as MySQL or Postgres ). • Debug.java – contains the code for printing out Debug messages...also provided. It is possible to output the results of queries to a MySQL or Postgres database for archival and the GUI can query those results

Development of new on-line statistical program for the Korean Society for Radiation Oncology

PubMed Central

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Choi, Eun Kyung; Cho, Kwan Ho

2015-01-01

Purpose To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. Materials and Methods The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Results Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. Conclusion The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology. PMID:26157684

The Cardiac Atlas Project--an imaging database for computational modeling and statistical atlases of the heart.

PubMed

Fonseca, Carissa G; Backhaus, Michael; Bluemke, David A; Britten, Randall D; Chung, Jae Do; Cowan, Brett R; Dinov, Ivo D; Finn, J Paul; Hunter, Peter J; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Medrano-Gracia, Pau; Shivkumar, Kalyanam; Suinesiaputra, Avan; Tao, Wenchao; Young, Alistair A

2011-08-15

Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups. Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt). http://www.cardiacatlas.org a.young@auckland.ac.nz Supplementary data are available at Bioinformatics online.

Mars @ ASDC

NASA Astrophysics Data System (ADS)

Carraro, Francesco

"Mars @ ASDC" is a project born with the goal of using the new web technologies to assist researches involved in the study of Mars. This project employs Mars map and javascript APIs provided by Google to visualize data acquired by space missions on the planet. So far, visualization of tracks acquired by MARSIS and regions observed by VIRTIS-Rosetta has been implemented. The main reason for the creation of this kind of tool is the difficulty in handling hundreds or thousands of acquisitions, like the ones from MARSIS, and the consequent difficulty in finding observations related to a particular region. This led to the development of a tool which allows to search for acquisitions either by defining the region of interest through a set of geometrical parameters or by manually selecting the region on the map through a few mouse clicks The system allows the visualization of tracks (acquired by MARSIS) or regions (acquired by VIRTIS-Rosetta) which intersect the user defined region. MARSIS tracks can be visualized both in Mercator and polar projections while the regions observed by VIRTIS can presently be visualized only in Mercator projection. The Mercator projection is the standard map provided by Google. The polar projections are provided by NASA and have been developed to be used in combination with APIs provided by Google The whole project has been developed following the "open source" philosophy: the client-side code which handles the functioning of the web page is written in javascript; the server-side code which executes the searches for tracks or regions is written in PHP and the DB which undergoes the system is MySQL.

Development of new on-line statistical program for the Korean Society for Radiation Oncology.

PubMed

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Shin, Kyung Hwan; Choi, Eun Kyung; Cho, Kwan Ho

2015-06-01

To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology.

Improving the User Experience of Finding and Visualizing Oceanographic Data

NASA Astrophysics Data System (ADS)

Rauch, S.; Allison, M. D.; Groman, R. C.; Chandler, C. L.; Galvarino, C.; Gegg, S. R.; Kinkade, D.; Shepherd, A.; Wiebe, P. H.; Glover, D. M.

2013-12-01

Searching for and locating data of interest can be a challenge to researchers as increasing volumes of data are made available online through various data centers, repositories, and archives. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is keenly aware of this challenge and, as a result, has implemented features and technologies aimed at improving data discovery and enhancing the user experience. BCO-DMO was created in 2006 to manage and publish data from research projects funded by the Division of Ocean Sciences (OCE) Biological and Chemical Oceanography Sections and the Division of Polar Programs (PLR) Antarctic Sciences Organisms and Ecosystems Program (ANT) of the US National Science Foundation (NSF). The BCO-DMO text-based and geospatial-based data access systems provide users with tools to search, filter, and visualize data in order to efficiently find data of interest. The geospatial interface, developed using a suite of open-source software (including MapServer [1], OpenLayers [2], ExtJS [3], and MySQL [4]), allows users to search and filter/subset metadata based on program, project, or deployment, or by using a simple word search. The map responds based on user selections, presents options that allow the user to choose specific data parameters (e.g., a species or an individual drifter), and presents further options for visualizing those data on the map or in "quick-view" plots. The data managed and made available by BCO-DMO are very heterogeneous in nature, from in-situ biogeochemical, ecological, and physical data, to controlled laboratory experiments. Due to the heterogeneity of the data types, a 'one size fits all' approach to visualization cannot be applied. Datasets are visualized in a way that will best allow users to assess fitness for purpose. An advanced geospatial interface, which contains a semantically-enabled faceted search [5], is also available. These search facets are highly interactive and responsive, allowing users to construct their own custom searches by applying multiple filters. New filtering and visualization tools are continually being added to the BCO-DMO system as new data types are encountered and as we receive feedback from our data contributors and users. As our system becomes more complex, teaching users about the many interactive features becomes increasingly important. Tutorials and videos are made available online. Recent in-person classroom-style tutorials have proven useful for both demonstrating our system to users and for obtaining feedback to further improve the user experience. References: [1] University of Minnesota. MapServer: Open source web mapping. http://www.mapserver.org [2] OpenLayers: Free Maps for the Web. http://www.openlayers.org [3] Sencha. ExtJS. http://www.sencha.com/products/extjs [4] MySQL. http://www.mysql.com/ [5] Maffei, A. R., Rozell, E. A., West, P., Zednik, S., and Fox, P. A. 2011. Open Standards and Technologies in the S2S Framework. Abstract IN31A-1435 presented at American Geophysical Union 2011 Fall Meeting, San Francisco, CA, 7 December 2011.

Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae.

PubMed

Swetha, Rayapadi G; Kala Sekar, Dinesh Kumar; Ramaiah, Sudha; Anbarasu, Anand; Sekar, Kanagaraj

2014-12-01

Haemophilus influenzae (H. Influenzae) is the causative agent of pneumonia, bacteraemia and meningitis. The organism is responsible for large number of deaths in both developed and developing countries. Even-though the first bacterial genome to be sequenced was that of H. Influenzae, there is no exclusive database dedicated for H. Influenzae. This prompted us to develop the Haemophilus influenzae Genome Database (HIGDB). All data of HIGDB are stored and managed in MySQL database. The HIGDB is hosted on Solaris server and developed using PERL modules. Ajax and JavaScript are used for the interface development. The HIGDB contains detailed information on 42,741 proteins, 18,077 genes including 10 whole genome sequences and also 284 three dimensional structures of proteins of H. influenzae. In addition, the database provides "Motif search" and "GBrowse". The HIGDB is freely accessible through the URL: http://bioserver1.physics.iisc.ernet.in/HIGDB/. The HIGDB will be a single point access for bacteriological, clinical, genomic and proteomic information of H. influenzae. The database can also be used to identify DNA motifs within H. influenzae genomes and to compare gene or protein sequences of a particular strain with other strains of H. influenzae. Copyright © 2014 Elsevier Ltd. All rights reserved.

Expert system for skin problem consultation in Thai traditional medicine.

PubMed

Nopparatkiat, Pornchai; na Nagara, Byaporn; Chansa-ngavej, Chuvej

2014-01-01

This paper aimed to demonstrate the research and development of a rule-based expert system for skin problem consulting in the areas of acne, melasma, freckle, wrinkle, and uneven skin tone, with recommended treatments from Thai traditional medicine knowledge. The tool selected for developing the expert system is a software program written in the PHP language. MySQL database is used to work together with PHP for building database of the expert system. The system is web-based and can be reached from anywhere with Internet access. The developed expert system gave recommendations on the skin problem treatment with Thai herbal recipes and Thai herbal cosmetics based on 416 rules derived from primary and secondary sources. The system had been tested by 50 users consisting of dermatologists, Thai traditional medicine doctors, and general users. The developed system was considered good for learning and consultation. The present work showed how such a scattered body of traditional knowledge as Thai traditional medicine and herbal recipes could be collected, organised and made accessible to users and interested parties. The expert system developed herein should contribute in a meaningful way towards preserving the knowledge and helping promote the use of Thai traditional medicine as a practical alternative medicine for the treatment of illnesses.

User-driven Cloud Implementation of environmental models and data for all

NASA Astrophysics Data System (ADS)

Gurney, R. J.; Percy, B. J.; Elkhatib, Y.; Blair, G. S.

2014-12-01

Environmental data and models come from disparate sources over a variety of geographical and temporal scales with different resolutions and data standards, often including terabytes of data and model simulations. Unfortunately, these data and models tend to remain solely within the custody of the private and public organisations which create the data, and the scientists who build models and generate results. Although many models and datasets are theoretically available to others, the lack of ease of access tends to keep them out of reach of many. We have developed an intuitive web-based tool that utilises environmental models and datasets located in a cloud to produce results that are appropriate to the user. Storyboards showing the interfaces and visualisations have been created for each of several exemplars. A library of virtual machine images has been prepared to serve these exemplars. Each virtual machine image has been tailored to run computer models appropriate to the end user. Two approaches have been used; first as RESTful web services conforming to the Open Geospatial Consortium (OGC) Web Processing Service (WPS) interface standard using the Python-based PyWPS; second, a MySQL database interrogated using PHP code. In all cases, the web client sends the server an HTTP GET request to execute the process with a number of parameter values and, once execution terminates, an XML or JSON response is sent back and parsed at the client side to extract the results. All web services are stateless, i.e. application state is not maintained by the server, reducing its operational overheads and simplifying infrastructure management tasks such as load balancing and failure recovery. A hybrid cloud solution has been used with models and data sited on both private and public clouds. The storyboards have been transformed into intuitive web interfaces at the client side using HTML, CSS and JavaScript, utilising plug-ins such as jQuery and Flot (for graphics), and Google Maps APIs. We have demonstrated that a cloud infrastructure can be used to assemble a virtual research environment that, coupled with a user-driven development approach, is able to cater to the needs of a wide range of user groups, from domain experts to concerned members of the general public.

Web-based auditory self-training system for adult and elderly users of hearing aids.

PubMed

Vitti, Simone Virginia; Blasca, Wanderléia Quinhoneiro; Sigulem, Daniel; Torres Pisa, Ivan

2015-01-01

Adults and elderly users of hearing aids suffer psychosocial reactions as a result of hearing loss. Auditory rehabilitation is typically carried out with support from a speech therapist, usually in a clinical center. For these cases, there is a lack of computer-based self-training tools for minimizing the psychosocial impact of hearing deficiency. To develop and evaluate a web-based auditory self-training system for adult and elderly users of hearing aids. Two modules were developed for the web system: an information module based on guidelines for using hearing aids; and an auditory training module presenting a sequence of training exercises for auditory abilities along the lines of the auditory skill steps within auditory processing. We built aweb system using PHP programming language and a MySQL database .from requirements surveyed through focus groups that were conducted by healthcare information technology experts. The web system was evaluated by speech therapists and hearing aid users. An initial sample of 150 patients at DSA/HRAC/USP was defined to apply the system with the inclusion criteria that: the individuals should be over the age of 25 years, presently have hearing impairment, be a hearing aid user, have a computer and have internet experience. They were divided into two groups: a control group (G1) and an experimental group (G2). These patients were evaluated clinically using the HHIE for adults and HHIA for elderly people, before and after system implementation. A third web group was formed with users who were invited through social networks for their opinions on using the system. A questionnaire evaluating hearing complaints was given to all three groups. The study hypothesis considered that G2 would present greater auditory perception, higher satisfaction and fewer complaints than G1 after the auditory training. It was expected that G3 would have fewer complaints regarding use and acceptance of the system. The web system, which was named SisTHA portal, was finalized, rated by experts and hearing aid users and approved for use. The system comprised auditory skills training along five lines: discrimination; recognition; comprehension and temporal sequencing; auditory closure; and cognitive-linguistic and communication strategies. Users needed to undergo auditory training over a minimum period of 1 month: 5 times a week for 30 minutes a day. Comparisons were made between G1 and G2 and web system use by G3. The web system developed was approved for release to hearing aid users. It is expected that the self-training will help improve effective use of hearing aids, thereby decreasing their rejection.

System Enhancements for Mechanical Inspection Processes

NASA Technical Reports Server (NTRS)

Hawkins, Myers IV

2011-01-01

Quality inspection of parts is a major component to any project that requires hardware implementation. Keeping track of all of the inspection jobs is essential to having a smooth running process. By using HTML, the programming language ColdFusion, and the MySQL database, I created a web-based job management system for the 170 Mechanical Inspection Group that will replace the Microsoft Access based management system. This will improve the ways inspectors and the people awaiting inspection view and keep track of hardware as it is in the inspection process. In the end, the management system should be able to insert jobs into a queue, place jobs in and out of a bonded state, pre-release bonded jobs, and close out inspection jobs.

Isfahan MISP Dataset.

PubMed

Kashefpur, Masoud; Kafieh, Rahele; Jorjandi, Sahar; Golmohammadi, Hadis; Khodabande, Zahra; Abbasi, Mohammadreza; Teifuri, Nilufar; Fakharzadeh, Ali Akbar; Kashefpoor, Maryam; Rabbani, Hossein

2017-01-01

An online depository was introduced to share clinical ground truth with the public and provide open access for researchers to evaluate their computer-aided algorithms. PHP was used for web programming and MySQL for database managing. The website was entitled "biosigdata.com." It was a fast, secure, and easy-to-use online database for medical signals and images. Freely registered users could download the datasets and could also share their own supplementary materials while maintaining their privacies (citation and fee). Commenting was also available for all datasets, and automatic sitemap and semi-automatic SEO indexing have been set for the site. A comprehensive list of available websites for medical datasets is also presented as a Supplementary (http://journalonweb.com/tempaccess/4800.584.JMSS_55_16I3253.pdf).

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

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.

VKCDB: voltage-gated K+ channel database updated and upgraded.

PubMed

Gallin, Warren J; Boutet, Patrick A

2011-01-01

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

Development of an electronic radiation oncology patient information management system.

PubMed

Mandal, Abhijit; Asthana, Anupam Kumar; Aggarwal, Lalit Mohan

2008-01-01

The quality of patient care is critically influenced by the availability of accurate information and its efficient management. Radiation oncology consists of many information components, for example there may be information related to the patient (e.g., profile, disease site, stage, etc.), to people (radiation oncologists, radiological physicists, technologists, etc.), and to equipment (diagnostic, planning, treatment, etc.). These different data must be integrated. A comprehensive information management system is essential for efficient storage and retrieval of the enormous amounts of information. A radiation therapy patient information system (RTPIS) has been developed using open source software. PHP and JAVA script was used as the programming languages, MySQL as the database, and HTML and CSF as the design tool. This system utilizes typical web browsing technology using a WAMP5 server. Any user having a unique user ID and password can access this RTPIS. The user ID and password is issued separately to each individual according to the person's job responsibilities and accountability, so that users will be able to only access data that is related to their job responsibilities. With this system authentic users will be able to use a simple web browsing procedure to gain instant access. All types of users in the radiation oncology department should find it user-friendly. The maintenance of the system will not require large human resources or space. The file storage and retrieval process would be be satisfactory, unique, uniform, and easily accessible with adequate data protection. There will be very little possibility of unauthorized handling with this system. There will also be minimal risk of loss or accidental destruction of information.

ESTree db: a Tool for Peach Functional Genomics

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Stella, Alessandra; Milanesi, Luciano; Pozzi, Carlo

2005-01-01

Background The ESTree db represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. Results The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. Conclusion The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig. PMID:16351742

ESTree db: a tool for peach functional genomics.

PubMed

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Stella, Alessandra; Milanesi, Luciano; Pozzi, Carlo

2005-12-01

The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.

Implementation of Simple and Functional Web Applications at the Alaska Volcano Observatory Remote Sensing Group

NASA Astrophysics Data System (ADS)

Skoog, R. A.

2007-12-01

Web pages are ubiquitous and accessible, but when compared to stand-alone applications they are limited in capability. The Alaska Volcano Observatory (AVO) Remote Sensing Group has implemented web pages and supporting server software that provide relatively advanced features to any user able to meet basic requirements. Anyone in the world with access to a modern web browser (such as Mozilla Firefox 1.5 or Internet Explorer 6) and reasonable internet connection can fully use the tools, with no software installation or configuration. This allows faculty, staff and students at AVO to perform many aspects of volcano monitoring from home or the road as easily as from the office. Additionally, AVO collaborators such as the National Weather Service and the Anchorage Volcanic Ash Advisory Center are able to use these web tools to quickly assess volcanic events. Capabilities of this web software include (1) ability to obtain accurate measured remote sensing data values on an semi- quantitative compressed image of a large area, (2) to view any data from a wide time range of data swaths, (3) to view many different satellite remote sensing spectral bands and combinations, to adjust color range thresholds, (4) and to export to KML files which are viewable virtual globes such as Google Earth. The technologies behind this implementation are primarily Javascript, PHP, and MySQL which are free to use and well documented, in addition to Terascan, a commercial software package used to extract data from level-0 data files. These technologies will be presented in conjunction with the techniques used to combine them into the final product used by AVO and its collaborators for operational volcanic monitoring.

Dr. John H. Hopps Jr. Research Scholars Program

DTIC Science & Technology

2014-10-20

Program staff, alumni and existing participants. Over the course of the last five months, SageFox has successfully obtained IRB approval for all...and awards. Progress made in development of the HoppsNet system included design and implementation of a relational database in MySQL , development of

Tropical Cyclone Information System

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Knosp, Brian W.; Vu, Quoc A.; Yi, Chao; Hristova-Veleva, Svetla M.

2009-01-01

The JPL Tropical Cyclone Infor ma tion System (TCIS) is a Web portal (http://tropicalcyclone.jpl.nasa.gov) that provides researchers with an extensive set of observed hurricane parameters together with large-scale and convection resolving model outputs. It provides a comprehensive set of high-resolution satellite (see figure), airborne, and in-situ observations in both image and data formats. Large-scale datasets depict the surrounding environmental parameters such as SST (Sea Surface Temperature) and aerosol loading. Model outputs and analysis tools are provided to evaluate model performance and compare observations from different platforms. The system pertains to the thermodynamic and microphysical structure of the storm, the air-sea interaction processes, and the larger-scale environment as depicted by ocean heat content and the aerosol loading of the environment. Currently, the TCIS is populated with satellite observations of all tropical cyclones observed globally during 2005. There is a plan to extend the database both forward in time till present as well as backward to 1998. The portal is powered by a MySQL database and an Apache/Tomcat Web server on a Linux system. The interactive graphic user interface is provided by Google Map.

Comparison of response times of a mobile-web EHRs system using PHP and JSP languages.

PubMed

De la Torre-Díez, Isabel; Antón-Rodríguez, Míriam; Díaz-Pernas, Francisco Javier; Perozo-Rondón, Freddy José

2012-12-01

Performance evaluation is highly important in the Electronic Health Records (EHRs) system implementation. Response time's measurement can be considered as one manner to make that evaluation. In the e-health field, after the creation of EHRs available through different platforms such as Web and/or mobile, a performance evaluation is necessary. The operation of the system in the right way is essential. In this paper, a comparison of the response times for the MEHRmobile system is presented. The first version uses PHP language with a MySQL database and the second one employs JSP with an eXist database. Both versions have got the same functionalities. In addition to the technological aspects, a significant difference is the way the information is stored. The main goal of this paper is choosing the version which offers better response times. We have created a new benchmark to calculate the response times. Better results have been obtained for the PHP version. Nowadays, this version is being used for specialists from Fundación Intras, Spain.

DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase.

PubMed

Nandy, Suman Kumar; Bhuyan, Rajabrata; Seal, Alpana

2012-01-01

Dehydrogenase enzymes are almost inevitable for metabolic processes. Shortage or malfunctioning of dehydrogenases often leads to several acute diseases like cancers, retinal diseases, diabetes mellitus, Alzheimer, hepatitis B & C etc. With advancement in modern-day research, huge amount of sequential, structural and functional data are generated everyday and widens the gap between structural attributes and its functional understanding. DB Dehydrogenase is an effort to relate the functionalities of dehydrogenase with its structures. It is a completely web-based structural database, covering almost all dehydrogenases [~150 enzyme classes, ~1200 entries from ~160 organisms] whose structures are known. It is created by extracting and integrating various online resources to provide the true and reliable data and implemented by MySQL relational database through user friendly web interfaces using CGI Perl. Flexible search options are there for data extraction and exploration. To summarize, sequence, structure, function of all dehydrogenases in one place along with the necessary option of cross-referencing; this database will be utile for researchers to carry out further work in this field. The database is available for free at http://www.bifku.in/DBD/

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

PubMed

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma.

Monitoring of small laboratory animal experiments by a designated web-based database.

PubMed

Frenzel, T; Grohmann, C; Schumacher, U; Krüll, A

2015-10-01

Multiple-parametric small animal experiments require, by their very nature, a sufficient number of animals which may need to be large to obtain statistically significant results.(1) For this reason database-related systems are required to collect the experimental data as well as to support the later (re-) analysis of the information gained during the experiments. In particular, the monitoring of animal welfare is simplified by the inclusion of warning signals (for instance, loss in body weight >20%). Digital patient charts have been developed for human patients but are usually not able to fulfill the specific needs of animal experimentation. To address this problem a unique web-based monitoring system using standard MySQL, PHP, and nginx has been created. PHP was used to create the HTML-based user interface and outputs in a variety of proprietary file formats, namely portable document format (PDF) or spreadsheet files. This article demonstrates its fundamental features and the easy and secure access it offers to the data from any place using a web browser. This information will help other researchers create their own individual databases in a similar way. The use of QR-codes plays an important role for stress-free use of the database. We demonstrate a way to easily identify all animals and samples and data collected during the experiments. Specific ways to record animal irradiations and chemotherapy applications are shown. This new analysis tool allows the effective and detailed analysis of huge amounts of data collected through small animal experiments. It supports proper statistical evaluation of the data and provides excellent retrievable data storage. © The Author(s) 2015.

ESTuber db: an online database for Tuber borchii EST sequences.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cosentino, Cristian; Stella, Alessandra; Milanesi, Luciano; Viotti, Angelo

2007-03-08

The ESTuber database (http://www.itb.cnr.it/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface. Sequences included in the ESTuber db were clustered and annotated against three databases: the GenBank nr database, the UniProtKB database and a third in-house prepared database of fungi genomic sequences. An algorithm was implemented to infer statistical classification among Gene Ontology categories from the ontology occurrences deduced from the annotation procedure against the UniProtKB database. Ontologies were also deduced from the annotation of more than 130,000 EST sequences from five filamentous fungi, for intra-species comparison purposes. Further analyses were performed on the ESTuber db dataset, including tandem repeats search and comparison of the putative protein dataset inferred from the EST sequences to the PROSITE database for protein patterns identification. All the analyses were performed both on the complete sequence dataset and on the contig consensus sequences generated by the EST assembly procedure. The resulting web site is a resource of data and links related to truffle expressed genes. The Sequence Report and Contig Report pages are the web interface core structures which, together with the Text search utility and the Blast utility, allow easy access to the data stored in the database.

Profile-IQ: Web-based data query system for local health department infrastructure and activities.

PubMed

Shah, Gulzar H; Leep, Carolyn J; Alexander, Dayna

2014-01-01

To demonstrate the use of National Association of County & City Health Officials' Profile-IQ, a Web-based data query system, and how policy makers, researchers, the general public, and public health professionals can use the system to generate descriptive statistics on local health departments. This article is a descriptive account of an important health informatics tool based on information from the project charter for Profile-IQ and the authors' experience and knowledge in design and use of this query system. Profile-IQ is a Web-based data query system that is based on open-source software: MySQL 5.5, Google Web Toolkit 2.2.0, Apache Commons Math library, Google Chart API, and Tomcat 6.0 Web server deployed on an Amazon EC2 server. It supports dynamic queries of National Profile of Local Health Departments data on local health department finances, workforce, and activities. Profile-IQ's customizable queries provide a variety of statistics not available in published reports and support the growing information needs of users who do not wish to work directly with data files for lack of staff skills or time, or to avoid a data use agreement. Profile-IQ also meets the growing demand of public health practitioners and policy makers for data to support quality improvement, community health assessment, and other processes associated with voluntary public health accreditation. It represents a step forward in the recent health informatics movement of data liberation and use of open source information technology solutions to promote public health.

Implementation monitoring temperature, humidity and mositure soil based on wireless sensor network for e-agriculture technology

NASA Astrophysics Data System (ADS)

Sumarudin, A.; Ghozali, A. L.; Hasyim, A.; Effendi, A.

2016-04-01

Indonesian agriculture has great potensial for development. Agriculture a lot yet based on data collection for soil or plant, data soil can use for analys soil fertility. We propose e-agriculture system for monitoring soil. This system can monitoring soil status. Monitoring system based on wireless sensor mote that sensing soil status. Sensor monitoring utilize soil moisture, humidity and temperature. System monitoring design with mote based on microcontroler and xbee connection. Data sensing send to gateway with star topology with one gateway. Gateway utilize with mini personal computer and connect to xbee cordinator mode. On gateway, gateway include apache server for store data based on My-SQL. System web base with YII framework. System done implementation and can show soil status real time. Result the system can connection other mote 40 meters and mote lifetime 7 hours and minimum voltage 7 volt. The system can help famer for monitoring soil and farmer can making decision for treatment soil based on data. It can improve the quality in agricultural production and would decrease the management and farming costs.

BioImaging Database

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

David Nix, Lisa Simirenko

2006-10-25

The Biolmaging Database (BID) is a relational database developed to store the data and meta-data for the 3D gene expression in early Drosophila embryo development on a cellular level. The schema was written to be used with the MySQL DBMS but with minor modifications can be used on any SQL compliant relational DBMS.

EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

PubMed

Montes-Grajales, Diana; Olivero-Verbel, Jesus

2015-01-02

Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. Copyright © 2014. Published by Elsevier Ireland Ltd.

Web-based application on employee performance assessment using exponential comparison method

NASA Astrophysics Data System (ADS)

Maryana, S.; Kurnia, E.; Ruyani, A.

2017-02-01

Employee performance assessment is also called a performance review, performance evaluation, or assessment of employees, is an effort to assess the achievements of staffing performance with the aim to increase productivity of employees and companies. This application helps in the assessment of employee performance using five criteria: Presence, Quality of Work, Quantity of Work, Discipline, and Teamwork. The system uses the Exponential Comparative Method and Weighting Eckenrode. Calculation results using graphs were provided to see the assessment of each employee. Programming language used in this system is written in Notepad++ and MySQL database. The testing result on the system can be concluded that this application is correspond with the design and running properly. The test conducted is structural test, functional test, and validation, sensitivity analysis, and SUMI testing.

Isfahan MISP Dataset

PubMed Central

Kashefpur, Masoud; Kafieh, Rahele; Jorjandi, Sahar; Golmohammadi, Hadis; Khodabande, Zahra; Abbasi, Mohammadreza; Teifuri, Nilufar; Fakharzadeh, Ali Akbar; Kashefpoor, Maryam; Rabbani, Hossein

2017-01-01

An online depository was introduced to share clinical ground truth with the public and provide open access for researchers to evaluate their computer-aided algorithms. PHP was used for web programming and MySQL for database managing. The website was entitled “biosigdata.com.” It was a fast, secure, and easy-to-use online database for medical signals and images. Freely registered users could download the datasets and could also share their own supplementary materials while maintaining their privacies (citation and fee). Commenting was also available for all datasets, and automatic sitemap and semi-automatic SEO indexing have been set for the site. A comprehensive list of available websites for medical datasets is also presented as a Supplementary (http://journalonweb.com/tempaccess/4800.584.JMSS_55_16I3253.pdf). PMID:28487832

Monitoring of IaaS and scientific applications on the Cloud using the Elasticsearch ecosystem

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Guarise, A.; Lusso, S.; Masera, M.; Vallero, S.

