CREDO: a structural interactomics database for drug discovery

PubMed Central

Schreyer, Adrian M.; Blundell, Tom L.

2013-01-01

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

P1198: software for tracing decision behavior in lending to small businesses.

PubMed

Andersson, P

2001-05-01

This paper describes a process-tracing software program specially designed to capture decision behavior in lending to small businesses. The source code was written in Lotus Notes. The software runs in a Web browser and consists of two interacting systems: a database and a user interface. The database includes three realistic loan applications. The user interface consists of different but interacting screens that enable the participant to operate the software. Log files register the decision behavior of the participant. An empirical example is presented in order to show the software's potential in providing insights into judgment and decision making. The implications of the software are discussed.

On the Suitability of Tcl/Tk for SYS

DTIC Science & Technology

2003-02-01

database design, or user interface. CMU/SEI-2003-TN-001 7 4.4 Legacy Systems SYS is not now complete. The system it replaced interfaced with a dozen...a database maintained by a parent organization. Before SYS was released, many of its current users interacted directly with JSYS, so that system...rating. Rather than shades of blue, the full rainbow is exploited. Rather than window proliferation, the usual result of an action is to replace the

Metadata tables to enable dynamic data modeling and web interface design: the SEER example.

PubMed

Weiner, Mark; Sherr, Micah; Cohen, Abigail

2002-04-01

A wealth of information addressing health status, outcomes and resource utilization is compiled and made available by various government agencies. While exploration of the data is possible using existing tools, in general, would-be users of the resources must acquire CD-ROMs or download data from the web, and upload the data into their own database. Where web interfaces exist, they are highly structured, limiting the kinds of queries that can be executed. This work develops a web-based database interface engine whose content and structure is generated through interaction with a metadata table. The result is a dynamically generated web interface that can easily accommodate changes in the underlying data model by altering the metadata table, rather than requiring changes to the interface code. This paper discusses the background and implementation of the metadata table and web-based front end and provides examples of its use with the NCI's Surveillance, Epidemiology and End-Results (SEER) database.

A database for TMT interface control documents

NASA Astrophysics Data System (ADS)

Gillies, Kim; Roberts, Scott; Brighton, Allan; Rogers, John

2016-08-01

The TMT Software System consists of software components that interact with one another through a software infrastructure called TMT Common Software (CSW). CSW consists of software services and library code that is used by developers to create the subsystems and components that participate in the software system. CSW also defines the types of components that can be constructed and their roles. The use of common component types and shared middleware services allows standardized software interfaces for the components. A software system called the TMT Interface Database System was constructed to support the documentation of the interfaces for components based on CSW. The programmer describes a subsystem and each of its components using JSON-style text files. A command interface file describes each command a component can receive and any commands a component sends. The event interface files describe status, alarms, and events a component publishes and status and events subscribed to by a component. A web application was created to provide a user interface for the required features. Files are ingested into the software system's database. The user interface allows browsing subsystem interfaces, publishing versions of subsystem interfaces, and constructing and publishing interface control documents that consist of the intersection of two subsystem interfaces. All published subsystem interfaces and interface control documents are versioned for configuration control and follow the standard TMT change control processes. Subsystem interfaces and interface control documents can be visualized in the browser or exported as PDF files.

EcoCyc: a comprehensive database resource for Escherichia coli

PubMed Central

Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro; Ingraham, John; Paley, Suzanne; Paulsen, Ian T.; Peralta-Gil, Martín; Karp, Peter D.

2005-01-01

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions. PMID:15608210

Databases and coordinated research projects at the IAEA on atomic processes in plasmas

NASA Astrophysics Data System (ADS)

Braams, Bastiaan J.; Chung, Hyun-Kyung

2012-05-01

The Atomic and Molecular Data Unit at the IAEA works with a network of national data centres to encourage and coordinate production and dissemination of fundamental data for atomic, molecular and plasma-material interaction (A+M/PMI) processes that are relevant to the realization of fusion energy. The Unit maintains numerical and bibliographical databases and has started a Wiki-style knowledge base. The Unit also contributes to A+M database interface standards and provides a search engine that offers a common interface to multiple numerical A+M/PMI databases. Coordinated Research Projects (CRPs) bring together fusion energy researchers and atomic, molecular and surface physicists for joint work towards the development of new data and new methods. The databases and current CRPs on A+M/PMI processes are briefly described here.