2015-05-01

The private Cloud at the Torino INFN computing centre offers IaaS services to different scientific computing applications. The infrastructure is managed with the OpenNebula cloud controller. The main stakeholders of the facility are a grid Tier-2 site for the ALICE collaboration at LHC, an interactive analysis facility for the same experiment and a grid Tier-2 site for the BES-III collaboration, plus an increasing number of other small tenants. Besides keeping track of the usage, the automation of dynamic allocation of resources to tenants requires detailed monitoring and accounting of the resource usage. As a first investigation towards this, we set up a monitoring system to inspect the site activities both in terms of IaaS and applications running on the hosted virtual instances. For this purpose we used the Elasticsearch, Logstash and Kibana stack. In the current implementation, the heterogeneous accounting information is fed to different MySQL databases and sent to Elasticsearch via a custom Logstash plugin. For the IaaS metering, we developed sensors for the OpenNebula API. The IaaS level information gathered through the API is sent to the MySQL database through an ad-hoc developed RESTful web service, which is also used for other accounting purposes. Concerning the application level, we used the Root plugin TProofMonSenderSQL to collect accounting data from the interactive analysis facility. The BES-III virtual instances used to be monitored with Zabbix, as a proof of concept we also retrieve the information contained in the Zabbix database. Each of these three cases is indexed separately in Elasticsearch. We are now starting to consider dismissing the intermediate level provided by the SQL database and evaluating a NoSQL option as a unique central database for all the monitoring information. We setup a set of Kibana dashboards with pre-defined queries in order to monitor the relevant information in each case. In this way we have achieved a uniform monitoring interface for both the IaaS and the scientific applications, mostly leveraging off-the-shelf tools.

Cellular Consequences of Telomere Shortening in Histologically Normal Breast Tissues

DTIC Science & Technology

2013-09-01

using the open source, JAVA -based image analysis software package ImageJ (http://rsb.info.nih.gov/ij/) and a custom designed plugin (“Telometer...Tabulated data were stored in a MySQL (http://www.mysql.com) database and viewed through Microsoft Access (Microsoft Corp.). Statistical Analysis For

The Colima Volcano WebGIS: system acquisition, application and database development in an open-source environment

NASA Astrophysics Data System (ADS)

Manea, M.; Norini, G.; Capra, L.; Manea, V. C.

2009-04-01

The Colima Volcano is currently the most active Mexican volcano. After the 1913 plinian activity the volcano presented several eruptive phases that lasted few years, but since 1991 its activity became more persistent with vulcanian eruptions, lava and dome extrusions. During the last 15 years the volcano suffered several eruptive episodes as in 1991, 1994, 1998-1999, 2001-2003, 2004 and 2005 with the emplacement of pyroclastic flows. During rain seasons lahars are frequent affecting several infrastructures such as bridges and electric towers. Researchers from different institutions (Mexico, USA, Germany, Italy, and Spain) are currently working on several aspects of the volcano, from remote sensing, field data of old and recent deposits, structural framework, monitoring (rain, seismicity, deformation and visual observations) and laboratory experiments (analogue models and numerical simulations). Each investigation is focused to explain a single process, but it is fundamental to visualize the global status of the volcano in order to understand its behavior and to mitigate future hazards. The Colima Volcano WebGIS represents an initiative aimed to collect and store on a systematic basis all the data obtained so far for the volcano and to continuously update the database with new information. The Colima Volcano WebGIS is hosted on the Computational Geodynamics Laboratory web server and it is based entirely on Open Source software. The web pages, written in php/html will extract information from a mysql relational database, which will host the information needed for the MapBender application. There will be two types of intended users: 1) researchers working on the Colima Volcano, interested in this project and collaborating in common projects will be provided with open access to the database and will be able to introduce their own data, results, interpretation or recommendations; 2) general users, interested in accessing information on Colima Volcano will be provided with restricted access and will be able to visualize maps, images, diagrams, and current activity. The website can be visited at: http://www.geociencias.unam.mx/colima

An End-to-End System to Enable Quick, Easy and Inexpensive Deployment of Hydrometeorological Stations

NASA Astrophysics Data System (ADS)

Celicourt, P.; Piasecki, M.

2014-12-01

The high cost of hydro-meteorological data acquisition, communication and publication systems along with limited qualified human resources is considered as the main reason why hydro-meteorological data collection remains a challenge especially in developing countries. Despite significant advances in sensor network technologies which gave birth to open hardware and software, low-cost (less than $50) and low-power (in the order of a few miliWatts) sensor platforms in the last two decades, sensors and sensor network deployment remains a labor-intensive, time consuming, cumbersome, and thus expensive task. These factors give rise for the need to develop a affordable, simple to deploy, scalable and self-organizing end-to-end (from sensor to publication) system suitable for deployment in such countries. The design of the envisioned system will consist of a few Sensed-And-Programmed Arduino-based sensor nodes with low-cost sensors measuring parameters relevant to hydrological processes and a Raspberry Pi micro-computer hosting the in-the-field back-end data management. This latter comprises the Python/Django model of the CUAHSI Observations Data Model (ODM) namely DjangODM backed by a PostgreSQL Database Server. We are also developing a Python-based data processing script which will be paired with the data autoloading capability of Django to populate the DjangODM database with the incoming data. To publish the data, the WOFpy (WaterOneFlow Web Services in Python) developed by the Texas Water Development Board for 'Water Data for Texas' which can produce WaterML web services from a variety of back-end database installations such as SQLite, MySQL, and PostgreSQL will be used. A step further would be the development of an appealing online visualization tool using Python statistics and analytics tools (Scipy, Numpy, Pandas) showing the spatial distribution of variables across an entire watershed as a time variant layer on top of a basemap.

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.

Agentless Cloud-Wide Monitoring of Virtual Disk State

DTIC Science & Technology

2015-10-01

packages include Apache, MySQL , PHP, Ruby on Rails, Java Application Servers, and many others. Figure 2.12 shows the results of a run of the Software...Linux, Apache, MySQL , PHP (LAMP) set of applications. Thus, many file-level update logs will contain the same versions of files repeated across many

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Design of a Web-tool for diagnostic clinical trials handling medical imaging research.

PubMed

Baltasar Sánchez, Alicia; González-Sistal, Angel

2011-04-01

New clinical studies in medicine are based on patients and controls using different imaging diagnostic modalities. Medical information systems are not designed for clinical trials employing clinical imaging. Although commercial software and communication systems focus on storage of image data, they are not suitable for storage and mining of new types of quantitative data. We sought to design a Web-tool to support diagnostic clinical trials involving different experts and hospitals or research centres. The image analysis of this project is based on skeletal X-ray imaging. It involves a computerised image method using quantitative analysis of regions of interest in healthy bone and skeletal metastases. The database is implemented with ASP.NET 3.5 and C# technologies for our Web-based application. For data storage, we chose MySQL v.5.0, one of the most popular open source databases. User logins were necessary, and access to patient data was logged for auditing. For security, all data transmissions were carried over encrypted connections. This Web-tool is available to users scattered at different locations; it allows an efficient organisation and storage of data (case report form) and images and allows each user to know precisely what his task is. The advantages of our Web-tool are as follows: (1) sustainability is guaranteed; (2) network locations for collection of data are secured; (3) all clinical information is stored together with the original images and the results derived from processed images and statistical analysis that enable us to perform retrospective studies; (4) changes are easily incorporated because of the modular architecture; and (5) assessment of trial data collected at different sites is centralised to reduce statistical variance.

Streamlining the Process of Acquiring Secure Open Architecture Software Systems

DTIC Science & Technology

2013-10-08

Microsoft.NET, Enterprise Java Beans, GNU Lesser General Public License (LGPL) libraries, and data communication protocols like the Hypertext Transfer...NetBeans development environments),  customer relationship management (SugarCRM),  database management systems (PostgreSQL, MySQL ),  operating

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Kunst, O.; Cubasch, U.

2014-12-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced by other users-saving CPU time, I/O and disk space. This study presents the different techniques and advantages of such a hybrid evaluation system making use of a Big Data HPC in climate science. website: www-miklip.dkrz.de visitor-login: guest password: miklip

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Ulbrich, Uwe; Cubasch, Ulrich

2015-04-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced by other users-saving CPU time, I/O and disk space. This study presents the different techniques and advantages of such a hybrid evaluation system making use of a Big Data HPC in climate science. website: www-miklip.dkrz.de visitor-login: click on "Guest"

Tobacco-Smoking, Alcohol-Drinking, and Betel-Quid-Chewing Behaviors: Development and Use of a Web-Based Survey System.

PubMed

Hsu, Kuo-Yao; Tsai, Yun-Fang; Huang, Chu-Ching; Yeh, Wen-Ling; Chang, Kai-Ping; Lin, Chen-Chun; Chen, Ching-Yen; Lee, Hsiu-Lan

2018-06-11

Smoking tobacco, drinking alcohol, and chewing betel quid are health-risk behaviors for several diseases, such as cancer, cardiovascular disease, and diabetes, with severe impacts on health. However, health care providers often have limited time to assess clients' behaviors regarding smoking tobacco, drinking alcohol, and chewing betel quid and intervene, if needed. The objective of this study was to develop a Web-based survey system; determine the rates of tobacco-smoking, alcohol-drinking, and betel-quid-chewing behaviors; and estimate the efficiency of the system (time to complete the survey). Patients and their family members or friends were recruited from gastrointestinal medical-surgical, otolaryngology, orthopedics, and rehabilitation clinics or wards at a medical center in northern Taiwan. Data for this descriptive, cross-sectional study were extracted from a large series of research studies. A Web-based survey system was developed using a Linux, Apache, MySQL, PHP stack solution. The Web survey was set up to include four questionnaires: the Chinese-version Fagerstrom Tolerance Questionnaire, the Chinese-version Alcohol Use Disorders Identification Test, the Betel Nut Dependency Scale, and a sociodemographic form with several chronic diseases. After the participants completed the survey, the system automatically calculated their score, categorized their risk level for each behavior, and immediately presented and explained their results. The system also recorded the time each participant took to complete the survey. Of 782 patient participants, 29.6% were addicted to nicotine, 13.3% were hazardous, harmful, or dependent alcohol drinkers, and 1.5% were dependent on chewing betel quid. Of 425 family or friend participants, 19.8% were addicted to nicotine, 5.6% were hazardous, harmful, or dependent alcohol drinkers, and 0.9% were dependent on chewing betel quid. Regarding the mean time to complete the survey, patients took 7.9 minutes (SD 3.0; range 3-20) and family members or friends took 7.7 minutes (SD 2.8; range 3-18). Most of the participants completed the survey within 5-10 minutes. The Web-based survey was easy to self-administer. Health care providers can use this Web-based survey system to save time in assessing these risk behaviors in clinical settings. All smokers had mild-to-severe nicotine addiction, and 5.6%-12.3% of patients and their family members or friends were at risk of alcohol dependence. Considering that these three behaviors, particularly in combination, dramatically increase the risk of esophageal cancer, appropriate and convenient interventions are necessary for preserving public health in Taiwan. ©Kuo-Yao Hsu, Yun-Fang Tsai, Chu-Ching Huang, Wen-Ling Yeh, Kai-Ping Chang, Chen-Chun Lin, Ching-Yen Chen, Hsiu-Lan Lee. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 11.06.2018.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

Lowering the Barrier for Standards-Compliant and Discoverable Hydrological Data Publication

NASA Astrophysics Data System (ADS)

Kadlec, J.

2013-12-01

The growing need for sharing and integration of hydrological and climate data across multiple organizations has resulted in the development of distributed, services-based, standards-compliant hydrological data management and data hosting systems. The problem with these systems is complicated set-up and deployment. Many existing systems assume that the data publisher has remote-desktop access to a locally managed server and experience with computer network setup. For corporate websites, shared web hosting services with limited root access provide an inexpensive, dynamic web presence solution using the Linux, Apache, MySQL and PHP (LAMP) software stack. In this paper, we hypothesize that a webhosting service provides an optimal, low-cost solution for hydrological data hosting. We propose a software architecture of a standards-compliant, lightweight and easy-to-deploy hydrological data management system that can be deployed on the majority of existing shared internet webhosting services. The architecture and design is validated by developing Hydroserver Lite: a PHP and MySQL-based hydrological data hosting package that is fully standards-compliant and compatible with the Consortium of Universities for Advancement of Hydrologic Sciences (CUAHSI) hydrologic information system. It is already being used for management of field data collection by students of the McCall Outdoor Science School in Idaho. For testing, the Hydroserver Lite software has been installed on multiple different free and low-cost webhosting sites including Godaddy, Bluehost and 000webhost. The number of steps required to set-up the server is compared with the number of steps required to set-up other standards-compliant hydrologic data hosting systems including THREDDS, IstSOS and MapServer SOS.

Investigating the Limitations of Advanced Design Methods through Real World Application

DTIC Science & Technology

2016-03-31

36 War Room Laptop Display ( MySQL , JMP 9 Pro, 64-bit Windows) Georgia Tech Secure Collaborative Visualization Environment ( MySQL , JMP 9 Pro...investigate expanding the EA for VC3ATS • Would like to consider both an expansion of the use of current Java -based BPM approach and other potential EA

Evolution of the LBT Telemetry System

NASA Astrophysics Data System (ADS)

Summers, K.; Biddick, C.; De La Peña, M. D.; Summers, D.

2014-05-01

The Large Binocular Telescope (LBT) Telescope Control System (TCS) records about 10GB of telemetry data per night. Additionally, the vibration monitoring system records about 9GB of telemetry data per night. Through 2013, we have amassed over 6TB of Hierarchical Data Format (HDF5) files and almost 9TB in a MySQL database of TCS and vibration data. The LBT telemetry system, in its third major revision since 2004, provides the mechanism to capture and store this data. The telemetry system has evolved from a simple HDF file system with MySQL stream definitions within the TCS, to a separate system using a MySQL database system for the definitions and data, and finally to no database use at all, using HDF5 files.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

PubMed

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

A MySQL Based EPICS Archiver

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

Christopher Slominski

2009-10-01

Archiving a large fraction of the EPICS signals within the Jefferson Lab (JLAB) Accelerator control system is vital for postmortem and real-time analysis of the accelerator performance. This analysis is performed on a daily basis by scientists, operators, engineers, technicians, and software developers. Archiving poses unique challenges due to the magnitude of the control system. A MySQL Archiving system (Mya) was developed to scale to the needs of the control system; currently archiving 58,000 EPICS variables, updating at a rate of 11,000 events per second. In addition to the large collection rate, retrieval of the archived data must also bemore » fast and robust. Archived data retrieval clients obtain data at a rate over 100,000 data points per second. Managing the data in a relational database provides a number of benefits. This paper describes an archiving solution that uses an open source database and standard off the shelf hardware to reach high performance archiving needs. Mya has been in production at Jefferson Lab since February of 2007.« less

Computerized database management system for breast cancer patients.

PubMed

Sim, Kok Swee; Chong, Sze Siang; Tso, Chih Ping; Nia, Mohsen Esmaeili; Chong, Aun Kee; Abbas, Siti Fathimah

2014-01-01

Data analysis based on breast cancer risk factors such as age, race, breastfeeding, hormone replacement therapy, family history, and obesity was conducted on breast cancer patients using a new enhanced computerized database management system. My Structural Query Language (MySQL) is selected as the application for database management system to store the patient data collected from hospitals in Malaysia. An automatic calculation tool is embedded in this system to assist the data analysis. The results are plotted automatically and a user-friendly graphical user interface is developed that can control the MySQL database. Case studies show breast cancer incidence rate is highest among Malay women, followed by Chinese and Indian. The peak age for breast cancer incidence is from 50 to 59 years old. Results suggest that the chance of developing breast cancer is increased in older women, and reduced with breastfeeding practice. The weight status might affect the breast cancer risk differently. Additional studies are needed to confirm these findings.

Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cestaro, Alessandro; Merelli, Ivan; Del Corvo, Marcello; Fontana, Paolo; Milanesi, Luciano; Velasco, Riccardo; Stella, Alessandra

2009-06-29

Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database. The application is available at http://www.itb.cnr.it/ptp/grapemirna/. The program FindMiRNA was used to detect putative microRNA genes in the grape genome. A very high number of predictions was retrieved, calling for validation. Nine parameters were calculated and, based on the grape microRNAs dataset available at miRBase, thresholds were defined and applied to FindMiRNA predictions having targets in gene exons. In the resulting subset, predictions were ranked according to precursor positions and sequence similarity, and to target identity. To further validate FindMiRNA predictions, comparisons to the Arabidopsis genome, to the grape Genoscope genome, and to the grape EST collection were performed. Results were stored in a MySQL database and a web interface was prepared to query the database and retrieve predictions of interest. The GrapeMiRNA database encompasses 5,778 microRNA predictions spanning the whole grape genome. Predictions are integrated with information that can be of use in selection procedures. Tools added in the web interface also allow to inspect predictions according to gene ontology classes and metabolic pathways of targets. The GrapeMiRNA database can be of help in selecting candidate microRNA genes to be validated.

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

PubMed Central

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-01-01

Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects. PMID:18402700

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

PubMed

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists

PubMed Central

Wiley, Laura K.; Sivley, R. Michael; Bush, William S.

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist PMID:23894185

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.

PubMed

Wiley, Laura K; Sivley, R Michael; Bush, William S

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist.

A MYSQL-BASED DATA ARCHIVER: PRELIMINARY RESULTS

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

Matthew Bickley; Christopher Slominski

2008-01-23

Following an evaluation of the archival requirements of the Jefferson Laboratory accelerator’s user community, a prototyping effort was executed to determine if an archiver based on MySQL had sufficient functionality to meet those requirements. This approach was chosen because an archiver based on a relational database enables the development effort to focus on data acquisition and management, letting the database take care of storage, indexing and data consistency. It was clear from the prototype effort that there were no performance impediments to successful implementation of a final system. With our performance concerns addressed, the lab undertook the design and developmentmore » of an operational system. The system is in its operational testing phase now. This paper discusses the archiver system requirements, some of the design choices and their rationale, and presents the acquisition, storage and retrieval performance.« less

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

PubMed Central

Johnson, Z. P.; Eady, R. D.; Ahmad, S. F.; Agravat, S.; Morris, T; Else, J; Lank, S. M.; Wiseman, R. W.; O’Connor, D. H.; Penedo, M. C. T.; Larsen, C. P.

2012-01-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permitsmultiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox onWindows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie. kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo, user name: imsdemo7@gmail.com and password: imsdemo. PMID:22080300

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets.

PubMed

Johnson, Z P; Eady, R D; Ahmad, S F; Agravat, S; Morris, T; Else, J; Lank, S M; Wiseman, R W; O'Connor, D H; Penedo, M C T; Larsen, C P; Kean, L S

2012-04-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO.

PubMed

Ni, Ming; Ye, Fuqiang; Zhu, Juanjuan; Li, Zongwei; Yang, Shuai; Yang, Bite; Han, Lu; Wu, Yongge; Chen, Ying; Li, Fei; Wang, Shengqi; Bo, Xiaochen

2014-12-01

Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users' own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as 'agent→drug→estrogen receptor antagonist→tamoxifen'. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

PubMed

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata

NASA Astrophysics Data System (ADS)

Roy, Anindya; Bhole, R. B.; Nandy, Partha P.; Yadav, R. C.; Pal, Sarbajit; Roy, Amitava

2015-03-01

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A set of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata.

PubMed

Roy, Anindya; Bhole, R B; Nandy, Partha P; Yadav, R C; Pal, Sarbajit; Roy, Amitava

2015-03-01

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A set of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.

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/

Managing hydrological measurements for small and intermediate projects: RObsDat

NASA Astrophysics Data System (ADS)

Reusser, Dominik E.

2014-05-01

Hydrological measurements need good management for the data not to be lost. Multiple, often overlapping files from various loggers with heterogeneous formats need to be merged. Data needs to be validated and cleaned and subsequently converted to the format for the hydrological target application. Preferably, all these steps should be easily tracable. RObsDat is an R package designed to support such data management. It comes with a command line user interface to support hydrologists to enter and adjust their data in a database following the Observations Data Model (ODM) standard by QUASHI. RObsDat helps in the setup of the database within one of the free database engines MySQL, PostgreSQL or SQLite. It imports the controlled water vocabulary from the QUASHI web service and provides a smart interface between the hydrologist and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designes to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. A new development is the use of spacetime objects for subsequent processing.

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.

DAPD: A Knowledgebase for Diabetes Associated Proteins.

PubMed

Gopinath, Krishnasamy; Jayakumararaj, Ramaraj; Karthikeyan, Muthusamy

2015-01-01

Recent advancements in genomics and proteomics provide a solid foundation for understanding the pathogenesis of diabetes. Proteomics of diabetes associated pathways help to identify the most potent target for the management of diabetes. The relevant datasets are scattered in various prominent sources which takes much time to select the therapeutic target for the clinical management of diabetes. However, additional information about target proteins is needed for validation. This lacuna may be resolved by linking diabetes associated genes, pathways and proteins and it will provide a strong base for the treatment and planning management strategies of diabetes. Thus, a web source "Diabetes Associated Proteins Database (DAPD)" has been developed to link the diabetes associated genes, pathways and proteins using PHP, MySQL. The current version of DAPD has been built with proteins associated with different types of diabetes. In addition, DAPD has been linked to external sources to gain the access to more participatory proteins and their pathway network. DAPD will reduce the time and it is expected to pave the way for the discovery of novel anti-diabetic leads using computational drug designing for diabetes management. DAPD is open accessed via following url www.mkarthikeyan.bioinfoau.org/dapd.

Magnetic Fields for All: The GPIPS Community Web-Access Portal

NASA Astrophysics Data System (ADS)

Carveth, Carol; Clemens, D. P.; Pinnick, A.; Pavel, M.; Jameson, K.; Taylor, B.

2007-12-01

The new GPIPS website portal provides community users with an intuitive and powerful interface to query the data products of the Galactic Plane Infrared Polarization Survey. The website, which was built using PHP for the front end and MySQL for the database back end, allows users to issue queries based on galactic or equatorial coordinates, GPIPS-specific identifiers, polarization information, magnitude information, and several other attributes. The returns are presented in HTML tables, with the added option of either downloading or being emailed an ASCII file including the same or more information from the database. Other functionalities of the website include providing details of the status of the Survey (which fields have been observed or are planned to be observed), techniques involved in data collection and analysis, and descriptions of the database contents and names. For this initial launch of the website, users may access the GPIPS polarization point source catalog and the deep coadd photometric point source catalog. Future planned developments include a graphics-based method for querying the database, as well as tools to combine neighboring GPIPS images into larger image files for both polarimetry and photometry. This work is partially supported by NSF grant AST-0607500.

HEROD: a human ethnic and regional specific omics database.

PubMed

Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

2017-10-15

Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Novel Advancements in Internet-Based Real Time Data Technologies

NASA Technical Reports Server (NTRS)

Myers, Gerry; Welch, Clara L. (Technical Monitor)

2002-01-01

AZ Technology has been working with MSFC Ground Systems Department to find ways to make it easier for remote experimenters (RPI's) to monitor their International Space Station (ISS) payloads in real-time from anywhere using standard/familiar devices. AZ Technology was awarded an SBIR Phase I grant to research the technologies behind and advancements of distributing live ISS data across the Internet. That research resulted in a product called "EZStream" which is in use on several ISS-related projects. Although the initial implementation is geared toward ISS, the architecture and lessons learned are applicable to other space-related programs. This paper presents the high-level architecture and components that make up EZStream. A combination of commercial-off-the-shelf (COTS) and custom components were used and their interaction will be discussed. The server is powered by Apache's Jakarta-Tomcat web server/servlet engine. User accounts are maintained in a My SQL database. Both Tomcat and MySQL are Open Source products. When used for ISS, EZStream pulls the live data directly from NASA's Telescience Resource Kit (TReK) API. TReK parses the ISS data stream into individual measurement parameters and performs on-the- fly engineering unit conversion and range checking before passing the data to EZStream for distribution. TReK is provided by NASA at no charge to ISS experimenters. By using a combination of well established Open Source, NASA-supplied. and AZ Technology-developed components, operations using EZStream are robust and economical. Security over the Internet is a major concern on most space programs. This paper describes how EZStream provides for secure connection to and transmission of space- related data over the public Internet. Display pages that show sensitive data can be placed under access control by EZStream. Users are required to login before being allowed to pull up those web pages. To enhance security, the EZStream client/server data transmissions can be encrypted to preclude interception. EZStream was developed to make use of a host of standard platforms and protocols. Each are discussed in detail in this paper. The I3ZStream server is written as Java Servlets. This allows different platforms (i.e. Windows, Unix, Linux . Mac) to host the server portion. The EZStream client component is written in two different flavors: JavaBean and ActiveX. The JavaBean component is used to develop Java Applet displays. The ActiveX component is used for developing ActiveX-based displays. Remote user devices will be covered including web browsers on PC#s and scaled-down displays for PDA's and smart cell phones. As mentioned. the interaction between EZStream (web/data server) and TReK (data source) will be covered as related to ISS. EZStream is being enhanced to receive and parse binary data stream directly. This makes EZStream beneficial to both the ISS International Partners and non-NASA applications (i.e. factory floor monitoring). The options for developing client-side display web pages will be addressed along with the development of tools to allow creation of display web pages by non-programmers.

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.

Subject-enabled analytics model on measurement statistics in health risk expert system for public health informatics.

PubMed

Chung, Chi-Jung; Kuo, Yu-Chen; Hsieh, Yun-Yu; Li, Tsai-Chung; Lin, Cheng-Chieh; Liang, Wen-Miin; Liao, Li-Na; Li, Chia-Ing; Lin, Hsueh-Chun

2017-11-01

This study applied open source technology to establish a subject-enabled analytics model that can enhance measurement statistics of case studies with the public health data in cloud computing. The infrastructure of the proposed model comprises three domains: 1) the health measurement data warehouse (HMDW) for the case study repository, 2) the self-developed modules of online health risk information statistics (HRIStat) for cloud computing, and 3) the prototype of a Web-based process automation system in statistics (PASIS) for the health risk assessment of case studies with subject-enabled evaluation. The system design employed freeware including Java applications, MySQL, and R packages to drive a health risk expert system (HRES). In the design, the HRIStat modules enforce the typical analytics methods for biomedical statistics, and the PASIS interfaces enable process automation of the HRES for cloud computing. The Web-based model supports both modes, step-by-step analysis and auto-computing process, respectively for preliminary evaluation and real time computation. The proposed model was evaluated by computing prior researches in relation to the epidemiological measurement of diseases that were caused by either heavy metal exposures in the environment or clinical complications in hospital. The simulation validity was approved by the commercial statistics software. The model was installed in a stand-alone computer and in a cloud-server workstation to verify computing performance for a data amount of more than 230K sets. Both setups reached efficiency of about 10 5 sets per second. The Web-based PASIS interface can be used for cloud computing, and the HRIStat module can be flexibly expanded with advanced subjects for measurement statistics. The analytics procedure of the HRES prototype is capable of providing assessment criteria prior to estimating the potential risk to public health. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

PubMed Central

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

A publication database for optical long baseline interferometry

NASA Astrophysics Data System (ADS)

Malbet, Fabien; Mella, Guillaume; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

2010-07-01

Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

PubMed

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Chemical and isotopic database of water and gas from hydrothermal systems with an emphasis for the western United States

USGS Publications Warehouse

Mariner, R.H.; Venezky, D.Y.; Hurwitz, S.

2006-01-01

Chemical and isotope data accumulated by two USGS Projects (led by I. Barnes and R. Mariner) over a time period of about 40 years can now be found using a basic web search or through an image search (left). The data are primarily chemical and isotopic analyses of waters (thermal, mineral, or fresh) and associated gas (free and/or dissolved) collected from hot springs, mineral springs, cold springs, geothermal wells, fumaroles, and gas seeps. Additional information is available about the collection methods and analysis procedures.The chemical and isotope data are stored in a MySQL database and accessed using PHP from a basic search form below. Data can also be accessed using an Open Source GIS called WorldKit by clicking on the image to the left. Additional information is available about WorldKit including the files used to set up the site.

An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.

PubMed

Sakurai, Nozomu; Ara, Takeshi; Kanaya, Shigehiko; Nakamura, Yukiko; Iijima, Yoko; Enomoto, Mitsuo; Motegi, Takeshi; Aoki, Koh; Suzuki, Hideyuki; Shibata, Daisuke

2013-01-15

High-accuracy mass values detected by high-resolution mass spectrometry analysis enable prediction of elemental compositions, and thus are used for metabolite annotations in metabolomic studies. Here, we report an application of a relational database to significantly improve the rate of elemental composition predictions. By searching a database of pre-calculated elemental compositions with fixed kinds and numbers of atoms, the approach eliminates redundant evaluations of the same formula that occur in repeated calculations with other tools. When our approach is compared with HR2, which is one of the fastest tools available, our database search times were at least 109 times shorter than those of HR2. When a solid-state drive (SSD) was applied, the search time was 488 times shorter at 5 ppm mass tolerance and 1833 times at 0.1 ppm. Even if the search by HR2 was performed with 8 threads in a high-spec Windows 7 PC, the database search times were at least 26 and 115 times shorter without and with the SSD. These improvements were enhanced in a low spec Windows XP PC. We constructed a web service 'MFSearcher' to query the database in a RESTful manner. Available for free at http://webs2.kazusa.or.jp/mfsearcher. The web service is implemented in Java, MySQL, Apache and Tomcat, with all major browsers supported. sakurai@kazusa.or.jp Supplementary data are available at Bioinformatics online.

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data

PubMed Central

Jupiter, Daniel; Chen, Hailin; VanBuren, Vincent

2009-01-01

Background Although expression microarrays have become a standard tool used by biologists, analysis of data produced by microarray experiments may still present challenges. Comparison of data from different platforms, organisms, and labs may involve complicated data processing, and inferring relationships between genes remains difficult. Results STARNET 2 is a new web-based tool that allows post hoc visual analysis of correlations that are derived from expression microarray data. STARNET 2 facilitates user discovery of putative gene regulatory networks in a variety of species (human, rat, mouse, chicken, zebrafish, Drosophila, C. elegans, S. cerevisiae, Arabidopsis and rice) by graphing networks of genes that are closely co-expressed across a large heterogeneous set of preselected microarray experiments. For each of the represented organisms, raw microarray data were retrieved from NCBI's Gene Expression Omnibus for a selected Affymetrix platform. All pairwise Pearson correlation coefficients were computed for expression profiles measured on each platform, respectively. These precompiled results were stored in a MySQL database, and supplemented by additional data retrieved from NCBI. A web-based tool allows user-specified queries of the database, centered at a gene of interest. The result of a query includes graphs of correlation networks, graphs of known interactions involving genes and gene products that are present in the correlation networks, and initial statistical analyses. Two analyses may be performed in parallel to compare networks, which is facilitated by the new HEATSEEKER module. Conclusion STARNET 2 is a useful tool for developing new hypotheses about regulatory relationships between genes and gene products, and has coverage for 10 species. Interpretation of the correlation networks is supported with a database of previously documented interactions, a test for enrichment of Gene Ontology terms, and heat maps of correlation distances that may be used to compare two networks. The list of genes in a STARNET network may be useful in developing a list of candidate genes to use for the inference of causal networks. The tool is freely available at , and does not require user registration. PMID:19828039

A database for coconut crop improvement.

PubMed

Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

2005-12-08

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. http://www.bioinfcpcri.org.

Architecture for biomedical multimedia information delivery on the World Wide Web

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

1997-10-01

Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

PubMed

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

PubMed Central

2011-01-01

Background Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Results Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Methods Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Conclusions Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. PMID:21995939

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata

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

Roy, Anindya, E-mail: r-ani@vecc.gov.in; Bhole, R. B.; Nandy, Partha P.

2015-03-15

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A setmore » of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.« less

Joint Battlespace Infosphere: Information Management Within a C2 Enterprise

DTIC Science & Technology

2005-06-01

using. In version 1.2, we support both MySQL and Oracle as underlying implementations where the XML metadata schema is mapped into relational tables in...Identity Servers, Role-Based Access Control, and Policy Representation – Databases: Oracle , MySQL , TigerLogic, Berkeley XML DB 15 Instrumentation Services...converted to SQL for execution. Invocations are then forwarded to the appropriate underlying IOR core components that have the responsibility of issuing

Factors Leading to Effectiveness and Satisfaction in Civil Engineer Information Systems

DTIC Science & Technology

2008-03-01

recently acquired MySQL in 2008 shortly after Oracle failed to acquire MySQL in 2007. For more information on policy implications concerning the use...individual level serves as the pertinent outcome variable and is used to evaluate and compare information systems in this study. Researchers have found...interim work information management system used by the Civil Engineer Operations Flight. The functions served by this system date back to the late

Large-scale Graph Computation on Just a PC

DTIC Science & Technology

2014-05-01

edges for several vertices simultaneously). We compared the performance of GraphChi-DB to Neo4j using their Java API (we discuss MySQL comparison in the...75 4.7.6 Comparison to RDBMS ( MySQL ) . . . . . . . . . . . . . . . . . . . . . 75 4.7.7 Summary of the...Windows method, GraphChi. The C++ implementation has circa 8,000 lines of code. We have also de- veloped a Java -version of GraphChi, but it does not

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

PubMed

Wong, Wing Chung; Kim, Dewey; Carter, Hannah; Diekhans, Mark; Ryan, Michael C; Karchin, Rachel

2011-08-01

Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

ToTem: a tool for variant calling pipeline optimization.

PubMed

Tom, Nikola; Tom, Ondrej; Malcikova, Jitka; Pavlova, Sarka; Kubesova, Blanka; Rausch, Tobias; Kolarik, Miroslav; Benes, Vladimir; Bystry, Vojtech; Pospisilova, Sarka

2018-06-26

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. ToTem is a tool for automated pipeline optimization which is freely available as a web application at  https://totem.software .

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

PubMed Central

2010-01-01

Background Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. Results In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. Conclusions CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu. PMID:20946609

Design and implementation of the first nationwide, web-based Chinese Renal Data System (CNRDS)

PubMed Central

2012-01-01

Background In April 2010, with an endorsement from the Ministry of Health of the People's Republic of China, the Chinese Society of Nephrology launched the first nationwide, web-based prospective renal data registration platform, the Chinese Renal Data System (CNRDS), to collect structured demographic, clinical, and laboratory data for dialysis cases, as well as to establish a kidney disease database for researchers and policy makers. Methods The CNRDS program uses information technology to facilitate healthcare professionals to create a blood purification registry and to deliver an evidence-based care and education protocol tailored to chronic kidney disease, as well as online forum for communication between nephrologists. The online portal https://www.cnrds.net is implemented as a Java web application using an Apache Tomcat web server and a MySQL database. All data are stored in a central databank to establish a Chinese renal database for research and publication purposes. Results Currently, over 270,000 clinical cases, including general patient information, diagnostics, therapies, medications, and laboratory tests, have been registered in CNRDS by 3,669 healthcare institutions qualified for hemodialysis therapy. At the 2011 annual blood purification forum of the Chinese Society of Nephrology, the CNRDS 2010 annual report was reviewed and accepted by the society members and government representatives. Conclusions CNRDS is the first national, web-based application for collecting and managing electronic medical records of patients with dialysis in China. It provides both an easily accessible platform for nephrologists to store and organize their patient data and acts as a communication platform among participating doctors. Moreover, it is the largest database for treatment and patient care of end-stage renal disease (ESRD) patients in China, which will be beneficial for scientific research and epidemiological investigations aimed at improving the quality of life of such patients. Furthermore, it is a model nationwide disease registry, which could potentially be used for other diseases. PMID:22369692

Design and implementation of the first nationwide, web-based Chinese Renal Data System (CNRDS).

PubMed

Xie, Fengbo; Zhang, Dong; Wu, Jinzhao; Zhang, Yunfeng; Yang, Qing; Sun, Xuefeng; Cheng, Jing; Chen, Xiangmei

2012-02-28

In April 2010, with an endorsement from the Ministry of Health of the People's Republic of China, the Chinese Society of Nephrology launched the first nationwide, web-based prospective renal data registration platform, the Chinese Renal Data System (CNRDS), to collect structured demographic, clinical, and laboratory data for dialysis cases, as well as to establish a kidney disease database for researchers and policy makers. The CNRDS program uses information technology to facilitate healthcare professionals to create a blood purification registry and to deliver an evidence-based care and education protocol tailored to chronic kidney disease, as well as online forum for communication between nephrologists. The online portal https://www.cnrds.net is implemented as a Java web application using an Apache Tomcat web server and a MySQL database. All data are stored in a central databank to establish a Chinese renal database for research and publication purposes. Currently, over 270,000 clinical cases, including general patient information, diagnostics, therapies, medications, and laboratory tests, have been registered in CNRDS by 3,669 healthcare institutions qualified for hemodialysis therapy. At the 2011 annual blood purification forum of the Chinese Society of Nephrology, the CNRDS 2010 annual report was reviewed and accepted by the society members and government representatives. CNRDS is the first national, web-based application for collecting and managing electronic medical records of patients with dialysis in China. It provides both an easily accessible platform for nephrologists to store and organize their patient data and acts as a communication platform among participating doctors. Moreover, it is the largest database for treatment and patient care of end-stage renal disease (ESRD) patients in China, which will be beneficial for scientific research and epidemiological investigations aimed at improving the quality of life of such patients. Furthermore, it is a model nationwide disease registry, which could potentially be used for other diseases.

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

PubMed

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu.

MicroRNA Gene Regulatory Networks in Peripheral Nerve Sheath Tumors

DTIC Science & Technology

2013-09-01

3.0 hierarchical clustering of both the X and the Y-axis using Centroid linkage. The resulting clustered matrixes were visualized using Java Treeview...To score potential ceRNA interactions, the 54979 human interactions were loaded into a mySQL database and when the user selects a given mRNA all...on the fly using PHP interactions with mySQL in a similar fashion as previously described in our publicly available databases such as sarcoma

Quantifying Uncertainty in Expert Judgment: Initial Results

DTIC Science & Technology

2013-03-01

lines of source code were added in . ---------- C++ = 32%; JavaScript = 29%; XML = 15%; C = 7%; CSS = 7%; Java = 5%; Oth- er = 5% LOC = 927,266...much total effort in person years has been spent on this project? CMU/SEI-2013-TR-001 | 33 5 MySQL , the most popular Open Source SQL...as MySQL , Oracle, PostgreSQL, MS SQL Server, ODBC, or Interbase. Features include email reminders, iCal/vCal import/export, re- mote subscriptions

A database for coconut crop improvement

PubMed Central

Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

2005-01-01

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. Availability http://www.bioinfcpcri.org PMID:17597858

Towards Monitoring-as-a-service for Scientific Computing Cloud applications using the ElasticSearch ecosystem

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Guarise, A.; Lusso, S.; Masera, M.; Vallero, S.

2015-12-01

The INFN computing centre in Torino hosts a private Cloud, which is managed with the OpenNebula cloud controller. The infrastructure offers Infrastructure-as-a-Service (IaaS) and Platform-as-a-Service (PaaS) services to different scientific computing applications. The main stakeholders of the facility are a grid Tier-2 site for the ALICE collaboration at LHC, an interactive analysis facility for the same experiment and a grid Tier-2 site for the BESIII collaboration, plus an increasing number of other small tenants. The dynamic allocation of resources to tenants is partially automated. This feature requires detailed monitoring and accounting of the resource usage. We set up a monitoring framework to inspect the site activities both in terms of IaaS and applications running on the hosted virtual instances. For this purpose we used the ElasticSearch, Logstash and Kibana (ELK) stack. The infrastructure relies on a MySQL database back-end for data preservation and to ensure flexibility to choose a different monitoring solution if needed. The heterogeneous accounting information is transferred from the database to the ElasticSearch engine via a custom Logstash plugin. Each use-case is indexed separately in ElasticSearch and we setup a set of Kibana dashboards with pre-defined queries in order to monitor the relevant information in each case. For the IaaS metering, we developed sensors for the OpenNebula API. The IaaS level information gathered through the API is sent to the MySQL database through an ad-hoc developed RESTful web service. Moreover, we have developed a billing system for our private Cloud, which relies on the RabbitMQ message queue for asynchronous communication to the database and on the ELK stack for its graphical interface. The Italian Grid accounting framework is also migrating to a similar set-up. Concerning the application level, we used the Root plugin TProofMonSenderSQL to collect accounting data from the interactive analysis facility. The BESIII virtual instances used to be monitored with Zabbix, as a proof of concept we also retrieve the information contained in the Zabbix database. In this way we have achieved a uniform monitoring interface for both the IaaS and the scientific applications, mostly leveraging off-the-shelf tools. At present, we are working to define a model for monitoring-as-a-service, based on the tools described above, which the Cloud tenants can easily configure to suit their specific needs.

Provenance Store Evaluation

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

Paulson, Patrick R.; Gibson, Tara D.; Schuchardt, Karen L.

2008-03-01

Requirements for the provenance store and access API are developed. Existing RDF stores and APIs are evaluated against the requirements and performance benchmarks. The team’s conclusion is to use MySQL as a database backend, with a possible move to Oracle in the near-term future. Both Jena and Sesame’s APIs will be supported, but new code will use the Jena API

Earthquake forecasting studies using radon time series data in Taiwan

NASA Astrophysics Data System (ADS)

Walia, Vivek; Kumar, Arvind; Fu, Ching-Chou; Lin, Shih-Jung; Chou, Kuang-Wu; Wen, Kuo-Liang; Chen, Cheng-Hong

2017-04-01

For few decades, growing number of studies have shown usefulness of data in the field of seismogeochemistry interpreted as geochemical precursory signals for impending earthquakes and radon is idendified to be as one of the most reliable geochemical precursor. Radon is recognized as short-term precursor and is being monitored in many countries. This study is aimed at developing an effective earthquake forecasting system by inspecting long term radon time series data. The data is obtained from a network of radon monitoring stations eastblished along different faults of Taiwan. The continuous time series radon data for earthquake studies have been recorded and some significant variations associated with strong earthquakes have been observed. The data is also examined to evaluate earthquake precursory signals against environmental factors. An automated real-time database operating system has been developed recently to improve the data processing for earthquake precursory studies. In addition, the study is aimed at the appraisal and filtrations of these environmental parameters, in order to create a real-time database that helps our earthquake precursory study. In recent years, automatic operating real-time database has been developed using R, an open source programming language, to carry out statistical computation on the data. To integrate our data with our working procedure, we use the popular and famous open source web application solution, AMP (Apache, MySQL, and PHP), creating a website that could effectively show and help us manage the real-time database.

Harmonize Pipeline and Archiving Aystem: PESSTO@IA2 Use Case

NASA Astrophysics Data System (ADS)

Smareglia, R.; Knapic, C.; Molinaro, M.; Young, D.; Valenti, S.

2013-10-01

Italian Astronomical Archives Center (IA2) is a research infrastructure project that aims at coordinating different national and international initiatives to improve the quality of astrophysical data services. IA2 is now also involved in the PESSTO (Public ESO Spectroscopic Survey of Transient Objects) collaboration, developing a complete archiving system to store calibrated post processed data (including sensitive intermediate products), a user interface to access private data and Virtual Observatory (VO) compliant web services to access public fast reduction data via VO tools. The archive system shall rely on the PESSTO Marshall to provide file data and its associated metadata output by the PESSTO data-reduction pipeline. To harmonize the object repository, data handling and archiving system, new tools are under development. These systems must have a strong cross-interaction without increasing the complexities of any single task, in order to improve the performances of the whole system and must have a sturdy logic in order to perform all operations in coordination with the other PESSTO tools. MySQL Replication technology and triggers are used for the synchronization of new data in an efficient, fault tolerant manner. A general purpose library is under development to manage data starting from raw observations to final calibrated ones, open to the overriding of different sources, formats, management fields, storage and publication policies. Configurations for all the systems are stored in a dedicated schema (no configuration files), but can be easily updated by a planned Archiving System Configuration Interface (ASCI).

Telemedicine: Development of a distance care system for pre-dialysis chronic kidney disease patients.

PubMed

Fernandes, Natália Maria da Silva; Bastos, Marcus Gomes; Oliveira, Nivalda A C de; Costa, Alex do Vale; Bernardino, Heder Soares

2015-01-01

The focus in the treatment of CKD is to prevent its progression through optimal medical control. The large number of patients with CKD has pressed nephrologists to assess more patients into ever-smaller periods of consultation. The use of light technologies as a promising form of health care. The internet offers the opportunity to manipulate the doctor in his professional contact with the user. To develop a web system to attend the patients with CKD not on dialysis and clinically stable stages at distance. Developed a system using the Java language, MySQL database and PrimeFaces framework; available on a Glassfish application server. The initial access is performed by the nephrologist, which registers the patients with their personal information and access data. After being registered, the patient (or family doctor) can enter the data of your query and these will be following, passed on to the nephrologist for evaluation. The form with the data of interest is pre-determined, but there is possibility to add free-form information. The system enables, in addition, there is exchange of messages between doctors and patients. In addition, users receive messages via e-mail alerting them of their duties. Confidentiality is guaranteed by individual passwords for doctors and patients. This tool will enable to increase the coverage area of nephrologists, reduce costs and bring the patient to the primary care physician, using the Family Health Program as an interface between the patient and the nephrology secondary care.

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.

An expression database for roots of the model legume Medicago truncatula under salt stress

PubMed Central

2009-01-01

Background Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. Description The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. Conclusion MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/. PMID:19906315

An expression database for roots of the model legume Medicago truncatula under salt stress.

PubMed

Li, Daofeng; Su, Zhen; Dong, Jiangli; Wang, Tao

2009-11-11

Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.

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.

Workstation Analytics in Distributed Warfighting Experimentation: Results from Coalition Attack Guidance Experiment 3A

DTIC Science & Technology

2014-06-01

central location. Each of the SQLite databases are converted and stored in one MySQL database and the pcap files are parsed to extract call information...from the specific communications applications used during the experiment. This extracted data is then stored in the same MySQL database. With all...rhythm of the event. Figure 3 demonstrates the application usage over the course of the experiment for the EXDIR. As seen, the EXDIR spent the majority

From design to implementation--the Joint Asia Diabetes Evaluation (JADE) program: a descriptive report of an electronic web-based diabetes management program.

PubMed

Ko, Gary T; So, Wing-Yee; Tong, Peter C; Le Coguiec, Francois; Kerr, Debborah; Lyubomirsky, Greg; Tamesis, Beaver; Wolthers, Troels; Nan, Jennifer; Chan, Juliana

2010-05-13

The Joint Asia Diabetes Evaluation (JADE) Program is a web-based program incorporating a comprehensive risk engine, care protocols, and clinical decision support to improve ambulatory diabetes care. The JADE Program uses information technology to facilitate healthcare professionals to create a diabetes registry and to deliver an evidence-based care and education protocol tailored to patients' risk profiles. With written informed consent from participating patients and care providers, all data are anonymized and stored in a databank to establish an Asian Diabetes Database for research and publication purpose. The JADE electronic portal (e-portal: http://www.jade-adf.org) is implemented as a Java application using the Apache web server, the mySQL database and the Cocoon framework. The JADE e-portal comprises a risk engine which predicts 5-year probability of major clinical events based on parameters collected during an annual comprehensive assessment. Based on this risk stratification, the JADE e-portal recommends a care protocol tailored to these risk levels with decision support triggered by various risk factors. Apart from establishing a registry for quality assurance and data tracking, the JADE e-portal also displays trends of risk factor control at each visit to promote doctor-patient dialogues and to empower both parties to make informed decisions. The JADE Program is a prototype using information technology to facilitate implementation of a comprehensive care model, as recommended by the International Diabetes Federation. It also enables health care teams to record, manage, track and analyze the clinical course and outcomes of people with diabetes.

Automated data processing architecture for the Gemini Planet Imager Exoplanet Survey

NASA Astrophysics Data System (ADS)

Wang, Jason J.; Perrin, Marshall D.; Savransky, Dmitry; Arriaga, Pauline; Chilcote, Jeffrey K.; De Rosa, Robert J.; Millar-Blanchaer, Maxwell A.; Marois, Christian; Rameau, Julien; Wolff, Schuyler G.; Shapiro, Jacob; Ruffio, Jean-Baptiste; Maire, Jérôme; Marchis, Franck; Graham, James R.; Macintosh, Bruce; Ammons, S. Mark; Bailey, Vanessa P.; Barman, Travis S.; Bruzzone, Sebastian; Bulger, Joanna; Cotten, Tara; Doyon, René; Duchêne, Gaspard; Fitzgerald, Michael P.; Follette, Katherine B.; Goodsell, Stephen; Greenbaum, Alexandra Z.; Hibon, Pascale; Hung, Li-Wei; Ingraham, Patrick; Kalas, Paul; Konopacky, Quinn M.; Larkin, James E.; Marley, Mark S.; Metchev, Stanimir; Nielsen, Eric L.; Oppenheimer, Rebecca; Palmer, David W.; Patience, Jennifer; Poyneer, Lisa A.; Pueyo, Laurent; Rajan, Abhijith; Rantakyrö, Fredrik T.; Schneider, Adam C.; Sivaramakrishnan, Anand; Song, Inseok; Soummer, Remi; Thomas, Sandrine; Wallace, J. Kent; Ward-Duong, Kimberly; Wiktorowicz, Sloane J.

2018-01-01

The Gemini Planet Imager Exoplanet Survey (GPIES) is a multiyear direct imaging survey of 600 stars to discover and characterize young Jovian exoplanets and their environments. We have developed an automated data architecture to process and index all data related to the survey uniformly. An automated and flexible data processing framework, which we term the Data Cruncher, combines multiple data reduction pipelines (DRPs) together to process all spectroscopic, polarimetric, and calibration data taken with GPIES. With no human intervention, fully reduced and calibrated data products are available less than an hour after the data are taken to expedite follow up on potential objects of interest. The Data Cruncher can run on a supercomputer to reprocess all GPIES data in a single day as improvements are made to our DRPs. A backend MySQL database indexes all files, which are synced to the cloud, and a front-end web server allows for easy browsing of all files associated with GPIES. To help observers, quicklook displays show reduced data as they are processed in real time, and chatbots on Slack post observing information as well as reduced data products. Together, the GPIES automated data processing architecture reduces our workload, provides real-time data reduction, optimizes our observing strategy, and maintains a homogeneously reduced dataset to study planet occurrence and instrument performance.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

PubMed Central

Köhler, Sebastian; Doelken, Sandra C.; Mungall, Christopher J.; Bauer, Sebastian; Firth, Helen V.; Bailleul-Forestier, Isabelle; Black, Graeme C. M.; Brown, Danielle L.; Brudno, Michael; Campbell, Jennifer; FitzPatrick, David R.; Eppig, Janan T.; Jackson, Andrew P.; Freson, Kathleen; Girdea, Marta; Helbig, Ingo; Hurst, Jane A.; Jähn, Johanna; Jackson, Laird G.; Kelly, Anne M.; Ledbetter, David H.; Mansour, Sahar; Martin, Christa L.; Moss, Celia; Mumford, Andrew; Ouwehand, Willem H.; Park, Soo-Mi; Riggs, Erin Rooney; Scott, Richard H.; Sisodiya, Sanjay; Vooren, Steven Van; Wapner, Ronald J.; Wilkie, Andrew O. M.; Wright, Caroline F.; Vulto-van Silfhout, Anneke T.; de Leeuw, Nicole; de Vries, Bert B. A.; Washingthon, Nicole L.; Smith, Cynthia L.; Westerfield, Monte; Schofield, Paul; Ruef, Barbara J.; Gkoutos, Georgios V.; Haendel, Melissa; Smedley, Damian; Lewis, Suzanna E.; Robinson, Peter N.

2014-01-01

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. PMID:24217912

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

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

PubMed Central

Carter, Hannah; Diekhans, Mark; Ryan, Michael C.; Karchin, Rachel

2011-01-01

Summary: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. Availability and Implementation: MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM. Contact: karchin@jhu.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21685053

SAMMD: Staphylococcus aureus microarray meta-database.

PubMed

Nagarajan, Vijayaraj; Elasri, Mohamed O

2007-10-02

Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes.

SAMMD: Staphylococcus aureus Microarray Meta-Database

PubMed Central

Nagarajan, Vijayaraj; Elasri, Mohamed O

2007-01-01

Background Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles. Description SAMMD is a relational database that uses MySQL as the back end and PHP/JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License (GPL). Conclusion SAMMD is hosted and available at . Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes. PMID:17910768

Implementation of an interactive database interface utilizing HTML, PHP, JavaScript, and MySQL in support of water quality assessments in the Northeastern North Carolina Pasquotank Watershed

NASA Astrophysics Data System (ADS)

Guion, A., Jr.; Hodgkins, H.

2015-12-01

The Center of Excellence in Remote Sensing Education and Research (CERSER) has implemented three research projects during the summer Research Experience for Undergraduates (REU) program gathering water quality data for local waterways. The data has been compiled manually utilizing pen and paper and then entered into a spreadsheet. With the spread of electronic devices capable of interacting with databases, the development of an electronic method of entering and manipulating the water quality data was pursued during this project. This project focused on the development of an interactive database to gather, display, and analyze data collected from local waterways. The database and entry form was built in MySQL on a PHP server allowing participants to enter data from anywhere Internet access is available. This project then researched applying this data to the Google Maps site to provide labeling and information to users. The NIA server at http://nia.ecsu.edu is used to host the application for download and for storage of the databases. Water Quality Database Team members included the authors plus Derek Morris Jr., Kathryne Burton and Mr. Jeff Wood as mentor.

A high-speed drug interaction search system for ease of use in the clinical environment.

PubMed

Takada, Masahiro; Inada, Hiroshi; Nakazawa, Kazuo; Tani, Shoko; Iwata, Michiaki; Sugimoto, Yoshihisa; Nagata, Satoru

2012-12-01

With the advancement of pharmaceutical development, drug interactions have become increasingly complex. As a result, a computer-based drug interaction search system is required to organize the whole of drug interaction data. To overcome problems faced with the existing systems, we developed a drug interaction search system using a hash table, which offers higher processing speeds and easier maintenance operations compared with relational databases (RDB). In order to compare the performance of our system and MySQL RDB in terms of search speed, drug interaction searches were repeated for all 45 possible combinations of two out of a group of 10 drugs for two cases: 5,604 and 56,040 drug interaction data. As the principal result, our system was able to process the search approximately 19 times faster than the system using the MySQL RDB. Our system also has several other merits such as that drug interaction data can be created in comma-separated value (CSV) format, thereby facilitating data maintenance. Although our system uses the well-known method of a hash table, it is expected to resolve problems common to existing systems and to be an effective system that enables the safe management of drugs.

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.

PubMed

McKain, Michael R; Hartsock, Ryan H; Wohl, Molly M; Kellogg, Elizabeth A

2017-01-01

Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/ It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. mrmckain@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Making generic tutorials content specific: recycling evidence-based practice (EBP) tutorials for two disciplines.

PubMed

Jeffery, Keven M; Maggio, Lauren; Blanchard, Mary

2009-01-01

Librarians at the Boston University Medical Center constructed two interactive online tutorials, "Introduction to EBM" and "Formulating a Clinical Question (PICO)," for a Family Medicine Clerkship and then quickly repurposed the existing tutorials to support an Evidence-based Dentistry course. Adobe's ColdFusion software was used to populate the tutorials with course-specific content based on the URL used to enter each tutorial, and a MySQL database was used to collect student input. Student responses were viewable immediately by course faculty on a password-protected Web site. The tutorials ensured that all students received the same baseline training and allowed librarians to tailor a subsequent library skills workshop to student tutorial answers. The tutorials were well-received by the medical and dental schools and have been added to mandatory first-year Evidence-based Medicine (EBM) and Evidence-based Dentistry (EBD) courses, meaning that every medical and dental student at BUMC will be expected to complete these tutorials.

Online Meta-data Collection and Monitoring Framework for the STAR Experiment at RHIC

NASA Astrophysics Data System (ADS)

Arkhipkin, D.; Lauret, J.; Betts, W.; Van Buren, G.

2012-12-01

The STAR Experiment further exploits scalable message-oriented model principles to achieve a high level of control over online data streams. In this paper we present an AMQP-powered Message Interface and Reliable Architecture framework (MIRA), which allows STAR to orchestrate the activities of Meta-data Collection, Monitoring, Online QA and several Run-Time and Data Acquisition system components in a very efficient manner. The very nature of the reliable message bus suggests parallel usage of multiple independent storage mechanisms for our meta-data. We describe our experience with a robust data-taking setup employing MySQL- and HyperTable-based archivers for meta-data processing. In addition, MIRA has an AJAX-enabled web GUI, which allows real-time visualisation of online process flow and detector subsystem states, and doubles as a sophisticated alarm system when combined with complex event processing engines like Esper, Borealis or Cayuga. The performance data and our planned path forward are based on our experience during the 2011-2012 running of STAR.

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data.

PubMed

Rosenfeld, Aaron M; Meng, Wenzhao; Luning Prak, Eline T; Hershberg, Uri

2017-01-15

As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: Uh25@drexel.eduSupplementary 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.

Gramene database in 2010: updates and extensions.

PubMed

Youens-Clark, Ken; Buckler, Ed; Casstevens, Terry; Chen, Charles; Declerck, Genevieve; Derwent, Paul; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul; Karthikeyan, A S; Lu, Jerry; McCouch, Susan R; Ren, Liya; Spooner, William; Stein, Joshua C; Thomason, Jim; Wei, Sharon; Ware, Doreen

2011-01-01

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

CGDSNPdb: a database resource for error-checked and imputed mouse SNPs.

PubMed

Hutchins, Lucie N; Ding, Yueming; Szatkiewicz, Jin P; Von Smith, Randy; Yang, Hyuna; de Villena, Fernando Pardo-Manuel; Churchill, Gary A; Graber, Joel H

2010-07-06

The Center for Genome Dynamics Single Nucleotide Polymorphism Database (CGDSNPdb) is an open-source value-added database with more than nine million mouse single nucleotide polymorphisms (SNPs), drawn from multiple sources, with genotypes assigned to multiple inbred strains of laboratory mice. All SNPs are checked for accuracy and annotated for properties specific to the SNP as well as those implied by changes to overlapping protein-coding genes. CGDSNPdb serves as the primary interface to two unique data sets, the 'imputed genotype resource' in which a Hidden Markov Model was used to assess local haplotypes and the most probable base assignment at several million genomic loci in tens of strains of mice, and the Affymetrix Mouse Diversity Genotyping Array, a high density microarray with over 600,000 SNPs and over 900,000 invariant genomic probes. CGDSNPdb is accessible online through either a web-based query tool or a MySQL public login. Database URL: http://cgd.jax.org/cgdsnpdb/

METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters.

PubMed

Geffers, Lars; Tetzlaff, Benjamin; Cui, Xiao; Yan, Jun; Eichele, Gregor

2013-01-01

METscout (http://metscout.mpg.de) brings together metabolism and gene expression landscapes. It is a MySQL relational database linking biochemical pathway information with 3D patterns of gene expression determined by robotic in situ hybridization in the E14.5 mouse embryo. The sites of expression of ∼1500 metabolic enzymes and of ∼350 solute carriers (SLCs) were included and are accessible as single cell resolution images and in the form of semi-quantitative image abstractions. METscout provides several graphical web-interfaces allowing navigation through complex anatomical and metabolic information. Specifically, the database shows where in the organism each of the many metabolic reactions take place and where SLCs transport metabolites. To link enzymatic reactions and transport, the KEGG metabolic reaction network was extended to include metabolite transport. This network in conjunction with spatial expression pattern of the network genes allows for a tracing of metabolic reactions and transport processes across the entire body of the embryo.

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

PubMed

Auerbach, Raymond K; Chen, Bin; Butte, Atul J

2013-08-01

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

Easily configured real-time CPOE Pick Off Tool supporting focused clinical research and quality improvement.

PubMed

Rosenbaum, Benjamin P; Silkin, Nikolay; Miller, Randolph A

2014-01-01

Real-time alerting systems typically warn providers about abnormal laboratory results or medication interactions. For more complex tasks, institutions create site-wide 'data warehouses' to support quality audits and longitudinal research. Sophisticated systems like i2b2 or Stanford's STRIDE utilize data warehouses to identify cohorts for research and quality monitoring. However, substantial resources are required to install and maintain such systems. For more modest goals, an organization desiring merely to identify patients with 'isolation' orders, or to determine patients' eligibility for clinical trials, may adopt a simpler, limited approach based on processing the output of one clinical system, and not a data warehouse. We describe a limited, order-entry-based, real-time 'pick off' tool, utilizing public domain software (PHP, MySQL). Through a web interface the tool assists users in constructing complex order-related queries and auto-generates corresponding database queries that can be executed at recurring intervals. We describe successful application of the tool for research and quality monitoring.

Architecture and Functionality of the Advanced Life Support On-Line Project Information System

NASA Technical Reports Server (NTRS)

Hogan, John A.; Levri, Julie A.; Morrow, Rich; Cavazzoni, Jim; Rodriguez, Luis F.; Riano, Rebecca; Whitaker, Dawn R.

2004-01-01

An ongoing effort is underway at NASA Ames Research Center (ARC) to develop an On-line Project Information System (OPIS) for the Advanced Life Support (ALS) Program. The objective of this three-year project is to develop, test, revise and deploy OPIS to enhance the quality of decision-making metrics and attainment of Program goals through improved knowledge sharing. OPIS will centrally locate detailed project information solicited from investigators on an annual basis and make it readily accessible by the ALS Community via a Web-accessible interface. The data will be stored in an object-oriented relational database (created in MySQL) located on a secure server at NASA ARC. OPE will simultaneously serve several functions, including being an research and technology development (R&TD) status information hub that can potentially serve as the primary annual reporting mechanism for ALS-funded projects. Using OPIS, ALS managers and element leads will be able to carry out informed R&TD investment decisions, and allow analysts to perform accurate systems evaluations. Additionally, the range and specificity of information solicited will serve to educate technology developers of programmatic needs. OPIS will collect comprehensive information from all ALS projects as well as highly detailed information specific to technology development in each ALS area (Waste, Water, Air, Biomass, Food, Thermal, Controls and Systems Analysis). Because the scope of needed information can vary dramatically between areas, element-specific technology information is being compiled with the aid of multiple specialized working groups. This paper presents the current development status in terms of the architecture and functionality of OPIS. Possible implementation approaches for OPIS are also discussed.

Salient Feature Selection Using Feed-Forward Neural Networks and Signal-to-Noise Ratios with a Focus Toward Network Threat Detection and Classification

DTIC Science & Technology

2014-03-27

0.8.0. The virtual machine’s network adapter was set to internal network only to keep any outside traffic from interfering. A MySQL -based query...primary output of Fullstats is the ARFF file format, intended for use with the WEKA Java -based data mining software developed at the University of Waikato

MotifNet: a web-server for network motif analysis.

PubMed

Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

2017-06-15

Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Lightweight application for generating clinical research information systems: MAGIC.

PubMed

Leskošek, Brane; Pajntar, Marjan

2015-12-01

Our purpose was to build and test a lightweight solution for generating clinical research information systems (CRIS) that would allow non-IT professionals with basic knowledge of computer usage to quickly define and build a ready-to-use, safe and secure web-based clinical research system for data management. We use the acronym MAGIC (Medical Application Generator InteraCtive) for the system. The generated CRIS should be very easy to build and use, so a common LAMP (Linux Apache MySQL Perl) platform was used, which also enables short development cycles. The application was built and tested using eXtreme Programming (XP) principles by a small development team consisting of one informatics specialist, one physician and one graphical designer/programmer. The parameter and graphical user interface (GUI) definitions for the CRIS can be made by non-IT professionals using an intuitive English-language-like formalism called application definition language (ADL). From these definitions, the MAGIC builds an end-user CRIS that can be used on a wide variety of platforms (from standard workstations to hand-held devices). A working example of a national health-care-quality assessment program is presented to illustrate this process. The lightweight application for generating CRIS (MAGIC) has proven to be useful for both clinical and analytical users in real working environment. To achieve better performance and interoperability, we are planning to recompile the application using XML schemas (XSD) in HL7 CDA or openEHR archetypes formats used for parameters definition and for data interchange between different information systems.

Knowledge portal for Six Sigma DMAIC process

NASA Astrophysics Data System (ADS)

ThanhDat, N.; Claudiu, K. V.; Zobia, R.; Lobont, Lucian

2016-08-01

Knowledge plays a crucial role in success of DMAIC (Define, Measure, Analysis, Improve, and Control) execution. It is therefore necessary to share and renew the knowledge. Yet, one problem arising is how to create a place where knowledge are collected and shared effectively. We believe that Knowledge Portal (KP) is an important solution for the problem. In this article, the works concerning with requirements and functionalities for KP are first reviewed. Afterwards, a procedure with necessary tools to develop and implement a KP for DMAIC (KPD) is proposed. Particularly, KPD is built on the basis of free and open-source content and learning management systems, and Ontology Engineering. In order to structure and store knowledge, tools such as Protégé, OWL, as well as OWL-RDF Parsers are used. A Knowledge Reasoner module is developed in PHP language, ARC2, MySQL and SPARQL endpoint for the purpose of querying and inferring knowledge available from Ontologies. In order to validate the availability of the procedure, a KPD is built with the proposed functionalities and tools. The authors find that the KPD benefits an organization in constructing Web sites by itself with simple steps of implementation and low initial costs. It creates a space of knowledge exchange and supports effectively collecting DMAIC reports as well as sharing knowledge created. The authors’ evaluation result shows that DMAIC knowledge is found exactly with a high success rate and a good level of response time of queries.

Open Scenario Study, Phase II Report: Assessment and Development of Approaches for Satisfying Unclassified Scenario Needs

DTIC Science & Technology

2010-01-01

interface, another providing the application logic (a program used to manipulate the data), and a server running Microsoft SQL Server or Oracle RDBMS... Oracle ) • Mysql (Open Source) • Other What application server software will be needed? • Application Server • CGI PHP/Perl (Open Source...are used throughout DoD and serve a variety of functions. While DoD has a codified and institutionalized process for the development of a common set

AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.

PubMed

Major, Sylvia M; Nishizuka, Satoshi; Morita, Daisaku; Rowland, Rick; Sunshine, Margot; Shankavaram, Uma; Washburn, Frank; Asin, Daniel; Kouros-Mehr, Hosein; Kane, David; Weinstein, John N

2006-04-06

Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different tissues of origin. AbMiner is a relational database that provides extensive information from our own laboratory and other sources on more than 600 available antibodies and the genes that encode the antibodies' antigens. The data will be made freely available at http://discover.nci.nih.gov/abminer.

TCW: Transcriptome Computational Workbench

PubMed Central

Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R.

2013-01-01

Background The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. Methodology The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. Conclusion It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw. PMID:23874959

TCW: transcriptome computational workbench.

PubMed

Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

2013-01-01

The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

From design to implementation - The Joint Asia Diabetes Evaluation (JADE) program: A descriptive report of an electronic web-based diabetes management program

PubMed Central

2010-01-01

Background The Joint Asia Diabetes Evaluation (JADE) Program is a web-based program incorporating a comprehensive risk engine, care protocols, and clinical decision support to improve ambulatory diabetes care. Methods The JADE Program uses information technology to facilitate healthcare professionals to create a diabetes registry and to deliver an evidence-based care and education protocol tailored to patients' risk profiles. With written informed consent from participating patients and care providers, all data are anonymized and stored in a databank to establish an Asian Diabetes Database for research and publication purpose. Results The JADE electronic portal (e-portal: http://www.jade-adf.org) is implemented as a Java application using the Apache web server, the mySQL database and the Cocoon framework. The JADE e-portal comprises a risk engine which predicts 5-year probability of major clinical events based on parameters collected during an annual comprehensive assessment. Based on this risk stratification, the JADE e-portal recommends a care protocol tailored to these risk levels with decision support triggered by various risk factors. Apart from establishing a registry for quality assurance and data tracking, the JADE e-portal also displays trends of risk factor control at each visit to promote doctor-patient dialogues and to empower both parties to make informed decisions. Conclusions The JADE Program is a prototype using information technology to facilitate implementation of a comprehensive care model, as recommended by the International Diabetes Federation. It also enables health care teams to record, manage, track and analyze the clinical course and outcomes of people with diabetes. PMID:20465815

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

The GEOSS Clearinghouse based on the GeoNetwork opensource

NASA Astrophysics Data System (ADS)

Liu, K.; Yang, C.; Wu, H.; Huang, Q.

2010-12-01

The Global Earth Observation System of Systems (GEOSS) is established to support the study of the Earth system in a global community. It provides services for social management, quick response, academic research, and education. The purpose of GEOSS is to achieve comprehensive, coordinated and sustained observations of the Earth system, improve monitoring of the state of the Earth, increase understanding of Earth processes, and enhance prediction of the behavior of the Earth system. In 2009, GEO called for a competition for an official GEOSS clearinghouse to be selected as a source to consolidating catalogs for Earth observations. The Joint Center for Intelligent Spatial Computing at George Mason University worked with USGS to submit a solution based on the open-source platform - GeoNetwork. In the spring of 2010, the solution is selected as the product for GEOSS clearinghouse. The GEOSS Clearinghouse is a common search facility for the Intergovernmental Group on Ea rth Observation (GEO). By providing a list of harvesting functions in Business Logic, GEOSS clearinghouse can collect metadata from distributed catalogs including other GeoNetwork native nodes, webDAV/sitemap/WAF, catalog services for the web (CSW)2.0, GEOSS Component and Service Registry (http://geossregistries.info/), OGC Web Services (WCS, WFS, WMS and WPS), OAI Protocol for Metadata Harvesting 2.0, ArcSDE Server and Local File System. Metadata in GEOSS clearinghouse are managed in a database (MySQL, Postgresql, Oracle, or MckoiDB) and an index of the metadata is maintained through Lucene engine. Thus, EO data, services, and related resources can be discovered and accessed. It supports a variety of geospatial standards including CSW and SRU for search, FGDC and ISO metadata, and WMS related OGC standards for data access and visualization, as linked from the metadata.

Novel Method of Storing and Reconstructing Events at Fermilab E-906/SeaQuest Using a MySQL Database

NASA Astrophysics Data System (ADS)

Hague, Tyler

2010-11-01

Fermilab E-906/SeaQuest is a fixed target experiment at Fermi National Accelerator Laboratory. We are investigating the antiquark asymmetry in the nucleon sea. By examining the ratio of the Drell- Yan cross sections of proton-proton and proton-deuterium collisions we can determine the asymmetry ratio. An essential feature in the development of the analysis software is to update the event reconstruction to modern software tools. We are doing this in a unique way by doing a majority of the calculations within an SQL database. Using a MySQL database allows us to take advantage of off-the-shelf software without sacrificing ROOT compatibility and avoid network bottlenecks with server-side data selection. Using our raw data we create stubs, or partial tracks, at each station which are pieced together to create full tracks. Our reconstruction process uses dynamically created SQL statements to analyze the data. These SQL statements create tables that contain the final reconstructed tracks as well as intermediate values. This poster will explain the reconstruction process and how it is being implemented.

Development of a Big Data Application Architecture for Navy Manpower, Personnel, Training, and Education

DTIC Science & Technology

2016-03-01

science IT information technology JBOD just a bunch of disks JDBC java database connectivity xviii JPME Joint Professional Military Education JSO...Joint Service Officer JVM java virtual machine MPP massively parallel processing MPTE Manpower, Personnel, Training, and Education NAVMAC Navy...27 external database, whether it is MySQL , Oracle, DB2, or SQL Server (Teller, 2015). Connectors optimize the data transfer by obtaining metadata

Automatic Publication of a MIS Product to GeoNetwork: Case of the AIS Indexer

DTIC Science & Technology

2012-11-01

installation and configuration The following instructions are for installing and configuring the software packages Java 1.6 and MySQL 5.5 which are...An Automatic Identification System (AIS) reception indexer Java application was developed in the summer of 2011, based on the work of Lapinski and...release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT An Automatic Identification System (AIS) reception indexer Java application was

An Open-source Meteorological Operational System and its Installation in Portuguese- speaking Countries

NASA Astrophysics Data System (ADS)

Almeida, W. G.; Ferreira, A. L.; Mendes, M. V.; Ribeiro, A.; Yoksas, T.

2007-05-01

CPTEC, a division of Brazil’s INPE, has been using several open-source software packages for a variety of tasks in its Data Division. Among these tools are ones traditionally used in research and educational communities such as GrADs (Grid Analysis and Display System from the Center for Ocean-Land-Atmosphere Studies (COLA)), the Local Data Manager (LDM) and GEMPAK (from Unidata), andl operational tools such the Automatic File Distributor (AFD) that are popular among National Meteorological Services. In addition, some tools developed locally at CPTEC are also being made available as open-source packages. One package is being used to manage the data from Automatic Weather Stations that INPE operates. This system uses only open- source tools such as MySQL database, PERL scripts and Java programs for web access, and Unidata’s Internet Data Distribution (IDD) system and AFD for data delivery. All of these packages are get bundled into a low-cost and easy to install and package called the Meteorological Data Operational System. Recently, in a cooperation with the SICLIMAD project, this system has been modified for use by Portuguese- speaking countries in Africa to manage data from many Automatic Weather Stations that are being installed in these countries under SICLIMAD sponsorship. In this presentation we describe the tools included-in and and architecture-of the Meteorological Data Operational System.

The automated data processing architecture for the GPI Exoplanet Survey

NASA Astrophysics Data System (ADS)

Wang, Jason J.; Perrin, Marshall D.; Savransky, Dmitry; Arriaga, Pauline; Chilcote, Jeffrey K.; De Rosa, Robert J.; Millar-Blanchaer, Maxwell A.; Marois, Christian; Rameau, Julien; Wolff, Schuyler G.; Shapiro, Jacob; Ruffio, Jean-Baptiste; Graham, James R.; Macintosh, Bruce

2017-09-01

The Gemini Planet Imager Exoplanet Survey (GPIES) is a multi-year direct imaging survey of 600 stars to discover and characterize young Jovian exoplanets and their environments. We have developed an automated data architecture to process and index all data related to the survey uniformly. An automated and flexible data processing framework, which we term the GPIES Data Cruncher, combines multiple data reduction pipelines together to intelligently process all spectroscopic, polarimetric, and calibration data taken with GPIES. With no human intervention, fully reduced and calibrated data products are available less than an hour after the data are taken to expedite follow-up on potential objects of interest. The Data Cruncher can run on a supercomputer to reprocess all GPIES data in a single day as improvements are made to our data reduction pipelines. A backend MySQL database indexes all files, which are synced to the cloud, and a front-end web server allows for easy browsing of all files associated with GPIES. To help observers, quicklook displays show reduced data as they are processed in real-time, and chatbots on Slack post observing information as well as reduced data products. Together, the GPIES automated data processing architecture reduces our workload, provides real-time data reduction, optimizes our observing strategy, and maintains a homogeneously reduced dataset to study planet occurrence and instrument performance.

GEOMAGIA50: An archeointensity database with PHP and MySQL

NASA Astrophysics Data System (ADS)

Korhonen, K.; Donadini, F.; Riisager, P.; Pesonen, L. J.

2008-04-01

The GEOMAGIA50 database stores 3798 archeomagnetic and paleomagnetic intensity determinations dated to the past 50,000 years. It also stores details of the measurement setup for each determination, which are used for ranking the data according to prescribed reliability criteria. The ranking system aims to alleviate the data reliability problem inherent in this kind of data. GEOMAGIA50 is based on two popular open source technologies. The MySQL database management system is used for storing the data, whereas the functionality and user interface are provided by server-side PHP scripts. This technical brief gives a detailed description of GEOMAGIA50 from a technical viewpoint.

Faust: Flexible Acquistion and Understanding System for Text

DTIC Science & Technology

2013-07-01

second version is still underway and it will continue in development as part of the DARPA DEFT program; it is written in Java and Clojure with MySQL and...SUTime, a Java library that recognizes and normalizes temporal expressions using deterministic patterns [101]. UIUC made another such framework... Java -based, large-scale inference engine called Tuffy. It leverages the full power of a relational optimizer in an RDBMS to perform the grounding of MLN

CBD: a biomarker database for colorectal cancer.

PubMed

Zhang, Xueli; Sun, Xiao-Feng; Cao, Yang; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD.Database URL: http://sysbio.suda.edu.cn/CBD/.

WordCluster: detecting clusters of DNA words and genomic elements

PubMed Central

2011-01-01

Background Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds. Results We introduce here an algorithm to detect clusters of DNA words (k-mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used WordCluster to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome. Conclusions WordCluster seems to predict biological meaningful clusters of DNA words (k-mers) and genomic entities. The implementation of the method into a web server is available at http://bioinfo2.ugr.es/wordCluster/wordCluster.php including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes. PMID:21261981

CBD: a biomarker database for colorectal cancer

PubMed Central

Zhang, Xueli; Sun, Xiao-Feng; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Abstract Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD. Database URL: http://sysbio.suda.edu.cn/CBD/ PMID:29846545

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB

PubMed Central

2013-01-01

Background Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and “finishing” expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. Description By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. Conclusion Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity. PMID:23336431

In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB.

PubMed

Sarika; Arora, Vasu; Iquebal, Mir Asif; Rai, Anil; Kumar, Dinesh

2013-01-19

Though India has sequenced water buffalo genome but its draft assembly is based on cattle genome BTau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. The existing radiation hybrid of buffalo and these reported STR can be used further in final gap plugging and "finishing" expected in de novo genome assembly. QTL and gene mapping needs mining of putative STR from buffalo genome at equal interval on each and every chromosome. Such markers have potential role in improvement of desirable characteristics, such as high milk yields, resistance to diseases, high growth rate. The STR mining from whole genome and development of user friendly database is yet to be done to reap the benefit of whole genome sequence. By in silico microsatellite mining of whole genome, we have developed first STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database (http://cabindb.iasri.res.in/buffsatdb/) which is a web based relational database of 910529 microsatellite markers, developed using PHP and MySQL database. Microsatellite markers have been generated using MIcroSAtellite tool. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes, motif type (mono-hexa), repeat motif and repeat kind (simple and composite). The search may be customised by limiting location of STR on chromosome as well as number of markers in that range. This is a novel approach and not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of the selected markers enabling researcher to select markers of choice at desired interval over the chromosome. The unique add-on of degenerate bases further helps in resolving presence of degenerate bases in current buffalo assembly. Being first buffalo STR database in the world , this would not only pave the way in resolving current assembly problem but shall be of immense use for global community in QTL/gene mapping critically required to increase knowledge in the endeavour to increase buffalo productivity, especially for third world country where rural economy is significantly dependent on buffalo productivity.

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events

PubMed Central

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-01-01

Background Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. Objective To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. Software architecture DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Results Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. Discussion This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. Conclusion The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License. PMID:17472749

Assessment of feasibility of running RSNA's MIRC on a Raspberry Pi: a cost-effective solution for teaching files in radiology.

PubMed

Pereira, Andre; Atri, Mostafa; Rogalla, Patrik; Huynh, Thien; O'Malley, Martin E

2015-11-01

The value of a teaching case repository in radiology training programs is immense. The allocation of resources for putting one together is a complex issue, given the factors that have to be coordinated: hardware, software, infrastructure, administration, and ethics. Costs may be significant and cost-effective solutions are desirable. We chose Medical Imaging Resource Center (MIRC) to build our teaching file. It is offered by RSNA for free. For the hardware, we chose the Raspberry Pi, developed by the Raspberry Foundation: a small control board developed as a low cost computer for schools also used in alternative projects such as robotics and environmental data collection. Its performance and reliability as a file server were unknown to us. For the operational system, we chose Raspbian, a variant of Debian Linux, along with Apache (web server), MySql (database server) and PHP, which enhance the functionality of the server. A USB hub and an external hard drive completed the setup. Installation of software was smooth. The Raspberry Pi was able to handle very well the task of hosting the teaching file repository for our division. Uptime was logged at 100 %, and loading times were similar to other MIRC sites available online. We setup two servers (one for backup), each costing just below $200.00 including external storage and USB hub. It is feasible to run RSNA's MIRC off a low-cost control board (Raspberry Pi). Performance and reliability are comparable to full-size servers for the intended purpose of hosting a teaching file within an intranet environment.

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events.

PubMed

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-05-01

Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. SOFTWARE ARCHITECTURE: DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License.

SLIMS--a user-friendly sample operations and inventory management system for genotyping labs.

PubMed

Van Rossum, Thea; Tripp, Ben; Daley, Denise

2010-07-15

We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers. Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.

ExportAid: database of RNA elements regulating nuclear RNA export in mammals.

PubMed

Giulietti, Matteo; Milantoni, Sara Armida; Armeni, Tatiana; Principato, Giovanni; Piva, Francesco

2015-01-15

Regulation of nuclear mRNA export or retention is carried out by RNA elements but the mechanism is not yet well understood. To understand the mRNA export process, it is important to collect all the involved RNA elements and their trans-acting factors. By hand-curated literature screening we collected, in ExportAid database, experimentally assessed data about RNA elements regulating nuclear export or retention of endogenous, heterologous or artificial RNAs in mammalian cells. This database could help to understand the RNA export language and to study the possible export efficiency alterations owing to mutations or polymorphisms. Currently, ExportAid stores 235 and 96 RNA elements, respectively, increasing and decreasing export efficiency, and 98 neutral assessed sequences. Freely accessible without registration at http://www.introni.it/ExportAid/ExportAid.html. Database and web interface are implemented in Perl, MySQL, Apache and JavaScript with all major browsers supported. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

SNPdbe: constructing an nsSNP functional impacts database.

PubMed

Schaefer, Christian; Meier, Alice; Rost, Burkhard; Bromberg, Yana

2012-02-15

Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; 'human' being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. http://www.rostlab.org/services/snpdbe.

mpMoRFsDB: a database of molecular recognition features in membrane proteins.

PubMed

Gypas, Foivos; Tsaousis, Georgios N; Hamodrakas, Stavros J

2013-10-01

Molecular recognition features (MoRFs) are small, intrinsically disordered regions in proteins that undergo a disorder-to-order transition on binding to their partners. MoRFs are involved in protein-protein interactions and may function as the initial step in molecular recognition. The aim of this work was to collect, organize and store all membrane proteins that contain MoRFs. Membrane proteins constitute ∼30% of fully sequenced proteomes and are responsible for a wide variety of cellular functions. MoRFs were classified according to their secondary structure, after interacting with their partners. We identified MoRFs in transmembrane and peripheral membrane proteins. The position of transmembrane protein MoRFs was determined in relation to a protein's topology. All information was stored in a publicly available mySQL database with a user-friendly web interface. A Jmol applet is integrated for visualization of the structures. mpMoRFsDB provides valuable information related to disorder-based protein-protein interactions in membrane proteins. http://bioinformatics.biol.uoa.gr/mpMoRFsDB

The HST/WFC3 Quicklook Project: A User Interface to Hubble Space Telescope Wide Field Camera 3 Data

NASA Astrophysics Data System (ADS)

Bourque, Matthew; Bajaj, Varun; Bowers, Ariel; Dulude, Michael; Durbin, Meredith; Gosmeyer, Catherine; Gunning, Heather; Khandrika, Harish; Martlin, Catherine; Sunnquist, Ben; Viana, Alex

2017-06-01

The Hubble Space Telescope's Wide Field Camera 3 (WFC3) instrument, comprised of two detectors, UVIS (Ultraviolet-Visible) and IR (Infrared), has been acquiring ~ 50-100 images daily since its installation in 2009. The WFC3 Quicklook project provides a means for instrument analysts to store, calibrate, monitor, and interact with these data through the various Quicklook systems: (1) a ~ 175 TB filesystem, which stores the entire WFC3 archive on disk, (2) a MySQL database, which stores image header data, (3) a Python-based automation platform, which currently executes 22 unique calibration/monitoring scripts, (4) a Python-based code library, which provides system functionality such as logging, downloading tools, database connection objects, and filesystem management, and (5) a Python/Flask-based web interface to the Quicklook system. The Quicklook project has enabled large-scale WFC3 analyses and calibrations, such as the monitoring of the health and stability of the WFC3 instrument, the measurement of ~ 20 million WFC3/UVIS Point Spread Functions (PSFs), the creation of WFC3/IR persistence calibration products, and many others.

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

Remote Numerical Simulations of the Interaction of High Velocity Clouds with Random Magnetic Fields

NASA Astrophysics Data System (ADS)

Santillan, Alfredo; Hernandez--Cervantes, Liliana; Gonzalez--Ponce, Alejandro; Kim, Jongsoo

The numerical simulations associated with the interaction of High Velocity Clouds (HVC) with the Magnetized Galactic Interstellar Medium (ISM) are a powerful tool to describe the evolution of the interaction of these objects in our Galaxy. In this work we present a new project referred to as Theoretical Virtual i Observatories. It is oriented toward to perform numerical simulations in real time through a Web page. This is a powerful astrophysical computational tool that consists of an intuitive graphical user interface (GUI) and a database produced by numerical calculations. In this Website the user can make use of the existing numerical simulations from the database or run a new simulation introducing initial conditions such as temperatures, densities, velocities, and magnetic field intensities for both the ISM and HVC. The prototype is programmed using Linux, Apache, MySQL, and PHP (LAMP), based on the open source philosophy. All simulations were performed with the MHD code ZEUS-3D, which solves the ideal MHD equations by finite differences on a fixed Eulerian mesh. Finally, we present typical results that can be obtained with this tool.

Building the Ferretome

PubMed Central

Sukhinin, Dmitrii I.; Engel, Andreas K.; Manger, Paul; Hilgetag, Claus C.

2016-01-01

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (https://bams1.org), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another animal model that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model. This data model was simplified and extended in order to accommodate new data modalities that were not represented previously, such as the cytoarchitecture of brain areas. The Ferretome uses a semantic parcellation of brain regions as well as a logical brain map transformation algorithm (objective relational transformation, ORT). The ORT algorithm was also adopted for the transformation of architecture data. The database is being developed in MySQL and has been populated with literature reports on tract-tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is equipped with a non-specialist web interface. This interface can be extended to produce connectivity matrices in several formats, including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system. Currently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei and 15 descriptions of regional brain architecture. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity. PMID:27242503

"One-Stop Shopping" for Ocean Remote-Sensing and Model Data

NASA Technical Reports Server (NTRS)

Li, P. Peggy; Vu, Quoc; Chao, Yi; Li, Zhi-Jin; Choi, Jei-Kook

2006-01-01

OurOcean Portal 2.0 (http:// ourocean.jpl.nasa.gov) is a software system designed to enable users to easily gain access to ocean observation data, both remote-sensing and in-situ, configure and run an Ocean Model with observation data assimilated on a remote computer, and visualize both the observation data and the model outputs. At present, the observation data and models focus on the California coastal regions and Prince William Sound in Alaska. This system can be used to perform both real-time and retrospective analyses of remote-sensing data and model outputs. OurOcean Portal 2.0 incorporates state-of-the-art information technologies (IT) such as MySQL database, Java Web Server (Apache/Tomcat), Live Access Server (LAS), interactive graphics with Java Applet at the Client site and MatLab/GMT at the server site, and distributed computing. OurOcean currently serves over 20 real-time or historical ocean data products. The data are served in pre-generated plots or their native data format. For some of the datasets, users can choose different plotting parameters and produce customized graphics. OurOcean also serves 3D Ocean Model outputs generated by ROMS (Regional Ocean Model System) using LAS. The Live Access Server (LAS) software, developed by the Pacific Marine Environmental Laboratory (PMEL) of the National Oceanic and Atmospheric Administration (NOAA), is a configurable Web-server program designed to provide flexible access to geo-referenced scientific data. The model output can be views as plots in horizontal slices, depth profiles or time sequences, or can be downloaded as raw data in different data formats, such as NetCDF, ASCII, Binary, etc. The interactive visualization is provided by graphic software, Ferret, also developed by PMEL. In addition, OurOcean allows users with minimal computing resources to configure and run an Ocean Model with data assimilation on a remote computer. Users may select the forcing input, the data to be assimilated, the simulation period, and the output variables and submit the model to run on a backend parallel computer. When the run is complete, the output will be added to the LAS server for

Building the Ferretome.

PubMed

Sukhinin, Dmitrii I; Engel, Andreas K; Manger, Paul; Hilgetag, Claus C

2016-01-01

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (https://bams1.org), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another animal model that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model. This data model was simplified and extended in order to accommodate new data modalities that were not represented previously, such as the cytoarchitecture of brain areas. The Ferretome uses a semantic parcellation of brain regions as well as a logical brain map transformation algorithm (objective relational transformation, ORT). The ORT algorithm was also adopted for the transformation of architecture data. The database is being developed in MySQL and has been populated with literature reports on tract-tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is equipped with a non-specialist web interface. This interface can be extended to produce connectivity matrices in several formats, including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system. Currently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei and 15 descriptions of regional brain architecture. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity.

Bridging the Gap - Networking Educators using Real-Time Seismic Data

NASA Astrophysics Data System (ADS)

Ortiz, A. M.; Renwald, M. D.; Baldwin, T. K.; Hall, M. K.

2004-12-01

After nearly a decade, the seismology community has made critical advances in identifying what is effective and what is needed for success in incorporating real-time seismic data in the classroom. Today's K-16 classroom teachers have many options and opportunities for incorporating short- and long-term inquiry activities for monitoring earthquakes and analyzing seismic data in their daily instruction. Through the SpiNet program, we are providing web-based tools that support educators working with real-time seismic data (http://www.scieds.com/spinet/). Our site includes a Recent Seismicity section, which allows users to share seismic data in real-time, and provides near real-time information about global seismicity. Our Activities section provides data and lessons to assist educators who wish to integrate seismology into their classroom. The Research section, currently under development, will allow educators to share general information about how they teach seismology in their classroom through a discussion board and by posting lesson plans. In addition, we are developing a user-friendly tool for students to post results of their research projects. Designing a website which targets a range of users requires a working knowledge of both user needs and website programming and design. User needs include providing a logical navigational structure and accounting for differences in browser functionality, internet access, and users' abilities. Using website development tools, such as PHP, MySQL, RDF feeds, and specialized geoscience applications, we are automating site maintenance; incorporating databases for information storage and retrieval; and providing accessibility for users with a range of skills and physical limitations. By incorporating these features, we have built a dynamic interface for a broad range of users interested in educational seismology.

Methods of formation of the knowledge base in the diagnosis of melanoma

NASA Astrophysics Data System (ADS)

Selchuk, V. Y.; Rodionova, O. V.; Sukhova, O. G.; Polyakov, E. V.; Grebennikova, O. P.; Burov, D. A.; Emelianova, G. S.

2017-01-01

The method of building of information systems for the diagnosis of skin melanoma is described in the presented work. Malignant tumors at the level of macro - and microimages in combination with clinical data are investigated. The development is made with the use of MySQL. An information system is a result of joint activities of the National research nuclear University “MEPhI” (Moscow Engineering Physics Institute) with N. N. Blokhin Russian Cancer Scientific Center.

The IEO Data Center Management System: Tools for quality control, analysis and access marine data

NASA Astrophysics Data System (ADS)

Casas, Antonia; Garcia, Maria Jesus; Nikouline, Andrei

2010-05-01

Since 1994 the Data Centre of the Spanish Oceanographic Institute develops system for archiving and quality control of oceanographic data. The work started in the frame of the European Marine Science & Technology Programme (MAST) when a consortium of several Mediterranean Data Centres began to work on the MEDATLAS project. Along the years, old software modules for MS DOS were rewritten, improved and migrated to Windows environment. Oceanographic data quality control includes now not only vertical profiles (mainly CTD and bottles observations) but also time series of currents and sea level observations. New powerful routines for analysis and for graphic visualization were added. Data presented originally in ASCII format were organized recently in an open source MySQL database. Nowadays, the IEO, as part of SeaDataNet Infrastructure, has designed and developed a new information system, consistent with the ISO 19115 and SeaDataNet standards, in order to manage the large and diverse marine data and information originated in Spain by different sources, and to interoperate with SeaDataNet. The system works with data stored in ASCII files (MEDATLAS, ODV) as well as data stored within the relational database. The components of the system are: 1.MEDATLAS Format and Quality Control - QCDAMAR: Quality Control of Marine Data. Main set of tools for working with data presented as text files. Includes extended quality control (searching for duplicated cruises and profiles, checking date, position, ship velocity, constant profiles, spikes, density inversion, sounding, acceptable data, impossible regional values,...) and input/output filters. - QCMareas: A set of procedures for the quality control of tide gauge data according to standard international Sea Level Observing System. These procedures include checking for unexpected anomalies in the time series, interpolation, filtering, computation of basic statistics and residuals. 2. DAMAR: A relational data base (MySql) designed to manage the wide variety of marine information as common vocabularies, Catalogues (CSR & EDIOS), Data and Metadata. 3.Other tools for analysis and data management - Import_DB: Script to import data and metadata from the Medatlas ASCII files into the database. - SelDamar/Selavi: interface with the database for local and web access. Allows selective retrievals applying the criteria introduced by the user, as geographical bounds, data responsible, cruises, platform, time periods, etc. Includes also statistical reference values calculation, plotting of original and mean profiles together with vertical interpolation. - ExtractDAMAR: Script to extract data when they are archived in ASCII files that meet the criteria upon an user request through SelDamar interface and export them in ODV format, making also a unit conversion.

GarlicESTdb: an online database and mining tool for garlic EST sequences.

PubMed

Kim, Dae-Won; Jung, Tae-Sung; Nam, Seong-Hyeuk; Kwon, Hyuk-Ryul; Kim, Aeri; Chae, Sung-Hwa; Choi, Sang-Haeng; Kim, Dong-Wook; Kim, Ryong Nam; Park, Hong-Seog

2009-05-18

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at http://garlicdb.kribb.re.kr. GarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Merelli, Ivan; Barale, Francesca; Milanesi, Luciano; Stella, Alessandra; Pozzi, Carlo

2008-01-01

Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention. PMID:18387211

Military Interoperable Digital Hospital Testbed (MIDHT)

DTIC Science & Technology

2013-10-01

activities are selected highlights completed by Northrop Grumman during the year. Cycle 4 development: - Increased the max_allowed_packet size in MySQL ...deployment with the Java install that is required by CONNECT v3.3.1.3. - Updated the MIDHT code base to work with the CONNECT v.3.3.1.3 Core Libraries...Provided TATRC the CONNECTUniversalClientGUI binaries for use with CONNECT v3.3.1.3 − Created and deployed a common Java library for the CONNECT

Information Mining Technologies to Enable Discovery of Actionable Intelligence to Facilitate Maritime Situational Awareness: I-MINE

DTIC Science & Technology

2013-01-01

website). Data mining tools are in-house code developed in Python, C++ and Java . • NGA The National Geospatial-Intelligence Agency (NGA) performs data...as PostgreSQL (with PostGIS), MySQL , Microsoft SQL Server, SQLite, etc. using the appropriate JDBC driver. 14 The documentation and ease to learn are...written in Java that is able to perform various types of regressions, classi- fications, and other data mining tasks. There is also a commercial version

Monitoring SLAC High Performance UNIX Computing Systems

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

Lettsome, Annette K.; /Bethune-Cookman Coll. /SLAC

2005-12-15

Knowledge of the effectiveness and efficiency of computers is important when working with high performance systems. The monitoring of such systems is advantageous in order to foresee possible misfortunes or system failures. Ganglia is a software system designed for high performance computing systems to retrieve specific monitoring information. An alternative storage facility for Ganglia's collected data is needed since its default storage system, the round-robin database (RRD), struggles with data integrity. The creation of a script-driven MySQL database solves this dilemma. This paper describes the process took in the creation and implementation of the MySQL database for use by Ganglia.more » Comparisons between data storage by both databases are made using gnuplot and Ganglia's real-time graphical user interface.« less

REDLetr: Workflow and tools to support the migration of legacy clinical data capture systems to REDCap.

PubMed

Dunn, William D; Cobb, Jake; Levey, Allan I; Gutman, David A

2016-09-01

A memory clinic at an academic medical center has relied on several ad hoc data capture systems including Microsoft Access and Excel for cognitive assessments over the last several years. However these solutions are challenging to maintain and limit the potential of hypothesis-driven or longitudinal research. REDCap, a secure web application based on PHP and MySQL, is a practical solution for improving data capture and organization. Here, we present a workflow and toolset to facilitate legacy data migration and real-time clinical research data collection into REDCap as well as challenges encountered. Legacy data consisted of neuropsychological tests stored in over 4000 Excel workbooks. Functions for data extraction, norm scoring, converting to REDCap-compatible formats, accessing the REDCap API, and clinical report generation were developed and executed in Python. Over 400 unique data points for each workbook were migrated and integrated into our REDCap database. Moving forward, our REDCap-based system replaces the Excel-based data collection method as well as eases the integration into the standard clinical research workflow and Electronic Health Record. In the age of growing data, efficient organization and storage of clinical and research data is critical for advancing research and providing efficient patient care. We believe that the workflow and tools described in this work to promote legacy data integration as well as real time data collection into REDCap ultimately facilitate these goals. Published by Elsevier Ireland Ltd.

REDLetr: Workflow and tools to support the migration of legacy clinical data capture systems to REDCap

PubMed Central

Dunn, William D; Cobb, Jake; Levey, Allan I; Gutman, David A

2017-01-01

Objective A memory clinic at an academic medical center has relied on several ad hoc data capture systems including Microsoft Access and Excel for cognitive assessments over the last several years. However these solutions are challenging to maintain and limit the potential of hypothesis-driven or longitudinal research. REDCap, a secure web application based on php and MySQL, is a practical solution for improving data capture and organization. Here, we present a workflow and toolset to facilitate legacy data migration and real-time clinical research data collection into REDCap as well as challenges encountered. Materials and Methods Legacy data consisted of neuropsychological tests stored in over 4,000 Excel workbooks. Functions for data extraction, norm scoring, converting to REDCap-compatible formats, accessing the REDCap API, and clinical report generation were developed and executed in Python. Results Over 400 unique data points for each workbook were migrated and integrated into our REDCap database. Moving forward, our REDCap-based system replaces the Excel-based data collection method as well as eases the integration to the Electronic Health Record. Conclusion In the age of growing data, efficient organization and storage of clinical and research data is critical for advancing research and providing efficient patient care. We believe that the tools and workflow described in this work to promote legacy data integration as well as real time data collection into REDCap ultimately facilitate these goals. PMID:27396629

ToxReporter: viewing the genome through the eyes of a toxicologist.

PubMed

Gosink, Mark

2016-01-01

One of the many roles of a toxicologist is to determine if an observed adverse event (AE) is related to a previously unrecognized function of a given gene/protein. Towards that end, he or she will search a variety of public and propriety databases for information linking that protein to the observed AE. However, these databases tend to present all available information about a protein, which can be overwhelming, limiting the ability to find information about the specific toxicity being investigated. ToxReporter compiles information from a broad selection of resources and limits display of the information to user-selected areas of interest. ToxReporter is a PERL-based web-application which utilizes a MySQL database to streamline this process by categorizing public and proprietary domain-derived information into predefined safety categories according to a customizable lexicon. Users can view gene information that is 'red-flagged' according to the safety issue under investigation. ToxReporter also uses a scoring system based on relative counts of the red-flags to rank all genes for the amount of information pertaining to each safety issue and to display their scored ranking as an easily interpretable 'Tox-At-A-Glance' chart. Although ToxReporter was originally developed to display safety information, its flexible design could easily be adapted to display disease information as well.Database URL: ToxReporter is freely available at https://github.com/mgosink/ToxReporter. © The Author(s) 2016. Published by Oxford University Press.

Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

PubMed

Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

2004-07-14

With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

MFIB: a repository of protein complexes with mutual folding induced by binding.

PubMed

Fichó, Erzsébet; Reményi, István; Simon, István; Mészáros, Bálint

2017-11-15

It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein-protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs. Here we present the Mutual Folding Induced by Binding (MFIB) database, the first systematic collection of complexes formed exclusively by IDPs. MFIB contains an order of magnitude more data than any dataset used in corresponding studies and offers a wide coverage of known IDP complexes in terms of flexibility, oligomeric composition and protein function from all domains of life. The included complexes are grouped using a hierarchical classification and are complemented with structural and functional annotations. MFIB is backed by a firm development team and infrastructure, and together with possible future community collaboration it will provide the cornerstone for structural and functional studies of IDP complexes. MFIB is freely accessible at http://mfib.enzim.ttk.mta.hu/. The MFIB application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. simon.istvan@ttk.mta.hu, meszaros.balint@ttk.mta.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Updates on Software development for a RICH detector

NASA Astrophysics Data System (ADS)

Voloshin, Andrew; Benmokhtar, Fatiha; Lendacky, Andrew; Goodwill, Justin

2017-01-01

The CLAS12 detector at Thomas Jefferson National Accelerator Facility (TJNAF) is undergoing an upgrade. One of the improvements is the addition of a Ring Imaging Cherenkov (RICH) detector to improve particle identification in the 3-8 GeV/c momentum range. Approximately 400 multi anode photomultiplier tubes (MAPMTs) are going to be used to detect Cherenkov Radiation in the single photoelectron spectra (SPS). Software development for slow control as well as online monitoring is under development. I will be presenting my work on the development of a java based programs for a monitor and explain its interaction with a Mysql database where the MAPMTs information is stored as well as the techniques used to visualize Cherenkov rings.

Database constraints applied to metabolic pathway reconstruction tools.

PubMed

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci.

PubMed

Falcone, Emmanuela; Grandoni, Luca; Garibaldi, Francesca; Manni, Isabella; Filligoi, Giancarlo; Piaggio, Giulia; Gurtner, Aymone

2016-01-01

miRNAs are potent regulators of gene expression and modulate multiple cellular processes in physiology and pathology. Deregulation of miRNAs expression has been found in various cancer types, thus, miRNAs may be potential targets for cancer therapy. However, the mechanisms through which miRNAs are regulated in cancer remain unclear. Therefore, the identification of transcriptional factor-miRNA crosstalk is one of the most update aspects of the study of miRNAs regulation. In the present study we describe the development of a fast and user-friendly software, named infinity, able to find the presence of DNA matrices, such as binding sequences for transcriptional factors, on ~65kb (kilobase) of 939 human miRNA genomic sequences, simultaneously. Of note, the power of this software has been validated in vivo by performing chromatin immunoprecipitation assays on a subset of new in silico identified target sequences (CCAAT) for the transcription factor NF-Y on colon cancer deregulated miRNA loci. Moreover, for the first time, we have demonstrated that NF-Y, through its CCAAT binding activity, regulates the expression of miRNA-181a, -181b, -21, -17, -130b, -301b in colon cancer cells. The infinity software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks. Infinity was implemented in pure Java using Eclipse framework, and runs on Linux and MS Windows machine, with MySQL database. The software is freely available on the web at https://github.com/bio-devel/infinity. The website is implemented in JavaScript, PHP and HTML with all major browsers supported.

Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci

PubMed Central

Garibaldi, Francesca; Manni, Isabella; Filligoi, Giancarlo; Piaggio, Giulia; Gurtner, Aymone

2016-01-01

Motivation miRNAs are potent regulators of gene expression and modulate multiple cellular processes in physiology and pathology. Deregulation of miRNAs expression has been found in various cancer types, thus, miRNAs may be potential targets for cancer therapy. However, the mechanisms through which miRNAs are regulated in cancer remain unclear. Therefore, the identification of transcriptional factor–miRNA crosstalk is one of the most update aspects of the study of miRNAs regulation. Results In the present study we describe the development of a fast and user-friendly software, named infinity, able to find the presence of DNA matrices, such as binding sequences for transcriptional factors, on ~65kb (kilobase) of 939 human miRNA genomic sequences, simultaneously. Of note, the power of this software has been validated in vivo by performing chromatin immunoprecipitation assays on a subset of new in silico identified target sequences (CCAAT) for the transcription factor NF-Y on colon cancer deregulated miRNA loci. Moreover, for the first time, we have demonstrated that NF-Y, through its CCAAT binding activity, regulates the expression of miRNA-181a, -181b, -21, -17, -130b, -301b in colon cancer cells. Conclusions The infinity software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks. Availability and Implementation Infinity was implemented in pure Java using Eclipse framework, and runs on Linux and MS Windows machine, with MySQL database. The software is freely available on the web at https://github.com/bio-devel/infinity. The website is implemented in JavaScript, PHP and HTML with all major browsers supported. PMID:27082112

Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

PubMed

Rahman, Mahabubur; Watabe, Hiroshi

2018-05-01

Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid achievement in cancer diagnosis and therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development of the prototype data management system of the solar H-alpha full disk observation

NASA Astrophysics Data System (ADS)

Wei, Ka-Ning; Zhao, Shi-Qing; Li, Qiong-Ying; Chen, Dong

2004-06-01

The Solar Chromospheric Telescope in Yunnan Observatory generates about 2G bytes fits format data per day. Huge amounts of data will bring inconvenience for people to use. Hence, data searching and sharing are important at present. Data searching, on-line browsing, remote accesses and download are developed with a prototype data management system of the solar H-alpha full disk observation, and improved by the working flow technology. Based on Windows XP operating system and MySQL data management system, a prototype system of browse/server model is developed by JAVA and JSP. Data compression, searching, browsing, deletion need authority and download in real-time have been achieved.

The Tri-Agency Climate Education (TrACE) Catalog: Promoting collaboration, effective practice, and a robust portfolio by sharing educational resources developed across NASA, NOAA & NSF climate education initiatives

NASA Astrophysics Data System (ADS)

McDougall, C.; Martin, A.; Givens, S. M.; Yue, S.; Wilson, C. E.; Karsten, J. L.

2012-12-01

The Tri-Agency Climate Education (TrACE) Catalog is an online, interactive, searchable and browsable web product driven by a database backend. TrACE was developed for and by the community of educators, scientists, and Federal agency representatives involved in a tri-agency collaboration for climate education. NASA, NOAA, and NSF are working together to strategically coordinate and support a portfolio of projects focused on climate literacy and education in formal and informal learning environments. The activities of the tri-agency collaboration, including annual meetings for principal investigators and the ongoing development of a nascent common evaluation framework, have created a strong national network for effectively engaging diverse audiences with the principles of climate literacy (see Eos Vol. 92, No. 24, 14 June 2011). TrACE is a tool for the climate education community that promotes the goals of the tri-agency collaboration to leverage existing resources, minimize duplicate efforts, and facilitate communication among this emergent community of scientists and educators. TrACE was born as "The Matrix," a product of the 2011 Second Annual NASA, NOAA and NSF Climate Change Education Principal Investigators Meeting (see McDougall, Wilson, Martin & Knippenberg, 2011, Abstract ED21B-0583 presented at 2011 Fall Meeting, AGU, San Francisco, CA.) Meeting attendees were asked to populate a pen-and-paper matrix with all of the activities or deliverables they had created or anticipated creating as part of their NOAA/NASA/NSF-funded project. During the 2012 Third Annual Tri-Agency PI Meeting, projects were given the opportunity to add and update their products and deliverables. In the intervening year, the dataset comprising the Matrix was converted to a MySQL database, with a standardized taxonomy and minimum criteria for inclusion, and further developed into the interactive TrACE Catalog. In the fall of 2012, the TrACE Catalog web product will be made publicly available. The catalog currently contains information about 204 educational products and resources, representing 81 federally funded projects, categorized by audience type (e.g., K-12 students, public, decision makers, scientists) and resource type (e.g., curriculum, electronic media & tools, exhibits). The web interface will allow for searching, sorting, and browsing of available educational resources by audience type, product type, funding agency, and geographical region. Using this tool, PIs working on similar efforts or in similar bioregions will be able to locate, learn from, and collaborate with each other. The dataset is also useful for visualizing and assessing the breadth and depth of the tri-agency portfolio. In this poster presentation, representatives from the three collaborating agencies will demonstrate the functionality of the TrACE Catalog and the dataset that drives it. We will invite others who are working on similar efforts to add their anticipated/existing products.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

A database of charged cosmic rays

NASA Astrophysics Data System (ADS)

Maurin, D.; Melot, F.; Taillet, R.

2014-09-01

Aims: This paper gives a description of a new online database and associated online tools (data selection, data export, plots, etc.) for charged cosmic-ray measurements. The experimental setups (type, flight dates, techniques) from which the data originate are included in the database, along with the references to all relevant publications. Methods: The database relies on the MySQL5 engine. The web pages and queries are based on PHP, AJAX and the jquery, jquery.cluetip, jquery-ui, and table-sorter third-party libraries. Results: In this first release, we restrict ourselves to Galactic cosmic rays with Z ≤ 30 and a kinetic energy per nucleon up to a few tens of TeV/n. This corresponds to more than 200 different sub-experiments (i.e., different experiments, or data from the same experiment flying at different times) in as many publications. Conclusions: We set up a cosmic-ray database (CRDB) and provide tools to sort and visualise the data. New data can be submitted, providing the community with a collaborative tool to archive past and future cosmic-ray measurements. http://lpsc.in2p3.fr/crdb; Contact: crdatabase@lpsc.in2p3.fr

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

A comparison of database systems for XML-type data.

PubMed

Risse, Judith E; Leunissen, Jack A M

2010-01-01

In the field of bioinformatics interchangeable data formats based on XML are widely used. XML-type data is also at the core of most web services. With the increasing amount of data stored in XML comes the need for storing and accessing the data. In this paper we analyse the suitability of different database systems for storing and querying large datasets in general and Medline in particular. All reviewed database systems perform well when tested with small to medium sized datasets, however when the full Medline dataset is queried a large variation in query times is observed. There is not one system that is vastly superior to the others in this comparison and, depending on the database size and the query requirements, different systems are most suitable. The best all-round solution is the Oracle 11~g database system using the new binary storage option. Alias-i's Lingpipe is a more lightweight, customizable and sufficiently fast solution. It does however require more initial configuration steps. For data with a changing XML structure Sedna and BaseX as native XML database systems or MySQL with an XML-type column are suitable.

S&MPO - An information system for ozone spectroscopy on the WEB

NASA Astrophysics Data System (ADS)

Babikov, Yurii L.; Mikhailenko, Semen N.; Barbe, Alain; Tyuterev, Vladimir G.

2014-09-01

Spectroscopy and Molecular Properties of Ozone ("S&MPO") is an Internet accessible information system devoted to high resolution spectroscopy of the ozone molecule, related properties and data sources. S&MPO contains information on original spectroscopic data (line positions, line intensities, energies, transition moments, spectroscopic parameters) recovered from comprehensive analyses and modeling of experimental spectra as well as associated software for data representation written in PHP Java Script, C++ and FORTRAN. The line-by-line list of vibration-rotation transitions and other information is organized as a relational database under control of MySQL database tools. The main S&MPO goal is to provide access to all available information on vibration-rotation molecular states and transitions under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for the S&MPO may include: education/training in molecular physics, radiative processes, laser physics; spectroscopic applications (analysis, Fourier transform spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The system is accessible via Internet on two sites: http://smpo.iao.ru and http://smpo.univ-reims.fr.

Master Metadata Repository and Metadata-Management System

NASA Technical Reports Server (NTRS)

Armstrong, Edward; Reed, Nate; Zhang, Wen

2007-01-01

A master metadata repository (MMR) software system manages the storage and searching of metadata pertaining to data from national and international satellite sources of the Global Ocean Data Assimilation Experiment (GODAE) High Resolution Sea Surface Temperature Pilot Project [GHRSSTPP]. These sources produce a total of hundreds of data files daily, each file classified as one of more than ten data products representing global sea-surface temperatures. The MMR is a relational database wherein the metadata are divided into granulelevel records [denoted file records (FRs)] for individual satellite files and collection-level records [denoted data set descriptions (DSDs)] that describe metadata common to all the files from a specific data product. FRs and DSDs adhere to the NASA Directory Interchange Format (DIF). The FRs and DSDs are contained in separate subdatabases linked by a common field. The MMR is configured in MySQL database software with custom Practical Extraction and Reporting Language (PERL) programs to validate and ingest the metadata records. The database contents are converted into the Federal Geographic Data Committee (FGDC) standard format by use of the Extensible Markup Language (XML). A Web interface enables users to search for availability of data from all sources.

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

PubMed

Arenillas, David J; Forrest, Alistair R R; Kawaji, Hideya; Lassmann, Timo; Wasserman, Wyeth W; Mathelier, Anthony

2016-09-15

With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions. The CAGEd-oPOSUM web tool is implemented in Perl, MySQL and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM CONTACTS: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

PubMed Central

Arenillas, David J.; Forrest, Alistair R. R.; Kawaji, Hideya; Lassmann, Timo; Wasserman, Wyeth W.; Mathelier, Anthony

2016-01-01

With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions. Availability and Implementation: The CAGEd-oPOSUM web tool is implemented in Perl, MySQL and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM. Contacts: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27334471

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study

PubMed Central

2018-01-01

Background Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. Objective The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Methods Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. Results All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. Conclusions To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. PMID:29699962

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

PubMed

Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

2012-01-01

Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and relationship errors in KEGG). We turn complicated and incompatible xml data formats and inconsistent gene and gene relationship representations from different source databases into normalized and unified pathway-gene and pathway-gene pair relationships neatly recorded in simple tab-delimited text format and MySQL tables, which facilitates convenient automatic computation and large-scale referencing in many related studies. IntPath data can be downloaded in text format or MySQL dump. IntPath data can also be retrieved and analyzed conveniently through web service by local programs or through web interface by mouse clicks. Several useful analysis tools are also provided in IntPath. We have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath.

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.

An image database management system for conducting CAD research

NASA Astrophysics Data System (ADS)

Gruszauskas, Nicholas; Drukker, Karen; Giger, Maryellen L.

2007-03-01

The development of image databases for CAD research is not a trivial task. The collection and management of images and their related metadata from multiple sources is a time-consuming but necessary process. By standardizing and centralizing the methods in which these data are maintained, one can generate subsets of a larger database that match the specific criteria needed for a particular research project in a quick and efficient manner. A research-oriented management system of this type is highly desirable in a multi-modality CAD research environment. An online, webbased database system for the storage and management of research-specific medical image metadata was designed for use with four modalities of breast imaging: screen-film mammography, full-field digital mammography, breast ultrasound and breast MRI. The system was designed to consolidate data from multiple clinical sources and provide the user with the ability to anonymize the data. Input concerning the type of data to be stored as well as desired searchable parameters was solicited from researchers in each modality. The backbone of the database was created using MySQL. A robust and easy-to-use interface for entering, removing, modifying and searching information in the database was created using HTML and PHP. This standardized system can be accessed using any modern web-browsing software and is fundamental for our various research projects on computer-aided detection, diagnosis, cancer risk assessment, multimodality lesion assessment, and prognosis. Our CAD database system stores large amounts of research-related metadata and successfully generates subsets of cases that match the user's desired search criteria.

Planetary Data Systems (PDS) Imaging Node Atlas II

NASA Technical Reports Server (NTRS)

Stanboli, Alice; McAuley, James M.

2013-01-01

The Planetary Image Atlas (PIA) is a Rich Internet Application (RIA) that serves planetary imaging data to the science community and the general public. PIA also utilizes the USGS Unified Planetary Coordinate system (UPC) and the on-Mars map server. The Atlas was designed to provide the ability to search and filter through greater than 8 million planetary image files. This software is a three-tier Web application that contains a search engine backend (MySQL, JAVA), Web service interface (SOAP) between server and client, and a GWT Google Maps API client front end. This application allows for the search, retrieval, and download of planetary images and associated meta-data from the following missions: 2001 Mars Odyssey, Cassini, Galileo, LCROSS, Lunar Reconnaissance Orbiter, Mars Exploration Rover, Mars Express, Magellan, Mars Global Surveyor, Mars Pathfinder, Mars Reconnaissance Orbiter, MESSENGER, Phoe nix, Viking Lander, Viking Orbiter, and Voyager. The Atlas utilizes the UPC to translate mission-specific coordinate systems into a unified coordinate system, allowing the end user to query across missions of similar targets. If desired, the end user can also use a mission-specific view of the Atlas. The mission-specific views rely on the same code base. This application is a major improvement over the initial version of the Planetary Image Atlas. It is a multi-mission search engine. This tool includes both basic and advanced search capabilities, providing a product search tool to interrogate the collection of planetary images. This tool lets the end user query information about each image, and ignores the data that the user has no interest in. Users can reduce the number of images to look at by defining an area of interest with latitude and longitude ranges.

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

PubMed Central

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

PubMed Central

Ebhardt, H Alexander; Wiese, Kay C; Unrau, Peter J

2006-01-01

Background DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. Results Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on Conclusion Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]. PMID:16584563

Black Sea GIS developed in MHI

NASA Astrophysics Data System (ADS)

Zhuk, E.; Khaliulin, A.; Zodiatis, G.; Nikolaidis, A.; Isaeva, E.

2016-08-01

The work aims at creating the Black Sea geoinformation system (GIS) and complementing it with a model bank. The software for data access and visualization was developed using client server architecture. A map service based on MapServer and MySQL data management system were chosen for the Black Sea GIS. Php-modules and python-scripts are used to provide data access, processing, and exchange between the client application and the server. According to the basic data types, the module structure of GIS was developed. Each type of data is matched to a module which allows selection and visualization of the data. At present, a GIS complement with a model bank (the models build in to the GIS) and users' models (programs launched on users' PCs but receiving and displaying data via GIS) is developed.

[Design and development of an online system of parasite's images for training and evaluation].

PubMed

Yuan-Chun, Mao; Sui, Xu; Jie, Wang; Hua-Yun, Zhou; Jun, Cao

2017-08-08

To design and develop an online training and evaluation system for parasitic pathogen recognition. The system was based on a Parasitic Diseases Specimen Image Digitization Construction Database by using MYSQL 5.0 as the system of database development software, and PHP 5 as the interface development language. It was mainly used for online training and evaluation of parasitic pathology diagnostic techniques. The system interface was designed simple, flexible, and easy to operate for medical staff. It enabled full day and 24 hours accessible to online training study and evaluation. Thus, the system broke the time and space constraints of the traditional training models. The system provides a shared platform for the professional training of parasitic diseases, and a reference for other training tasks.

Toxicity ForeCaster (ToxCast™) Data

EPA Pesticide Factsheets

Data is organized into different data sets and includes descriptions of ToxCast chemicals and assays and files summarizing the screening results, a MySQL database, chemicals screened through Tox21, and available data generated from animal toxicity studies.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Military Interoperable Digital Hospital Testbed (MIDHT) Phase III

DTIC Science & Technology

2014-10-01

silently changed, it is common knowledge  that some  Java  Development  Kit (JDK) implementations create slightly differently  formatted PEM and  DER...tracking software  JKS  Java  KeyStore  LDAP  Lightweight Directory Access Protocol  MHS  Military Health System  MIMC  Conemaugh Miners Medical... MySQL ~ Conemaugh Health System ’-J Common Access Layer (CAL) Interface I I t J J AIIScripts I I McKe-n J Sunque.st Horizon EHR Lab Patient

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study.

PubMed

Lizarraga, Gabriel; Li, Chunfei; Cabrerizo, Mercedes; Barker, Warren; Loewenstein, David A; Duara, Ranjan; Adjouadi, Malek

2018-04-26

Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. ©Gabriel Lizarraga, Chunfei Li, Mercedes Cabrerizo, Warren Barker, David A Loewenstein, Ranjan Duara, Malek Adjouadi. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 26.04.2018.

76 FR 63575 - Transportation Conformity Rule: MOVES Regional Grace Period Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-13

... written in FORTRAN and used simple text files for data input and output, MOVES2010a is written in JAVA and uses a relational database structure in MYSQL to handle input and output as data tables. These changes...

76 FR 63554 - Transportation Conformity Rule: MOVES Regional Grace Period Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-13

... written in FORTRAN and used simple text files for data input and output, MOVES2010a is written in JAVA and uses a relational database structure in MYSQL to handle input and output as data tables. These changes...

77 FR 11394 - Transportation Conformity Rule: MOVES Regional Grace Period Extension

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-27

... written in FORTRAN and used simple text files for data input and output, MOVES is written in JAVA and uses a relational database structure in MYSQL to handle input and output as data tables.\\13\\ \\13\\ Some...

An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B.

PubMed

Rallapalli, P M; Kemball-Cook, G; Tuddenham, E G; Gomez, K; Perkins, S J

2013-07-01

Factor IX (FIX) is important in the coagulation cascade, being activated to FIXa on cleavage. Defects in the human F9 gene frequently lead to hemophilia B. To assess 1113 unique F9 mutations corresponding to 3721 patient entries in a new and up-to-date interactive web database alongside the FIXa protein structure. The mutations database was built using MySQL and structural analyses were based on a homology model for the human FIXa structure based on closely-related crystal structures. Mutations have been found in 336 (73%) out of 461 residues in FIX. There were 812 unique point mutations, 182 deletions, 54 polymorphisms, 39 insertions and 26 others that together comprise a total of 1113 unique variants. The 64 unique mild severity mutations in the mature protein with known circulating protein phenotypes include 15 (23%) quantitative type I mutations and 41 (64%) predominantly qualitative type II mutations. Inhibitors were described in 59 reports (1.6%) corresponding to 25 unique mutations. The interactive database provides insights into mechanisms of hemophilia B. Type II mutations are deduced to disrupt predominantly those structural regions involved with functional interactions. The interactive features of the database will assist in making judgments about patient management. © 2013 International Society on Thrombosis and Haemostasis.

EcoGene 3.0

PubMed Central

Zhou, Jindan; Rudd, Kenneth E.

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection. PMID:23197660

Oasis 2: improved online analysis of small RNA-seq data.

PubMed

Rahman, Raza-Ur; Gautam, Abhivyakti; Bethune, Jörn; Sattar, Abdul; Fiosins, Maksims; Magruder, Daniel Sumner; Capece, Vincenzo; Shomroni, Orr; Bonn, Stefan

2018-02-14

Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing. Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module. Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment. Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.

JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs.

PubMed

Beauclair, Guillaume; Bridier-Nahmias, Antoine; Zagury, Jean-François; Saïb, Ali; Zamborlini, Alessia

2015-11-01

Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs. JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files. JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported. guillaume.beauclair@inserm.fr Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

PubMed

Schad, Eva; Fichó, Erzsébet; Pancsa, Rita; Simon, István; Dosztányi, Zsuzsanna; Mészáros, Bálint

2018-02-01

Intrinsically Disordered Proteins (IDPs) mediate crucial protein-protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode. Here, we present DIBS, the first comprehensive, curated collection of complexes between IDPs and ordered proteins. DIBS not only describes by far the highest number of cases, it also provides the dissociation constants of their interactions, as well as the description of potential post-translational modifications modulating the binding strength and linear motifs involved in the binding. Together with the wide range of structural and functional annotations, DIBS will provide the cornerstone for structural and functional studies of IDP complexes. DIBS is freely accessible at http://dibs.enzim.ttk.mta.hu/. The DIBS application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. dosztanyi@caesar.elte.hu or bmeszaros@caesar.elte.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

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.

EcoGene 3.0.

PubMed

Zhou, Jindan; Rudd, Kenneth E

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.

Product competitiveness analysis for e-commerce platform of special agricultural products

NASA Astrophysics Data System (ADS)

Wan, Fucheng; Ma, Ning; Yang, Dongwei; Xiong, Zhangyuan

2017-09-01

On the basis of analyzing the influence factors of the product competitiveness of the e-commerce platform of the special agricultural products and the characteristics of the analytical methods for the competitiveness of the special agricultural products, the price, the sales volume, the postage included service, the store reputation, the popularity, etc. were selected in this paper as the dimensionality for analyzing the competitiveness of the agricultural products, and the principal component factor analysis was taken as the competitiveness analysis method. Specifically, the web crawler was adopted to capture the information of various special agricultural products in the e-commerce platform ---- chi.taobao.com. Then, the original data captured thereby were preprocessed and MYSQL database was adopted to establish the information library for the special agricultural products. Then, the principal component factor analysis method was adopted to establish the analysis model for the competitiveness of the special agricultural products, and SPSS was adopted in the principal component factor analysis process to obtain the competitiveness evaluation factor system (support degree factor, price factor, service factor and evaluation factor) of the special agricultural products. Then, the linear regression method was adopted to establish the competitiveness index equation of the special agricultural products for estimating the competitiveness of the special agricultural products.

MODBASE, a database of annotated comparative protein structure models

PubMed Central

Pieper, Ursula; Eswar, Narayanan; Stuart, Ashley C.; Ilyin, Valentin A.; Sali, Andrej

2002-01-01

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server. PMID:11752309

Advancing Future Network Science through Content Understanding

DTIC Science & Technology

2014-05-01

BitTorrent, PostgreSQL, MySQL , and GRSecurity) and emerging technologies (HadoopDFS, Tokutera, Sector/Sphere, HBase, and other BigTable-like...result. • Multi-Source Network Pulse Analyzer and Correlator provides course of action planning by enhancing the understanding of the complex dynamics

SAMSON Technology Demonstrator

DTIC Science & Technology

2014-06-01

requested. The SAMSON TD was testing with two different policy engines: 1. A custom XACML-based element matching engine using a MySQL database for...performed during the course of the event. Full information protection across the sphere of access management, information protection and auditing was in...

Scale-Independent Relational Query Processing

DTIC Science & Technology

2013-10-04

source options are also available, including Postgresql, MySQL , and SQLite. These mod- ern relational databases are generally very complex software systems...and Their Application to Data Stream Management. IGI Global, 2010. [68] George Reese. Database Programming with JDBC and Java , Second Edition. Ed. by

Toward an open-access global database for mapping, control, and surveillance of neglected tropical diseases.

PubMed

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F L; Utzinger, Jürg; Kristensen, Thomas K; Vounatsou, Penelope

2011-12-01

After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and 'grey literature'), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay.

Ensembl variation resources

PubMed Central

2010-01-01

Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

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.

A phenome database (NEAUHLFPD) designed and constructed for broiler lines divergently selected for abdominal fat content.

PubMed

Li, Min; Dong, Xiang-yu; Liang, Hao; Leng, Li; Zhang, Hui; Wang, Shou-zhi; Li, Hui; Du, Zhi-Qiang

2017-05-20

Effective management and analysis of precisely recorded phenotypic traits are important components of the selection and breeding of superior livestocks. Over two decades, we divergently selected chicken lines for abdominal fat content at Northeast Agricultural University (Northeast Agricultural University High and Low Fat, NEAUHLF), and collected large volume of phenotypic data related to the investigation on molecular genetic basis of adipose tissue deposition in broilers. To effectively and systematically store, manage and analyze phenotypic data, we built the NEAUHLF Phenome Database (NEAUHLFPD). NEAUHLFPD included the following phenotypic records: pedigree (generations 1-19) and 29 phenotypes, such as body sizes and weights, carcass traits and their corresponding rates. The design and construction strategy of NEAUHLFPD were executed as follows: (1) Framework design. We used Apache as our web server, MySQL and Navicat as database management tools, and PHP as the HTML-embedded language to create dynamic interactive website. (2) Structural components. On the main interface, detailed introduction on the composition, function, and the index buttons of the basic structure of the database could be found. The functional modules of NEAUHLFPD had two main components: the first module referred to the physical storage space for phenotypic data, in which functional manipulation on data can be realized, such as data indexing, filtering, range-setting, searching, etc.; the second module related to the calculation of basic descriptive statistics, where data filtered from the database can be used for the computation of basic statistical parameters and the simultaneous conditional sorting. NEAUHLFPD could be used to effectively store and manage not only phenotypic, but also genotypic and genomics data, which can facilitate further investigation on the molecular genetic basis of chicken adipose tissue growth and development, and expedite the selection and breeding of broilers with low fat content.

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens

PubMed Central

2012-01-01

Background Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. Results In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and relationship errors in KEGG). We turn complicated and incompatible xml data formats and inconsistent gene and gene relationship representations from different source databases into normalized and unified pathway-gene and pathway-gene pair relationships neatly recorded in simple tab-delimited text format and MySQL tables, which facilitates convenient automatic computation and large-scale referencing in many related studies. IntPath data can be downloaded in text format or MySQL dump. IntPath data can also be retrieved and analyzed conveniently through web service by local programs or through web interface by mouse clicks. Several useful analysis tools are also provided in IntPath. Conclusions We have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath. PMID:23282057

An improved design method for EPC middleware

NASA Astrophysics Data System (ADS)

Lou, Guohuan; Xu, Ran; Yang, Chunming

2014-04-01

For currently existed problems and difficulties during the small and medium enterprises use EPC (Electronic Product Code) ALE (Application Level Events) specification to achieved middleware, based on the analysis of principle of EPC Middleware, an improved design method for EPC middleware is presented. This method combines the powerful function of MySQL database, uses database to connect reader-writer with upper application system, instead of development of ALE application program interface to achieve a middleware with general function. This structure is simple and easy to implement and maintain. Under this structure, different types of reader-writers added can be configured conveniently and the expandability of the system is improved.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

Using Controlled Vocabularies and Semantics to Improve Ocean Data Discovery (Invited)

NASA Astrophysics Data System (ADS)

Chandler, C. L.; Groman, R. C.; Shepherd, A.; Allison, M. D.; Kinkade, D.; Rauch, S.; Wiebe, P. H.; Glover, D. M.

2013-12-01

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was created in late 2006, by combining the formerly independent data management offices for the U.S. GLOBal Ocean ECosystems Dynamics (GLOBEC) and U.S. Joint Global Ocean flux Study (JGOFS) programs. BCO-DMO staff members work with investigators to publish data from research projects funded by the NSF Geosciences Directorate (GEO) Division of Ocean Sciences (OCE) Biological and Chemical Oceanography Sections and Polar Programs (PLR) Antarctic Sciences Organisms & Ecosystems Program (ANT). Since 2006, researchers have been contributing new data to the BCO-DMO data system. As the data from new research efforts have been added to the data previously shared by U.S. GLOBEC and U.S. JGOFS researchers, the BCO-DMO system has developed into a rich repository of data from ocean, coastal, and Great Lakes research programs. The metadata records for the original research program data (prior to 2006) were stored in human-readable flat files of text, translated on-demand to Web-retrievable files. Beginning in 2006, the metadata records from multiple data systems managed by BCO-DMO were ingested into a relational database (MySQL). Since that time, efforts have been made to incorporate lists of controlled vocabulary terms for key information concepts stored in the MySQL database (e.g. names of research programs, deployments, instruments and measurements). This presents a challenge for a data system that includes legacy data and is continually expanding with the addition of new contributions. Over the years, BCO-DMO has developed a series of data delivery systems driven by the supporting metadata. Improved access to research data, a primary goal of the BCO-DMO project, is achieved through geospatial and text-based data access systems that support data discovery, access, display, assessment, integration, and export of data resources. The addition of a semantically-enabled search capability improves data discovery options particularly for those investigators whose research interests are cross-domain and multi-disciplinary. Current efforts by BCO-DMO staff members are focused on identifying globally unique, persistent identifiers to unambiguously identify resources of interest curated by and available from BCO-DMO. The process involves several essential components: (1) identifying a trusted authoritative source of complementary content and the appropriate contact; (2) determining the globally unique, persistent identifier system for resources of interest and (3) negotiating the requisite syntactic and semantic exchange systems. A variety of technologies have been deployed including: (1) controlled vocabulary term lists for some of the essential concepts/classes; (2) the Ocean Data Ontology; (3) publishing content as Linked Open Data and (4) SPARQL queries and inference. The final results are emerging as a semantic layer comprising domain-specific controlled vocabularies typed to community standard definitions, an ontology with the concepts and relationships needed to describe ocean data, a semantically-enabled faceted search, and inferencing services. We are exploring use of these technologies to improve the accuracy of the BCO-DMO data collection and to facilitate exchange of information with complementary ocean data repositories. Integrating a semantic layer into the BCO-DMO data system architecture improves data and information resource discovery, access and integration.

Windows Memory Forensic Data Visualization

DTIC Science & Technology

2014-06-12

clustering characteristics (Bastian, et al, 2009). The software is written in Java and utilizes the OpenGL library for rendering graphical content...Toolkit 2 nd ed. Burlington MA: Syngress. D3noob. (2013, February 8). Using a MYSQL database as a source of data. Message posted to http

tcpl: The ToxCast Pipeline for High-Throughput Screening Data

EPA Science Inventory

Motivation: The large and diverse high-throughput chemical screening efforts carried out by the US EPAToxCast program requires an efficient, transparent, and reproducible data pipeline.Summary: The tcpl R package and its associated MySQL database provide a generalized platform fo...

An MRspec database query and visualization engine with applications as a clinical diagnostic and research tool.

PubMed

Miscevic, Filip; Foong, Justin; Schmitt, Benjamin; Blaser, Susan; Brudno, Michael; Schulze, Andreas

2016-12-01

Proton magnetic resonance spectroscopy (MRspec), one of the very few techniques for in vivo assessment of neuro-metabolic profiles, is often complicated by lack of standard population norms and paucity of computational tools. 7035 scans and clinical information from 4430 pediatric patients were collected from 2008 to 2014. Scans were conducted using a 1.5T (n=3664) or 3T scanner (n=3371), and with either a long (144ms, n=5559) or short echo time (35ms, n=1476). 3055 of these scans were localized in the basal ganglia (BG), 1211 in parieto-occipital white matter (WM). 34 metabolites were quantified using LCModel. A web application using MySQL, Python and Flask was developed to facilitate the exploration of the data set. Already piloting the application revealed numerous insights. (1), N-acetylaspartate (NAA) increased throughout all ages. During early infancy, total choline was highly varied and myo-inositol demonstrated a downward trend. (2), Total creatine (tCr) and creatine increased throughout childhood and adolescence, though phosphocreatine (PCr) remained constant beyond 200days. (3), tCr was higher in BG than WM. (4), No obvious gender-related differences were observed. (5), Field strength affects quantification using LCModel for some metabolites, most prominently for tCr and total NAA. (6), Outlier analysis identified patients treated with vigabatrin through elevated γ-aminobutyrate, and patients with Klippel-Feil syndrome, Leigh disease and L2-hydroxyglutaric aciduria through low choline in BG. We have established the largest MRSpec database and developed a robust and flexible computational tool for facilitating the exploration of vast metabolite datasets that proved its value for discovering neurochemical trends for clinical diagnosis, treatment monitoring, and research. Open access will lead to its widespread use, improving the diagnostic yield and contributing to better understanding of metabolic processes and conditions in the brain. Copyright © 2016 Elsevier Inc. All rights reserved.

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

PubMed Central

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K.

2018-01-01

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly. PMID:29470400

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

PubMed

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

2018-02-22

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly.

Integrated Autonomous Network Management (IANM) Multi-Topology Route Manager and Analyzer

DTIC Science & Technology

2008-02-01

zebra tmg mtrcli xinetd (tftp) mysql configuration file (mtrrm.conf) configuration file (mtrrmAggregator.properties) tftp files /tftpboot NetFlow PDUs...configuration upload/download snmp, telnet OSPFv2 user interface tmg Figure 6-2. Internal software organization Figure 6-2 illustrates the main

Acoustic Metadata Management and Transparent Access to Networked Oceanographic Data Sets

DTIC Science & Technology

2013-09-30

connectivity (ODBC) compliant data source for which drivers are available (e.g. MySQL , Oracle database, Postgres) can now be imported. Implementation...the possibility of speeding data transmission through compression (implemented) or the potential to use alternative data formats such as Java script

The AMMA database

NASA Astrophysics Data System (ADS)

Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

2010-05-01

The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can concern local, satellite and model data. - Documentation: catalogue of all the available data and their metadata. These tools have been developed using standard and free languages and softwares: - Linux system with an Apache web server and a Tomcat application server; - J2EE tools : JSF and Struts frameworks, hibernate; - relational database management systems: PostgreSQL and MySQL; - OpenLDAP directory. In order to facilitate the access to the data by African scientists, the complete system has been mirrored at AGHRYMET Regional Centre in Niamey and is operational there since January 2009. Users can now access metadata and request data through one or the other of two equivalent portals: http://database.amma-international.org or http://amma.agrhymet.ne/amma-data.

A Reusable Framework for Regional Climate Model Evaluation

NASA Astrophysics Data System (ADS)

Hart, A. F.; Goodale, C. E.; Mattmann, C. A.; Lean, P.; Kim, J.; Zimdars, P.; Waliser, D. E.; Crichton, D. J.

2011-12-01

Climate observations are currently obtained through a diverse network of sensors and platforms that include space-based observatories, airborne and seaborne platforms, and distributed, networked, ground-based instruments. These global observational measurements are critical inputs to the efforts of the climate modeling community and can provide a corpus of data for use in analysis and validation of climate models. The Regional Climate Model Evaluation System (RCMES) is an effort currently being undertaken to address the challenges of integrating this vast array of observational climate data into a coherent resource suitable for performing model analysis at the regional level. Developed through a collaboration between the NASA Jet Propulsion Laboratory (JPL) and the UCLA Joint Institute for Regional Earth System Science and Engineering (JIFRESSE), the RCMES uses existing open source technologies (MySQL, Apache Hadoop, and Apache OODT), to construct a scalable, parametric, geospatial data store that incorporates decades of observational data from a variety of NASA Earth science missions, as well as other sources into a consistently annotated, highly available scientific resource. By eliminating arbitrary partitions in the data (individual file boundaries, differing file formats, etc), and instead treating each individual observational measurement as a unique, geospatially referenced data point, the RCMES is capable of transforming large, heterogeneous collections of disparate observational data into a unified resource suitable for comparison to climate model output. This facility is further enhanced by the availability of a model evaluation toolkit which consists of a set of Python libraries, a RESTful web service layer, and a browser-based graphical user interface that allows for orchestration of model-to-data comparisons by composing them visually through web forms. This combination of tools and interfaces dramatically simplifies the process of interacting with and utilizing large volumes of observational data for model evaluation research. We feel that the RCMES is particularly appealing in that it represents a principled, reusable architectural approach rather than a one-off technological implementation. In fact, early RCMES prototypes have already utilized a variety of implementation technologies in an effort to address different performance and scalability concerns. This has been greatly facilitated by the fact that, at the architectural level, the RCMES is fundamentally domain agnostic. Strictly separating the data model from the implementation has enabled us to create a reusable architecture that we believe can be modified and configured to suit the demands of researchers in other domains.

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

PubMed Central

Thibaud-Nissen, Françoise; Campbell, Matthew; Hamilton, John P; Zhu, Wei; Buell, C Robin

2007-01-01

Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1) the submission of gene annotation to an annotation project, 2) the review of the submitted models by project annotators, and 3) the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP), an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA) has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs) in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website , as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the structural and/or functional annotation of 1,094 genes representing 57 families have been deposited and integrated into the current gene set. All of the EuCAP components are open-source, thereby allowing the implementation of EuCAP for the annotation of other genomes. EuCAP is available at . PMID:17961238

Mysql Data-Base Applications for Dst-Like Physics Analysis

NASA Astrophysics Data System (ADS)

Tsenov, Roumen

2004-07-01

The data and analysis model developed and being used in the HARP experiment for studying hadron production at CERN Proton Synchrotron is discussed. Emphasis is put on usage of data-base (DB) back-ends for persistent storing and retrieving "alive" C++ objects encapsulating raw and reconstructed data. Concepts of "Data Summary Tape" (DST) as a logical collection of DB-persistent data of different types, and of "intermediate DST" (iDST) as a physical "tag" of DST, are introduced. iDST level of persistency allows a powerful, DST-level of analysis to be performed by applications running on an isolated machine (even laptop) with no connection to the experiment's main data storage. Implementation of these concepts is considered.

Directed use of the internet for health information by patients with chronic kidney disease: prospective cohort study.

PubMed

Diamantidis, Clarissa Jonas; Fink, Wanda; Yang, Shiming; Zuckerman, Marni R; Ginsberg, Jennifer; Hu, Peter; Xiao, Yan; Fink, Jeffrey C

2013-11-15

Health information technology has become common in the care of patients with chronic diseases; however, there are few such applications employed in kidney disease. The aim of the study was to evaluate the use of a website providing disease-specific safety information by patients with predialysis chronic kidney disease. As part of the Safe Kidney Care (SKC) study, an educational website was designed to provide information on safety concerns in chronic kidney disease. Phase I study participants were provided a medical alert accessory with a unique ID number, the Safe Kidney Care website, and an in-person tutorial on the use of the Internet and accessing the SKC website at baseline. Participants were asked to visit the website and enter their unique ID as frequently as they desired over the next 365 days or until their annual follow-up visit, whichever occurred first. Participants' visits and dwell times on specific safety modules were tracked using embedded webpage PHP scripts linked to a MySQL database, enabling the collection of website usage statistics. Of 108 Phase I participants, 28.7% (31/108) visited the website from 1-6 times during the observation period (median follow-up 365 days). Median access time was 7 minutes per visit (range <1-46) and 13 minutes per person (range <1-123). The three most frequently visited pages were "Renal function calculator", "Pills to avoid", and "Foods to avoid". High school education and frequent Internet use were significantly associated with website entry (P=.02 and P=.03, respectively). Preliminary results show general interest in a Web-based platform designed to improve patient safety in chronic kidney disease. Clinicaltrials.gov NCT01407367; http://clinicaltrials.gov/show/NCT01407367 (Archived by WebCite at http://www.webcitation.org/6KvxFKA6M).

The HISTMAG database: combining historical, archaeomagnetic and volcanic data

NASA Astrophysics Data System (ADS)

Arneitz, Patrick; Leonhardt, Roman; Schnepp, Elisabeth; Heilig, Balázs; Mayrhofer, Franziska; Kovacs, Peter; Hejda, Pavel; Valach, Fridrich; Vadasz, Gergely; Hammerl, Christa; Egli, Ramon; Fabian, Karl; Kompein, Niko

2017-09-01

Records of the past geomagnetic field can be divided into two main categories. These are instrumental historical observations on the one hand, and field estimates based on the magnetization acquired by rocks, sediments and archaeological artefacts on the other hand. In this paper, a new database combining historical, archaeomagnetic and volcanic records is presented. HISTMAG is a relational database, implemented in MySQL, and can be accessed via a web-based interface (http://www.conrad-observatory.at/zamg/index.php/data-en/histmag-database). It combines available global historical data compilations covering the last ∼500 yr as well as archaeomagnetic and volcanic data collections from the last 50 000 yr. Furthermore, new historical and archaeomagnetic records, mainly from central Europe, have been acquired. In total, 190 427 records are currently available in the HISTMAG database, whereby the majority is related to historical declination measurements (155 525). The original database structure was complemented by new fields, which allow for a detailed description of the different data types. A user-comment function provides the possibility for a scientific discussion about individual records. Therefore, HISTMAG database supports thorough reliability and uncertainty assessments of the widely different data sets, which are an essential basis for geomagnetic field reconstructions. A database analysis revealed systematic offset for declination records derived from compass roses on historical geographical maps through comparison with other historical records, while maps created for mining activities represent a reliable source.

DB-PABP: a database of polyanion-binding proteins

PubMed Central

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Russell Middaugh, C.

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references. PMID:17916573

DB-PABP: a database of polyanion-binding proteins.

PubMed

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

WebaCGH: an interactive online tool for the analysis and display of array comparative genomic hybridisation data.

PubMed

Frankenberger, Casey; Wu, Xiaolin; Harmon, Jerry; Church, Deanna; Gangi, Lisa M; Munroe, David J; Urzúa, Ulises

2006-01-01

Gene copy number variations occur both in normal cells and in numerous pathologies including cancer and developmental diseases. Array comparative genomic hybridisation (aCGH) is an emerging technology that allows detection of chromosomal gains and losses in a high-resolution format. When aCGH is performed on cDNA and oligonucleotide microarrays, the impact of DNA copy number on gene transcription profiles may be directly compared. We have created an online software tool, WebaCGH, that functions to (i) upload aCGH and gene transcription results from multiple experiments; (ii) identify significant aberrant regions using a local Z-score threshold in user-selected chromosomal segments subjected to smoothing with moving averages; and (iii) display results in a graphical format with full genome and individual chromosome views. In the individual chromosome display, data can be zoomed in/out in both dimensions (i.e. ratio and physical location) and plotted features can have 'mouse over' linking to outside databases to identify loci of interest. Uploaded data can be stored indefinitely for subsequent retrieval and analysis. WebaCGH was created as a Java-based web application using the open-source database MySQL. WebaCGH is freely accessible at http://129.43.22.27/WebaCGH/welcome.htm Xiaolin Wu (forestwu@mail.nih.gov) or Ulises Urzúa (uurzua@med.uchile.cl).

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2014-01-15

Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

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 Development and Preliminary Application Ofplant Quarantine Remote Teaching System Inchina

NASA Astrophysics Data System (ADS)

Wu, Zhigang; Li, Zhihong; Yang, Ding; Zhang, Guozhen

With the development of modern information technology, the traditional teaching mode becomes more deficient for the requirement of modern education. Plant Quarantine has been accepted as the common course for the universities of agriculture in China after the entry of WTO. But the teaching resources of this course are not enough especially for most universities with lack base. The characteristic of e-learning is regarded as one way to solve the problem of short teaching resource. PQRTS (Plant Quarantine Remote Teaching System) was designed and developed with JSP (Java Sever Pages), MySQL and Tomcat in this study. The system included many kinds of plant quarantine teaching resources, such as international glossary, regulations and standards, multimedia information of quarantine process and pests, ppt files of teaching, and training exercise. The system prototype implemented the functions of remote learning, querying, management, examination and remote discussion. It could be a tool for teaching, teaching assistance and learning online.

Development of computer-assisted instruction application for statistical data analysis android platform as learning resource

NASA Astrophysics Data System (ADS)

Hendikawati, P.; Arifudin, R.; Zahid, M. Z.

2018-03-01

This study aims to design an android Statistics Data Analysis application that can be accessed through mobile devices to making it easier for users to access. The Statistics Data Analysis application includes various topics of basic statistical along with a parametric statistics data analysis application. The output of this application system is parametric statistics data analysis that can be used for students, lecturers, and users who need the results of statistical calculations quickly and easily understood. Android application development is created using Java programming language. The server programming language uses PHP with the Code Igniter framework, and the database used MySQL. The system development methodology used is the Waterfall methodology with the stages of analysis, design, coding, testing, and implementation and system maintenance. This statistical data analysis application is expected to support statistical lecturing activities and make students easier to understand the statistical analysis of mobile devices.

The VERITAS Facility: A Virtual Environment Platform for Human Performance Research

DTIC Science & Technology

2016-01-01

IAE The IAE supports the audio environment that users experience during the course of an experiment. This includes environmental sounds, user-to...future, we are looking towards a database-based system that would use MySQL or an equivalent product to store the large data sets and provide standard

Mining Bug Databases for Unidentified Software Vulnerabilities

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

Dumidu Wijayasekara; Milos Manic; Jason Wright

2012-06-01

Identifying software vulnerabilities is becoming more important as critical and sensitive systems increasingly rely on complex software systems. It has been suggested in previous work that some bugs are only identified as vulnerabilities long after the bug has been made public. These vulnerabilities are known as hidden impact vulnerabilities. This paper discusses the feasibility and necessity to mine common publicly available bug databases for vulnerabilities that are yet to be identified. We present bug database analysis of two well known and frequently used software packages, namely Linux kernel and MySQL. It is shown that for both Linux and MySQL, amore » significant portion of vulnerabilities that were discovered for the time period from January 2006 to April 2011 were hidden impact vulnerabilities. It is also shown that the percentage of hidden impact vulnerabilities has increased in the last two years, for both software packages. We then propose an improved hidden impact vulnerability identification methodology based on text mining bug databases, and conclude by discussing a few potential problems faced by such a classifier.« less

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies.

PubMed

Cannistraci, Carlo V; Ogorevc, Jernej; Zorc, Minja; Ravasi, Timothy; Dovc, Peter; Kunej, Tanja

2013-02-14

Cryptorchidism is the most frequent congenital disorder in male children; however the genetic causes of cryptorchidism remain poorly investigated. Comparative integratomics combined with systems biology approach was employed to elucidate genetic factors and molecular pathways underlying testis descent. Literature mining was performed to collect genomic loci associated with cryptorchidism in seven mammalian species. Information regarding the collected candidate genes was stored in MySQL relational database. Genomic view of the loci was presented using Flash GViewer web tool (http://gmod.org/wiki/Flashgviewer/). DAVID Bioinformatics Resources 6.7 was used for pathway enrichment analysis. Cytoscape plug-in PiNGO 1.11 was employed for protein-network-based prediction of novel candidate genes. Relevant protein-protein interactions were confirmed and visualized using the STRING database (version 9.0). The developed cryptorchidism gene atlas includes 217 candidate loci (genes, regions involved in chromosomal mutations, and copy number variations) identified at the genomic, transcriptomic, and proteomic level. Human orthologs of the collected candidate loci were presented using a genomic map viewer. The cryptorchidism gene atlas is freely available online: http://www.integratomics-time.com/cryptorchidism/. Pathway analysis suggested the presence of twelve enriched pathways associated with the list of 179 literature-derived candidate genes. Additionally, a list of 43 network-predicted novel candidate genes was significantly associated with four enriched pathways. Joint pathway analysis of the collected and predicted candidate genes revealed the pivotal importance of the muscle-contraction pathway in cryptorchidism and evidence for genomic associations with cardiomyopathy pathways in RASopathies. The developed gene atlas represents an important resource for the scientific community researching genetics of cryptorchidism. The collected data will further facilitate development of novel genetic markers and could be of interest for functional studies in animals and human. The proposed network-based systems biology approach elucidates molecular mechanisms underlying co-presence of cryptorchidism and cardiomyopathy in RASopathies. Such approach could also aid in molecular explanation of co-presence of diverse and apparently unrelated clinical manifestations in other syndromes.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

PubMed Central

2014-01-01

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow. PMID:25565494

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.

PubMed

Merelli, Ivan; Caprera, Andrea; Stella, Alessandra; Del Corvo, Marcello; Milanesi, Luciano; Lazzari, Barbara

2009-10-15

The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can be inspected according to biologically relevant criteria. EST data can be browsed using different dedicated web resources, which allow to investigate library specific gene expression levels and to make comparisons among libraries, highlighting significant differences in gene expression. Nonetheless, no tool is available to examine distributions of quantitative EST collections in Gene Ontology (GO) categories, nor to retrieve information concerning library-dependent EST involvement in metabolic pathways. In this work we present the Human EST Ontology Explorer (HEOE) http://www.itb.cnr.it/ptp/human_est_explorer, a web facility for comparison of expression levels among libraries from several healthy and diseased tissues. The HEOE provides library-dependent statistics on the distribution of sequences in the GO Direct Acyclic Graph (DAG) that can be browsed at each GO hierarchical level. The tool is based on large-scale BLAST annotation of EST sequences. Due to the huge number of input sequences, this BLAST analysis was performed with the aid of grid computing technology, which is particularly suitable to address data parallel task. Relying on the achieved annotation, library-specific distributions of ESTs in the GO Graph were inferred. A pathway-based search interface was also implemented, for a quick evaluation of the representation of libraries in metabolic pathways. EST processing steps were integrated in a semi-automatic procedure that relies on Perl scripts and stores results in a MySQL database. A PHP-based web interface offers the possibility to simultaneously visualize, retrieve and compare data from the different libraries. Statistically significant differences in GO categories among user selected libraries can also be computed. The HEOE provides an alternative and complementary way to inspect EST expression levels with respect to approaches currently offered by other resources. Furthermore, BLAST computation on the whole human EST dataset was a suitable test of grid scalability in the context of large-scale bioinformatics analysis. The HEOE currently comprises sequence analysis from 70 non-normalized libraries, representing a comprehensive overview on healthy and unhealthy tissues. As the analysis procedure can be easily applied to other libraries, the number of represented tissues is intended to increase.

A Magnetic Petrology Database for Satellite Magnetic Anomaly Interpretations

NASA Astrophysics Data System (ADS)

Nazarova, K.; Wasilewski, P.; Didenko, A.; Genshaft, Y.; Pashkevich, I.

2002-05-01

A Magnetic Petrology Database (MPDB) is now being compiled at NASA/Goddard Space Flight Center in cooperation with Russian and Ukrainian Institutions. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via Internet for more realistic interpretation of satellite magnetic anomalies. Magnetic Petrology Data had been accumulated in NASA/Goddard Space Flight Center, United Institute of Physics of the Earth (Russia) and Institute of Geophysics (Ukraine) over several decades and now consists of many thousands of records of data in our archives. The MPDB was, and continues to be in big demand especially since recent launching in near Earth orbit of the mini-constellation of three satellites - Oersted (in 1999), Champ (in 2000), and SAC-C (in 2000) which will provide lithospheric magnetic maps with better spatial and amplitude resolution (about 1 nT). The MPDB is focused on lower crustal and upper mantle rocks and will include data on mantle xenoliths, serpentinized ultramafic rocks, granulites, iron quartzites and rocks from Archean-Proterozoic metamorphic sequences from all around the world. A substantial amount of data is coming from the area of unique Kursk Magnetic Anomaly and Kola Deep Borehole (which recovered 12 km of continental crust). A prototype MPDB can be found on the Geodynamics Branch web server of Goddard Space Flight Center at http://core2.gsfc.nasa.gov/terr_mag/magnpetr.html. The MPDB employs a searchable relational design and consists of 7 interrelated tables. The schema of database is shown at http://core2.gsfc.nasa.gov/terr_mag/doc.html. MySQL database server was utilized to implement MPDB. The SQL (Structured Query Language) is used to query the database. To present the results of queries on WEB and for WEB programming we utilized PHP scripting language and CGI scripts. The prototype MPDB is designed to search database by major satellite magnetic anomaly, tectonic structure, geographical location, rock type, magnetic properties, chemistry and reference, see http://core2.gsfc.nasa.gov/terr_mag/query1.html. The output of database is HTML structured table, text file, and downloadable file. This database will be very useful for studies of lithospheric satellite magnetic anomalies on the Earth and other terrestrial planets.

FCDD: A Database for Fruit Crops Diseases.

PubMed

Chauhan, Rupal; Jasrai, Yogesh; Pandya, Himanshu; Chaudhari, Suman; Samota, Chand Mal

2014-01-01

Fruit Crops Diseases Database (FCDD) requires a number of biotechnology and bioinformatics tools. The FCDD is a unique bioinformatics resource that compiles information about 162 details on fruit crops diseases, diseases type, its causal organism, images, symptoms and their control. The FCDD contains 171 phytochemicals from 25 fruits, their 2D images and their 20 possible sequences. This information has been manually extracted and manually verified from numerous sources, including other electronic databases, textbooks and scientific journals. FCDD is fully searchable and supports extensive text search. The main focus of the FCDD is on providing possible information of fruit crops diseases, which will help in discovery of potential drugs from one of the common bioresource-fruits. The database was developed using MySQL. The database interface is developed in PHP, HTML and JAVA. FCDD is freely available. http://www.fruitcropsdd.com/

[The development and evaluation of software to verify diagnostic accuracy].

PubMed

Jensen, Rodrigo; de Moraes Lopes, Maria Helena Baena; Silveira, Paulo Sérgio Panse; Ortega, Neli Regina Siqueira

2012-02-01

This article describes the development and evaluation of software that verifies the accuracy of diagnoses made by nursing students. The software was based on a model that uses fuzzy logic concepts, including PERL, the MySQL database for Internet accessibility, and the NANDA-I 2007-2008 classification system. The software was evaluated in terms of its technical quality and usability through specific instruments. The activity proposed in the software involves four stages in which students establish the relationship values between nursing diagnoses, defining characteristics/risk factors and clinical cases. The relationship values determined by students are compared to those of specialists, generating performance scores for the students. In the evaluation, the software demonstrated satisfactory outcomes regarding the technical quality and, according to the students, helped in their learning and may become an educational tool to teach the process of nursing diagnosis.

CGDM: collaborative genomic data model for molecular profiling data using NoSQL.

PubMed

Wang, Shicai; Mares, Mihaela A; Guo, Yi-Ke

2016-12-01

High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets. However, more improvement can be achieved, particularly through better indexing techniques of the Key Value models, taking advantage of the types of queries which are specific for the high-throughput molecular profiling data. In this article, we introduce a Collaborative Genomic Data Model (CGDM), aimed at significantly increasing the query processing speed for the main classes of queries on genomic databases. CGDM creates three Collaborative Global Clustering Index Tables (CGCITs) to solve the velocity and variety issues at the cost of limited extra volume. Several benchmarking experiments were carried out, comparing CGDM implemented on HBase to the traditional SQL data model (TDM) implemented on both HBase and MySQL Cluster, using large publicly available molecular profiling datasets taken from NCBI and HapMap. In the microarray case, CGDM on HBase performed up to 246 times faster than TDM on HBase and 7 times faster than TDM on MySQL Cluster. In single nucleotide polymorphism case, CGDM on HBase outperformed TDM on HBase by up to 351 times and TDM on MySQL Cluster by up to 9 times. The CGDM source code is available at https://github.com/evanswang/CGDM. y.guo@imperial.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Look Under the Hood: How the JPL Tropical Cyclone Information System Uses Database Technologies to Present Big Data to Users

NASA Astrophysics Data System (ADS)

Knosp, B.; Gangl, M.; Hristova-Veleva, S. M.; Kim, R. M.; Li, P.; Turk, J.; Vu, Q. A.

2015-12-01

The JPL Tropical Cyclone Information System (TCIS) brings together satellite, aircraft, and model forecast data from several NASA, NOAA, and other data centers to assist researchers in comparing and analyzing data and model forecast related to tropical cyclones. The TCIS has been running a near-real time (NRT) data portal during North Atlantic hurricane season that typically runs from June through October each year, since 2010. Data collected by the TCIS varies by type, format, contents, and frequency and is served to the user in two ways: (1) as image overlays on a virtual globe and (2) as derived output from a suite of analysis tools. In order to support these two functions, the data must be collected and then made searchable by criteria such as date, mission, product, pressure level, and geospatial region. Creating a database architecture that is flexible enough to manage, intelligently interrogate, and ultimately present this disparate data to the user in a meaningful way has been the primary challenge. The database solution for the TCIS has been to use a hybrid MySQL + Solr implementation. After testing other relational database and NoSQL solutions, such as PostgreSQL and MongoDB respectively, this solution has given the TCIS the best offerings in terms of query speed and result reliability. This database solution also supports the challenging (and memory overwhelming) geospatial queries that are necessary to support analysis tools requested by users. Though hardly new technologies on their own, our implementation of MySQL + Solr had to be customized and tuned to be able to accurately store, index, and search the TCIS data holdings. In this presentation, we will discuss how we arrived on our MySQL + Solr database architecture, why it offers us the most consistent fast and reliable results, and how it supports our front end so that we can offer users a look into our "big data" holdings.

Shark: Fast Data Analysis Using Coarse-grained Distributed Memory

DTIC Science & Technology

2013-05-01

Schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 7.1.1 Java Objects...often MySQL or Derby) with a namespace for tables, table metadata, and par- tition information. Table data is stored in an HDFS directory, while a...saving time and space for large data sets. This is achieved with support for custom SerDe (serialization/deserialization) java interface implementations

searchSCF: Using MongoDB to Enable Richer Searches of Locally Hosted Science Data Repositories

NASA Astrophysics Data System (ADS)

Knosp, B.

2016-12-01

Science teams today are in the unusual position of almost having too much data available to them. Modern sensors and models are capable of outputting terabytes of data per day, which can make it difficult to find specific subsets of data. The sheer size of files can also make it time consuming to retrieve this big data from national data archive centers. Thus, many science teams choose to store what data they can on their local systems, but they are not always equipped with tools to help them intelligently organize and search their data. In its local data repository, the Aura Microwave Limb Sounder (MLS) science team at NASA's Jet Propulsion Laboratory has collected over 300TB of atmospheric science data from 71 missions/models that aid in validation, algorithm development, and research activities. When the project began, the team developed a MySQL database to aid in data queries, but this database was only designed to keep track of MLS and a few ancillary data sets, leving much of the data uncatalogued. The team has also seen database query time rise over the life of the mission. Even though the MLS science team's data holdings are not the size of a national data center's, team members still need tools to help them discover and utilize the data that they have on-hand. Over the past year, members of the science team have been looking for solutions to (1) store information on all the data sets they have collected in a single database, (2) store more metadata about each data file, (3) develop queries that can find relationships among these disparate data types, and (4) plug any new functions developed around this database into existing analysis, visualization, and web tools, transparently to users. In this presentation, I will discuss the searchSCF package that is currently under development. This package includes a NoSQL database management system (MongoDB) and a set of Python tools that both ingests data into the database and supports user queries. I will also highlight case studies of how this system could be used by the MLS science team, and how it could be implemented by other science teams with local data repositories.

Automating Data Submission to a National Archive

NASA Astrophysics Data System (ADS)

Work, T. T.; Chandler, C. L.; Groman, R. C.; Allison, M. D.; Gegg, S. R.; Biological; Chemical Oceanography Data Management Office

2010-12-01

In late 2006, the U.S. National Science Foundation (NSF) funded the Biological and Chemical Oceanographic Data Management Office (BCO-DMO) at Woods Hole Oceanographic Institution (WHOI) to work closely with investigators to manage oceanographic data generated from their research projects. One of the final data management tasks is to ensure that the data are permanently archived at the U.S. National Oceanographic Data Center (NODC) or other appropriate national archiving facility. In the past, BCO-DMO submitted data to NODC as an email with attachments including a PDF file (a manually completed metadata record) and one or more data files. This method is no longer feasible given the rate at which data sets are contributed to BCO-DMO. Working with collaborators at NODC, a more streamlined and automated workflow was developed to keep up with the increased volume of data that must be archived at NODC. We will describe our new workflow; a semi-automated approach for contributing data to NODC that includes a Federal Geographic Data Committee (FGDC) compliant Extensible Markup Language (XML) metadata file accompanied by comma-delimited data files. The FGDC XML file is populated from information stored in a MySQL database. A crosswalk described by an Extensible Stylesheet Language Transformation (XSLT) is used to transform the XML formatted MySQL result set to a FGDC compliant XML metadata file. To ensure data integrity, the MD5 algorithm is used to generate a checksum and manifest of the files submitted to NODC for permanent archive. The revised system supports preparation of detailed, standards-compliant metadata that facilitate data sharing and enable accurate reuse of multidisciplinary information. The approach is generic enough to be adapted for use by other data management groups.

GenomeVista

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

Poliakov, Alexander; Couronne, Olivier

2002-11-04

Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program tomore » find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

OpenElectrophy: An Electrophysiological Data- and Analysis-Sharing Framework

PubMed Central

Garcia, Samuel; Fourcaud-Trocmé, Nicolas

2008-01-01

Progress in experimental tools and design is allowing the acquisition of increasingly large datasets. Storage, manipulation and efficient analyses of such large amounts of data is now a primary issue. We present OpenElectrophy, an electrophysiological data- and analysis-sharing framework developed to fill this niche. It stores all experiment data and meta-data in a single central MySQL database, and provides a graphic user interface to visualize and explore the data, and a library of functions for user analysis scripting in Python. It implements multiple spike-sorting methods, and oscillation detection based on the ridge extraction methods due to Roux et al. (2007). OpenElectrophy is open source and is freely available for download at http://neuralensemble.org/trac/OpenElectrophy. PMID:19521545

Promoting Teachers' Positive Attitude towards Web Use: A Study in Web Site Development

ERIC Educational Resources Information Center

Akpinar, Yavuz; Bayramoglu, Yusuf

2008-01-01

The purpose of the study was to examine effects of a compact training for developing web sites on teachers' web attitude, as composed of: web self efficacy, perceived web enjoyment, perceived web usefulness and behavioral intention to use the web. To measure the related constructs, the Web Attitude Scale was adapted into Turkish and tested with a…

Development of Integrated Information System for Travel Bureau Company

NASA Astrophysics Data System (ADS)

Karma, I. G. M.; Susanti, J.

2018-01-01

Related to the effectiveness of decision-making by the management of travel bureau company, especially by managers, information serves frequent delays or incomplete. Although already computer-assisted, the existing application-based is used only handle one particular activity only, not integrated. This research is intended to produce an integrated information system that handles the overall operational activities of the company. By applying the object-oriented system development approach, the system is built with Visual Basic. Net programming language and MySQL database package. The result is a system that consists of 4 (four) separated program packages, including Reservation System, AR System, AP System and Accounting System. Based on the output, we can conclude that this system is able to produce integrated information that related to the problem of reservation, operational and financial those produce up-to-date information in order to support operational activities and decisionmaking process by related parties.

Project Management Software for Distributed Industrial Companies

NASA Astrophysics Data System (ADS)

Dobrojević, M.; Medjo, B.; Rakin, M.; Sedmak, A.

This paper gives an overview of the development of a new software solution for project management, intended mainly to use in industrial environment. The main concern of the proposed solution is application in everyday engineering practice in various, mainly distributed industrial companies. Having this in mind, special care has been devoted to development of appropriate tools for tracking, storing and analysis of the information about the project, and in-time delivering to the right team members or other responsible persons. The proposed solution is Internet-based and uses LAMP/WAMP (Linux or Windows - Apache - MySQL - PHP) platform, because of its stability, versatility, open source technology and simple maintenance. Modular structure of the software makes it easy for customization according to client specific needs, with a very short implementation period. Its main advantages are simple usage, quick implementation, easy system maintenance, short training and only basic computer skills needed for operators.

Design of Experiment and Analysis for the Joint Dynamic Allocation of Fires and Sensors (JDAFS) Simulation

DTIC Science & Technology

2007-06-01

other databases such as MySQL , Oracle , and Derby will be added to future versions of the program. Setting a factor requires more than changing a single...Non-Penetrating vs . Penetrating Results.............106 a. Coverage...Interaction Profile for D U-2 and C RQ-4 .......................................................89 Figure 59. R-Squared vs . Number of Regression Tree

Using Learning Analytics to Identify Medical Student Misconceptions in an Online Virtual Patient Environment

ERIC Educational Resources Information Center

Poitras, Eric G.; Naismith, Laura M.; Doleck, Tenzin; Lajoie, Susanne P.

2016-01-01

This study aimed to identify misconceptions in medical student knowledge by mining user interactions in the MedU online learning environment. Data from 13000 attempts at a single virtual patient case were extracted from the MedU MySQL database. A subgroup discovery method was applied to identify patterns in learner-generated annotations and…

Looking toward the Future: A Case Study of Open Source Software in the Humanities

ERIC Educational Resources Information Center

Quamen, Harvey

2006-01-01

In this article Harvey Quamen examines how the philosophy of open source software might be of particular benefit to humanities scholars in the near future--particularly for academic journals with limited financial resources. To this end he provides a case study in which he describes his use of open source technology (MySQL database software and…

PylotDB - A Database Management, Graphing, and Analysis Tool Written in Python

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

Barnette, Daniel W.

2012-01-04

PylotDB, written completely in Python, provides a user interface (UI) with which to interact with, analyze, graph data from, and manage open source databases such as MySQL. The UI mitigates the user having to know in-depth knowledge of the database application programming interface (API). PylotDB allows the user to generate various kinds of plots from user-selected data; generate statistical information on text as well as numerical fields; backup and restore databases; compare database tables across different databases as well as across different servers; extract information from any field to create new fields; generate, edit, and delete databases, tables, and fields;more » generate or read into a table CSV data; and similar operations. Since much of the database information is brought under control of the Python computer language, PylotDB is not intended for huge databases for which MySQL and Oracle, for example, are better suited. PylotDB is better suited for smaller databases that might be typically needed in a small research group situation. PylotDB can also be used as a learning tool for database applications in general.« less

Experience with Multi-Tier Grid MySQL Database Service Resiliency at BNL

NASA Astrophysics Data System (ADS)

Wlodek, Tomasz; Ernst, Michael; Hover, John; Katramatos, Dimitrios; Packard, Jay; Smirnov, Yuri; Yu, Dantong

2011-12-01

We describe the use of F5's BIG-IP smart switch technology (3600 Series and Local Traffic Manager v9.0) to provide load balancing and automatic fail-over to multiple Grid services (GUMS, VOMS) and their associated back-end MySQL databases. This resiliency is introduced in front of the external application servers and also for the back-end database systems, which is what makes it "multi-tier". The combination of solutions chosen to ensure high availability of the services, in particular the database replication and fail-over mechanism, are discussed in detail. The paper explains the design and configuration of the overall system, including virtual servers, machine pools, and health monitors (which govern routing), as well as the master-slave database scheme and fail-over policies and procedures. Pre-deployment planning and stress testing will be outlined. Integration of the systems with our Nagios-based facility monitoring and alerting is also described. And application characteristics of GUMS and VOMS which enable effective clustering will be explained. We then summarize our practical experiences and real-world scenarios resulting from operating a major US Grid center, and assess the applicability of our approach to other Grid services in the future.

Service architecture challenges in building the KNMI Data Centre

NASA Astrophysics Data System (ADS)

Som de Cerff, Wim; van de Vegte, John; Plieger, Maarten; de Vreede, Ernst; Sluiter, Raymond; Willem Noteboom, Jan; van der Neut, Ian; Verhoef, Hans; van Versendaal, Robert; van Binnendijk, Martin; Kalle, Henk; Knopper, Arthur; Calis, Gijs; Ha, Siu Siu; van Moosel, WIm; Klein Ikkink, Henk-Jan; Tosun, Tuncay

2013-04-01

One of the objectives of KNMI is to act as a National Data centre for weather, climate and seismological data. KNMI has experience in curation of data for many years however important scientific data is not well accessible. New technologies also are available to improve the current infrastructure. Therefore a data curation program is initiated with two main goals: setup a Satellite Data Platform (SDP) and a KNMI data centre (KDC). KDC will provide, besides curation, data access, and storage and retrieval portal for KNMI data. In 2010 first requirements were gathered, in 2011 the main architecture was sketched, KDC was implemented in 2012 and is available on: http://data.knmi.nl KDC is built with the data providers involved with as key challenge: 'adding a dataset should be as simple as creating an HTML page'. This is enabled by a three step process, in which the data provider is responsible for two steps: 1. Provide dataset metadata: An easy to use web interface for providing metadata, with automated validation. Metadata consists of an ISO 19115 profile (matching INSPIRE and WMO requirements) and additional technical metadata regarding the data structure and access rights to the data. The interface hides certain metadata fields, which are filed by KDC automatically. 2. Provide data: after metadata has been entered, an upload location for uploading the dataset is provided. Also scripts for pushing large datasets are available. 3. Process and publish: once files are uploaded, they are processed for metadata (e.g., geolocation, time, version) and made available in KDC. The data is put into archive and made available using the in-house developed Virtual File System, which provides a persistent virtual path to the data. For the end-user of the data, KDC provides a web interface with search filters on key words, geolocation and time. Data can be downloaded using HTTP or FTP and can be scripted. Users can register to gain access to restricted datasets. The architecture combines Open Source software components (e.g. Geonetwork, Magnolia, MongoDB, MySQL) with in-house built software (ADAGUC, NADC) and newly developed software. Challenges faced and solved are: How to deal with the different file formats used at KNMI? (e.g. NetCDF, GRIB, BUFR, ASCII); How to deal with the different metadata profiles while hiding the complexity of this to the user? How to incorporate the existing archives? KDC is a node in several networks (WMO WIS, INSPIRE, Open Data): how to do this? In the presentation/poster we will describe what has been done for each of these challenges and how it is implemented in KDC.

ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

PubMed

Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

2012-09-08

The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

PubMed Central

2012-01-01

Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system

PubMed Central

Diener, Stephen E; Houfek, Thomas D; Kalat, Sam E; Windham, DE; Burke, Mark; Opperman, Charles; Dean, Ralph A

2005-01-01

Background - Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. Results - Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. Conclusion - This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists. PMID:15958161

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information.

PubMed

Knowlton, Michelle N; Li, Tongbin; Ren, Yongliang; Bill, Brent R; Ellis, Lynda Bm; Ekker, Stephen C

2008-01-07

The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies. The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced. MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.

Integrated image data and medical record management for rare disease registries. A general framework and its instantiation to theGerman Calciphylaxis Registry.

PubMed

Deserno, Thomas M; Haak, Daniel; Brandenburg, Vincent; Deserno, Verena; Classen, Christoph; Specht, Paula

2014-12-01

Especially for investigator-initiated research at universities and academic institutions, Internet-based rare disease registries (RDR) are required that integrate electronic data capture (EDC) with automatic image analysis or manual image annotation. We propose a modular framework merging alpha-numerical and binary data capture. In concordance with the Office of Rare Diseases Research recommendations, a requirement analysis was performed based on several RDR databases currently hosted at Uniklinik RWTH Aachen, Germany. With respect to the study management tool that is already successfully operating at the Clinical Trial Center Aachen, the Google Web Toolkit was chosen with Hibernate and Gilead connecting a MySQL database management system. Image and signal data integration and processing is supported by Apache Commons FileUpload-Library and ImageJ-based Java code, respectively. As a proof of concept, the framework is instantiated to the German Calciphylaxis Registry. The framework is composed of five mandatory core modules: (1) Data Core, (2) EDC, (3) Access Control, (4) Audit Trail, and (5) Terminology as well as six optional modules: (6) Binary Large Object (BLOB), (7) BLOB Analysis, (8) Standard Operation Procedure, (9) Communication, (10) Pseudonymization, and (11) Biorepository. Modules 1-7 are implemented in the German Calciphylaxis Registry. The proposed RDR framework is easily instantiated and directly integrates image management and analysis. As open source software, it may assist improved data collection and analysis of rare diseases in near future.

Wolf Testing: Open Source Testing Software

NASA Astrophysics Data System (ADS)

Braasch, P.; Gay, P. L.

2004-12-01

Wolf Testing is software for easily creating and editing exams. Wolf Testing allows the user to create an exam from a database of questions, view it on screen, and easily print it along with the corresponding answer guide. The questions can be multiple choice, short answer, long answer, or true and false varieties. This software can be accessed securely from any location, allowing the user to easily create exams from home. New questions, which can include associated pictures, can be added through a web-interface. After adding in questions, they can be edited, deleted, or duplicated into multiple versions. Long-term test creation is simplified, as you are able to quickly see what questions you have asked in the past and insert them, with or without editing, into future tests. All tests are archived in the database. Written in PHP and MySQL, this software can be installed on any UNIX / Linux platform, including Macintosh OS X. The secure interface keeps students out, and allows you to decide who can create tests and who can edit information already in the database. Tests can be output as either html with pictures or rich text without pictures, and there are plans to add PDF and MS Word formats as well. We would like to thank Dr. Wolfgang Rueckner and the Harvard University Science Center for providing incentive to start this project, computers and resources to complete this project, and inspiration for the project's name. We would also like to thank Dr. Ronald Newburgh for his assistance in beta testing.

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean.

PubMed

Pagliosa, Paulo R; Doria, João G; Misturini, Dairana; Otegui, Mariana B P; Oortman, Mariana S; Weis, Wilson A; Faroni-Perez, Larisse; Alves, Alexandre P; Camargo, Maurício G; Amaral, A Cecília Z; Marques, Antonio C; Lana, Paulo C

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/.

LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory

PubMed Central

Milsted, Andrew J.; Hale, Jennifer R.; Frey, Jeremy G.; Neylon, Cameron

2013-01-01

Background The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research. Methodology/Principal Findings We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system. Conclusions/Significance LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment. PMID:23935832

Toward an Open-Access Global Database for Mapping, Control, and Surveillance of Neglected Tropical Diseases

PubMed Central

Hürlimann, Eveline; Schur, Nadine; Boutsika, Konstantina; Stensgaard, Anna-Sofie; Laserna de Himpsl, Maiti; Ziegelbauer, Kathrin; Laizer, Nassor; Camenzind, Lukas; Di Pasquale, Aurelio; Ekpo, Uwem F.; Simoonga, Christopher; Mushinge, Gabriel; Saarnak, Christopher F. L.; Utzinger, Jürg; Kristensen, Thomas K.; Vounatsou, Penelope

2011-01-01

Background After many years of general neglect, interest has grown and efforts came under way for the mapping, control, surveillance, and eventual elimination of neglected tropical diseases (NTDs). Disease risk estimates are a key feature to target control interventions, and serve as a benchmark for monitoring and evaluation. What is currently missing is a georeferenced global database for NTDs providing open-access to the available survey data that is constantly updated and can be utilized by researchers and disease control managers to support other relevant stakeholders. We describe the steps taken toward the development of such a database that can be employed for spatial disease risk modeling and control of NTDs. Methodology With an emphasis on schistosomiasis in Africa, we systematically searched the literature (peer-reviewed journals and ‘grey literature’), contacted Ministries of Health and research institutions in schistosomiasis-endemic countries for location-specific prevalence data and survey details (e.g., study population, year of survey and diagnostic techniques). The data were extracted, georeferenced, and stored in a MySQL database with a web interface allowing free database access and data management. Principal Findings At the beginning of 2011, our database contained more than 12,000 georeferenced schistosomiasis survey locations from 35 African countries available under http://www.gntd.org. Currently, the database is expanded to a global repository, including a host of other NTDs, e.g. soil-transmitted helminthiasis and leishmaniasis. Conclusions An open-access, spatially explicit NTD database offers unique opportunities for disease risk modeling, targeting control interventions, disease monitoring, and surveillance. Moreover, it allows for detailed geostatistical analyses of disease distribution in space and time. With an initial focus on schistosomiasis in Africa, we demonstrate the proof-of-concept that the establishment and running of a global NTD database is feasible and should be expanded without delay. PMID:22180793

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

PubMed Central

Pagliosa, Paulo R.; Doria, João G.; Misturini, Dairana; Otegui, Mariana B. P.; Oortman, Mariana S.; Weis, Wilson A.; Faroni-Perez, Larisse; Alves, Alexandre P.; Camargo, Maurício G.; Amaral, A. Cecília Z.; Marques, Antonio C.; Lana, Paulo C.

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/ PMID:24573879

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 .

The AVO Website - a Comprehensive Tool for Information Management and Dissemination

NASA Astrophysics Data System (ADS)

Snedigar, S.; Cameron, C.; Nye, C. J.

2008-12-01

The Alaska Volcano Observatory (AVO) website serves as a primary information management, browsing, and dissemination tool. It is database-driven, thus easy to maintain and update. There are two different, yet fully integrated parts of the website. An external site (www.avo.alaska.edu) allows the general public to track eruptive activity by viewing the latest photographs, webcam images, seismic data, and official information releases about the volcano, as well as maps, previous eruption information, and bibliographies. This website is also the single most comprehensive source of Alaska volcano information available. The database now contains 14,000 images, 3,300 of which are publicly viewable, and 4,300 bibliographic citations - many linked to full-text downloadable files.. The internal portion of the website is essential to routine observatory operations, and hosts browse images of diverse geophysical and geological data in a format accessible by AVO staff regardless of location. An observation log allows users to enter information about anything from satellite passes to seismic activity to ash fall reports into a searchable database, and has become the permanent record of observatory function. The individual(s) on duty at home, at the watch office, or elsewhere use forms on the internal website to log information about volcano activity. These data are then automatically parsed into a number of primary activity notices which are the formal communication to appropriate agencies and interested individuals. Geochemistry, geochronology, and geospatial data modules are currently being developed. The website receives over 100 million hits, and serves 1,300 GB of data annually. It is dynamically generated from a MySQL database with over 300 tables and several thousand lines of php code which write the actual web display. The primary webserver is housed at (but not owned by) the University of Alaska Fairbanks, and currently holds 200 GB of data. Webcam images, webicorder graphs, earthquake location plots, and spectrograms are pulled and generated by other servers in Fairbanks and Anchorage.

LabTrove: a lightweight, web based, laboratory "blog" as a route towards a marked up record of work in a bioscience research laboratory.

PubMed

Milsted, Andrew J; Hale, Jennifer R; Frey, Jeremy G; Neylon, Cameron

2013-01-01

The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research. We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system. LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.

Automatic helmet-wearing detection for law enforcement using CCTV cameras

NASA Astrophysics Data System (ADS)

Wonghabut, P.; Kumphong, J.; Satiennam, T.; Ung-arunyawee, R.; Leelapatra, W.

2018-04-01

The objective of this research is to develop an application for enforcing helmet wearing using CCTV cameras. The developed application aims to help law enforcement by police, and eventually resulting in changing risk behaviours and consequently reducing the number of accidents and its severity. Conceptually, the application software implemented using C++ language and OpenCV library uses two different angle of view CCTV cameras. Video frames recorded by the wide-angle CCTV camera are used to detect motorcyclists. If any motorcyclist without helmet is found, then the zoomed (narrow-angle) CCTV is activated to capture image of the violating motorcyclist and the motorcycle license plate in real time. Captured images are managed by database implemented using MySQL for ticket issuing. The results show that the developed program is able to detect 81% of motorcyclists on various motorcycle types during daytime and night-time. The validation results reveal that the program achieves 74% accuracy in detecting the motorcyclist without helmet.

An experiment in big data: storage, querying and visualisation of data taken from the Liverpool Telescope's wide field cameras

NASA Astrophysics Data System (ADS)

Barnsley, R. M.; Steele, Iain A.; Smith, R. J.; Mawson, Neil R.

2014-07-01

The Small Telescopes Installed at the Liverpool Telescope (STILT) project has been in operation since March 2009, collecting data with three wide field unfiltered cameras: SkycamA, SkycamT and SkycamZ. To process the data, a pipeline was developed to automate source extraction, catalogue cross-matching, photometric calibration and database storage. In this paper, modifications and further developments to this pipeline will be discussed, including a complete refactor of the pipeline's codebase into Python, migration of the back-end database technology from MySQL to PostgreSQL, and changing the catalogue used for source cross-matching from USNO-B1 to APASS. In addition to this, details will be given relating to the development of a preliminary front-end to the source extracted database which will allow a user to perform common queries such as cone searches and light curve comparisons of catalogue and non-catalogue matched objects. Some next steps and future ideas for the project will also be presented.

Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface.

PubMed

Dupl'áková, Nikoleta; Renák, David; Hovanec, Patrik; Honysová, Barbora; Twell, David; Honys, David

2007-07-23

Microarray technologies now belong to the standard functional genomics toolbox and have undergone massive development leading to increased genome coverage, accuracy and reliability. The number of experiments exploiting microarray technology has markedly increased in recent years. In parallel with the rapid accumulation of transcriptomic data, on-line analysis tools are being introduced to simplify their use. Global statistical data analysis methods contribute to the development of overall concepts about gene expression patterns and to query and compose working hypotheses. More recently, these applications are being supplemented with more specialized products offering visualization and specific data mining tools. We present a curated gene family-oriented gene expression database, Arabidopsis Gene Family Profiler (aGFP; http://agfp.ueb.cas.cz), which gives the user access to a large collection of normalised Affymetrix ATH1 microarray datasets. The database currently contains NASC Array and AtGenExpress transcriptomic datasets for various tissues at different developmental stages of wild type plants gathered from nearly 350 gene chips. The Arabidopsis GFP database has been designed as an easy-to-use tool for users needing an easily accessible resource for expression data of single genes, pre-defined gene families or custom gene sets, with the further possibility of keyword search. Arabidopsis Gene Family Profiler presents a user-friendly web interface using both graphic and text output. Data are stored at the MySQL server and individual queries are created in PHP script. The most distinguishable features of Arabidopsis Gene Family Profiler database are: 1) the presentation of normalized datasets (Affymetrix MAS algorithm and calculation of model-based gene-expression values based on the Perfect Match-only model); 2) the choice between two different normalization algorithms (Affymetrix MAS4 or MAS5 algorithms); 3) an intuitive interface; 4) an interactive "virtual plant" visualizing the spatial and developmental expression profiles of both gene families and individual genes. Arabidopsis GFP gives users the possibility to analyze current Arabidopsis developmental transcriptomic data starting with simple global queries that can be expanded and further refined to visualize comparative and highly selective gene expression profiles.

SMITH: a LIMS for handling next-generation sequencing workflows

PubMed Central

2014-01-01

Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. Conclusions SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis. PMID:25471934

Using a centralised database system and server in the European Union Framework Programme 7 project SEPServer

NASA Astrophysics Data System (ADS)

Heynderickx, Daniel

2012-07-01

The main objective of the SEPServer project (EU FP7 project 262773) is to produce a new tool, which greatly facilitates the investigation of solar energetic particles (SEPs) and their origin: a server providing SEP data, related electromagnetic (EM) observations and analysis methods, a comprehensive catalogue of the observed SEP events, and educational/outreach material on solar eruptions. The project is coordinated by the University of Helsinki. The project will combine data and knowledge from 11 European partners and several collaborating parties from Europe and US. The datasets provided by the consortium partners are collected in a MySQL database (using the ESA Open Data Interface under licence) on a server operated by DH Consultancy, which also hosts a web interface providing browsing, plotting and post-processing and analysis tools developed by the consortium, as well as a Solar Energetic Particle event catalogue. At this stage of the project, a prototype server has been established, which is presently undergoing testing by users inside the consortium. Using a centralized database has numerous advantages, including: homogeneous storage of the data, which eliminates the need for dataset specific file access routines once the data are ingested in the database; a homogeneous set of metadata describing the datasets on both a global and detailed level, allowing for automated access to and presentation of the various data products; standardised access to the data in different programming environments (e.g. php, IDL); elimination of the need to download data for individual data requests. SEPServer will, thus, add value to several space missions and Earth-based observations by facilitating the coordinated exploitation of and open access to SEP data and related EM observations, and promoting correct use of these data for the entire space research community. This will lead to new knowledge on the production and transport of SEPs during solar eruptions and facilitate the development of models for predicting solar radiation storms and calculation of expected fluxes/fluences of SEPs encountered by spacecraft in the interplanetary medium.

SMITH: a LIMS for handling next-generation sequencing workflows.

PubMed

Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

2014-01-01

Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis.

WebSat--a web software for microsatellite marker development.

PubMed

Martins, Wellington Santos; Lucas, Divino César Soares; Neves, Kelligton Fabricio de Souza; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. The web tool may be accessed at http://purl.oclc.org/NET/websat/

A Novel Database to Rank and Display Archeomagnetic Intensity Data

NASA Astrophysics Data System (ADS)

Donadini, F.; Korhonen, K.; Riisager, P.; Pesonen, L. J.; Kahma, K.

2005-12-01

To understand the content and the causes of the changes in the Earth's magnetic field beyond the observatory records one has to rely on archeomagnetic and lake sediment paleomagnetic data. The regional archeointensity curves are often of different quality and temporally variable which hampers the global analysis of the data in terms of dipole vs non-dipole field. We have developed a novel archeointensity database application utilizing MySQL, PHP (PHP Hypertext Preprocessor), and the Generic Mapping Tools (GMT) for ranking and displaying geomagnetic intensity data from the last 12000 years. Our application has the advantage that no specific software is required to query the database and view the results. Querying the database is performed using any Web browser; a fill-out form is used to enter the site location and a minimum ranking value to select the data points to be displayed. The form also features the possibility to select plotting of the data as an archeointensity curve with error bars, and a Virtual Axial Dipole Moment (VADM) or ancient field value (Ba) curve calculated using the CALS7K model (Continuous Archaeomagnetic and Lake Sediment geomagnetic model) of (Korte and Constable, 2005). The results of a query are displayed on a Web page containing a table summarizing the query parameters, a table showing the archeointensity values satisfying the query parameters, and a plot of VADM or Ba as a function of sample age. The database consists of eight related tables. The main one, INTENSITIES, stores the 3704 archeointensity measurements collected from 159 publications as VADM (and VDM when available) and Ba values, including their standard deviations and sampling locations. It also contains the number of samples and specimens measured from each site. The REFS table stores the references to a particular study. The names, latitudes, and longitudes of the regions where the samples were collected are stored in the SITES table. The MATERIALS, METHODS, SPECIMEN_TYPES and DATING_METHODS tables store information about the sample materials, intensity determination methods, specimen types and age determination methods. The SIGMA_COUNT table is used indirectly for ranking data according to the number of samples measured and their standard deviations. Each intensity measurement is assigned a score (0--2) depending on the number of specimens measured and their standard deviations, the intensity determination method, the type of specimens measured and materials. The ranking of each data point is calculated as the sum of the four scores and varies between 0 and 8. Additionally, users can select the parameters that will be included in the ranking.

Geologic data management at AVO: building authoritative coverage with radical availability (Invited)

NASA Astrophysics Data System (ADS)

Cameron, C.; Snedigar, S. F.; Nye, C. J.

2009-12-01

In 2002, the Alaska Volcano Observatory (AVO) began creating the Geologic Database of Information on Volcanoes in Alaska (GeoDIVA) to create a system that contains complete, flexible, timely, and accurate geologic and geographic information on Pleistocene and younger volcanoes in Alaska. This system was primarily intended to be a tool for scientific investigation, crisis response, and public information - delivered in a dynamic, digital format to both internal and external users. It is now the back-end of the AVO public website. GeoDIVA does not interface with our daily monitoring activities, however -- seismic and satellite data are handled by different database efforts. GeoDIVA also doesn’t store volcanic unrest data, although we hope WOVOdat will. GeoDIVA does include modules for the following datasets: bibliography (every subsequent piece of data in GeoDIVA is tied to a reference), basic volcano information (~137 edifices), historical eruption history information (~550 events), images (~17,000), sample information (~4400), geochemistry (~1500; population in progress), petrography (very early stages of data creation), sample storage (~14,000), and Quaternary vent information (~1200 vents). Modules in progress include GIS data, tephra data, and geochronologic data. In recent years, we have been doing maintenance work on older modules (for example, adding new references to the bibliography, and creating new queries and data fields in response to user feedback) as well as developing, designing, and populating new modules. Population can be quite time consuming, as there are no pre-compiled comprehensive existing sources for most information on Alaskan volcanoes, and we carefully reference each item. Newer modules also require more complex data arrangements than older modules. To meet the needs of a diverse group of users on widely varying computer platforms, GeoDIVA data is primarily stored in a MySQL DBMS; PostGIS/PostgreSQL are currently used to store and search spatial point data such as sample and volcano location. The spatial data storage system is evolving rapidly, and may change to a different DBMS in the future. Data upload is done via a web browser (one-record-at-a-time, tedious), or through automated .csv upload. Because we use open-source software and provide access through web browsers, AVO staff can view and update information from anywhere. In the future, we hope GeoDIVA will be a complete site for all geologic information about Alaskan volcanoes; because all data points are linked together (by references, sample IDs, volcanoes, geologists, etc.) we’ll be able to draw a box on a map and retrieve information on edifices, vents, samples, and all associated metadata, images, references, analytical data, and accompanying GIS files. As we look toward our goals, remaining challenges include: linking our data with other national and international efforts, creating easier ways for all to upload data, GIS development, and balancing the speed of new module development with the need for older module maintenance.

The Role of the Web Server in a Capstone Web Application Course

ERIC Educational Resources Information Center

Umapathy, Karthikeyan; Wallace, F. Layne

2010-01-01

Web applications have become commonplace in the Information Systems curriculum. Much of the discussion about Web development for capstone courses has centered on the scripting tools. Very little has been discussed about different ways to incorporate the Web server into Web application development courses. In this paper, three different ways of…

Tethys: A Platform for Water Resources Modeling and Decision Support Apps

NASA Astrophysics Data System (ADS)

Nelson, J.; Swain, N. R.

2015-12-01

The interactive nature of web applications or "web apps" makes it an excellent medium for conveying complex scientific concepts to lay audiences and creating decision support tools that harness cutting edge modeling techniques. However, the technical expertise required to develop web apps represents a barrier for would-be developers. This barrier can be characterized by the following hurdles that developers must overcome: (1) identify, select, and install software that meet the spatial and computational capabilities commonly required for water resources modeling; (2) orchestrate the use of multiple free and open source (FOSS) projects and navigate their differing application programming interfaces; (3) learn the multi-language programming skills required for modern web development; and (4) develop a web-secure and fully featured web portal to host the app. Tethys Platform has been developed to lower the technical barrier and minimize the initial development investment that prohibits many scientists and engineers from making use of the web app medium. It includes (1) a suite of FOSS that address the unique data and computational needs common to water resources web app development, (2) a Python software development kit that streamlines development, and (3) a customizable web portal that is used to deploy the completed web apps. Tethys synthesizes several software projects including PostGIS, 52°North WPS, GeoServer, Google Maps™, OpenLayers, and Highcharts. It has been used to develop a broad array of web apps for water resources modeling and decision support for several projects including CI-WATER, HydroShare, and the National Flood Interoperability Experiment. The presentation will include live demos of some of the apps that have been developed using Tethys to demonstrate its capabilities.

Research on high availability architecture of SQL and NoSQL

NASA Astrophysics Data System (ADS)

Wang, Zhiguo; Wei, Zhiqiang; Liu, Hao

2017-03-01

With the advent of the era of big data, amount and importance of data have increased dramatically. SQL database develops in performance and scalability, but more and more companies tend to use NoSQL database as their databases, because NoSQL database has simpler data model and stronger extension capacity than SQL database. Almost all database designers including SQL database and NoSQL database aim to improve performance and ensure availability by reasonable architecture which can reduce the effects of software failures and hardware failures, so that they can provide better experiences for their customers. In this paper, I mainly discuss the architectures of MySQL, MongoDB, and Redis, which are high available and have been deployed in practical application environment, and design a hybrid architecture.

The Best of all Possible Worlds: Applying the Model Driven Architecture Approach to a JC3IEDM OWL Ontology Modeled in UML

DTIC Science & Technology

2014-04-25

EA’s Java application programming interface (API), the team built a tool called OWL2EA that can ingest an OWL file and generate the corresponding UML...ObjectItemStructure specification shown in Figure 10. Running this script in the relational database server MySQL creates the physical schema that

Software Architecture Evolution

DTIC Science & Technology

2013-12-01

system’s major components occurring via a Java Message Service message bus [69]. This architecture was designed to promote loose coupling of soft- ware...play reconfiguration of the system. The components were Java -based and platform-independent; the interfaces by which they communicated were based on...The MPCS database, a MySQL database used for storing telemetry as well as some other information, such as logs and commanding data [68]. This

Examining the Relationship between Teachers' Attitudes and Motivation toward Web-Based Professional Development: A Structural Equation Modeling Approach

ERIC Educational Resources Information Center

Chien, Hui-Min; Kao, Chia-Pin; Yeh, I-Jan; Lin, Kuen-Yi

2012-01-01

This study was conducted to investigate elementary school teachers' attitudes and motivation toward web-based professional development. The relationship between teachers' attitudes and motivation was explored using the AWPD (Attitudes toward Web-based Professional Development) and MWPD (Motivation toward Web-based Professional Development)…

WebSat ‐ A web software for microsatellite marker development

PubMed Central

Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

PubMed

Nadkarni, P M; Brandt, C M; Marenco, L

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

Development of high efficiency solar cells on silicon web

NASA Technical Reports Server (NTRS)

Rohatgi, A.; Meier, D. L.; Campbell, R. B.; Schmidt, D. N.; Rai-Choudhury, P.

1984-01-01

Web base material is being improved with a goal toward obtaining solar cell efficiencies in excess of 18% (AM1). Carrier loss mechanisms in web silicon was investigated, techniques were developed to reduce carrier recombination in the web, and web cells were fabricated using effective surface passivation. The effect of stress on web cell performance was also investigated.

Practical guidelines for development of web-based interventions.

PubMed

Chee, Wonshik; Lee, Yaelim; Chee, Eunice; Im, Eun-Ok

2014-10-01

Despite a recent high funding priority on technological aspects of research and a high potential impact of Web-based interventions on health, few guidelines for the development of Web-based interventions are currently available. In this article, we propose practical guidelines for development of Web-based interventions based on an empirical study and an integrative literature review. The empirical study aimed at development of a Web-based physical activity promotion program that was specifically tailored to Korean American midlife women. The literature review included a total of 202 articles that were retrieved through multiple databases. On the basis of the findings of the study and the literature review, we propose directions for development of Web-based interventions in the following steps: (1) meaningfulness and effectiveness, (2) target population, (3) theoretical basis/program theory, (4) focus and objectives, (5) components, (6) technological aspects, and (7) logistics for users. The guidelines could help promote further development of Web-based interventions at this early stage of Web-based interventions in nursing.

Silicon dendritic web growth

NASA Technical Reports Server (NTRS)

Duncan, S.

1984-01-01

Technological goals for a silicon dendritic web growth program effort are presented. Principle objectives for this program include: (1) grow long web crystals front continuously replenished melt; (2) develop temperature distribution in web and melt; (3) improve reproductibility of growth; (4) develop configurations for increased growth rates (width and speed); (5) develop new growth system components as required for improved growth; and (6) evaluate quality of web growth.

Use of WebQuest Design for Inservice Teacher Professional Development

ERIC Educational Resources Information Center

Iskeceli-Tunc, Sinem; Oner, Diler

2016-01-01

This study investigated whether a teacher professional development module built around designing WebQuests could improve teachers' technological and pedagogical skills. The technological skills examined included Web searching and Web evaluating skills. The pedagogical skills targeted were developing a working definition for higher-order thinking…

Teaching Web Security Using Portable Virtual Labs

ERIC Educational Resources Information Center

Chen, Li-Chiou; Tao, Lixin

2012-01-01

We have developed a tool called Secure WEb dEvelopment Teaching (SWEET) to introduce security concepts and practices for web application development. This tool provides introductory tutorials, teaching modules utilizing virtualized hands-on exercises, and project ideas in web application security. In addition, the tool provides pre-configured…

Development and Evaluation of an Interactive WebQuest Environment: "Web Macerasi"

ERIC Educational Resources Information Center

Gulbahar, Yasemin; Madran, R. Orcun; Kalelioglu, Filiz

2010-01-01

This study was conducted to develop a web-based interactive system, Web Macerasi, for teaching-learning and evaluation purposes, and to find out the possible effects of this system. The study has two stages. In the first stage, a WebQuest site was designed as an interactive system in which various Internet and web technologies were used for…