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server

NASA Astrophysics Data System (ADS)

Reyes, J. C.; Vernon, F. L.; Newman, R. L.; Steidl, J. H.

2010-12-01

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base has been fundamentally modified to now present waveform data stored in cluster-based databases using a multi-threaded architecture, in addition to supporting the pre-existing single database model. This allows interactive web-based access to high-density (broadband @ 40Hz to strong motion @ 200Hz) waveform data that can span multiple years; the common lifetime of broadband seismic networks. The client-side interface expands on it's use of simple JSON-based AJAX queries to now incorporate a variety of User Interface (UI) improvements including standardized calendars for defining time ranges, applying on-the-fly data calibration to display SI-unit data, and increased rendering speed. This presentation will outline the various cyber infrastructure challenges we have faced while developing this application, the use-cases currently in existence, and the limitations of web-based application development.

Bright Ideas, Creative People, Teamwork, and Money: Developing Courseware for Teaching Scottish History.

ERIC Educational Resources Information Center

Munro, R. K.; Hillis, P. L. M.

1996-01-01

Describes three hypermedia databases designed to support secondary education classes in Scottish history. The databases contain mostly 19th-century census information with links to subjects such as fashion, education, and entertainment. Interactive interfaces allow students to create original research applications. (MJP)

hPDI: a database of experimental human protein-DNA interactions.

PubMed

Xie, Zhi; Hu, Shaohui; Blackshaw, Seth; Zhu, Heng; Qian, Jiang

2010-01-15

The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for >500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes. http://bioinfo.wilmer.jhu.edu/PDI/.

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

Databases and coordinated research projects at the IAEA on atomic processes in plasmas

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

Braams, Bastiaan J.; Chung, Hyun-Kyung

2012-05-25

The Atomic and Molecular Data Unit at the IAEA works with a network of national data centres to encourage and coordinate production and dissemination of fundamental data for atomic, molecular and plasma-material interaction (A+M/PMI) processes that are relevant to the realization of fusion energy. The Unit maintains numerical and bibliographical databases and has started a Wiki-style knowledge base. The Unit also contributes to A+M database interface standards and provides a search engine that offers a common interface to multiple numerical A+M/PMI databases. Coordinated Research Projects (CRPs) bring together fusion energy researchers and atomic, molecular and surface physicists for joint workmore » towards the development of new data and new methods. The databases and current CRPs on A+M/PMI processes are briefly described here.« less

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

Experiments and Analysis on a Computer Interface to an Information-Retrieval Network.

ERIC Educational Resources Information Center

Marcus, Richard S.; Reintjes, J. Francis

A primary goal of this project was to develop an interface that would provide direct access for inexperienced users to existing online bibliographic information retrieval networks. The experiment tested the concept of a virtual-system mode of access to a network of heterogeneous interactive retrieval systems and databases. An experimental…

Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies.

PubMed

Sukhwal, Anshul; Sowdhamini, Ramanathan

2013-07-01

Protein-protein interactions are important in carrying out many biological processes and functions. These interactions may be either permanent or of temporary nature. Several studies have employed tools like solvent accessibility and graph theory to identify these interactions, but still more studies need to be performed to quantify and validate them. Although we now have many databases available with predicted and experimental results on protein-protein interactions, we still do not have many databases which focus on providing structural details of the interacting complexes, their oligomerisation state and homologues. In this work, protein-protein interactions have been thoroughly investigated within the structural regime and quantified for their strength using calculated pseudoenergies. The PPCheck server, an in-house webserver, has been used for calculating the pseudoenergies like van der Waals, hydrogen bonds and electrostatic energy based on distances between atoms of amino acids from two interacting proteins. PPCheck can be visited at . Based on statistical data, as obtained by studying established protein-protein interacting complexes from earlier studies, we came to a conclusion that an average protein-protein interface consisted of about 51 to 150 amino acid residues and the generalized energy per residue ranged from -2 kJ mol(-1) to -6 kJ mol(-1). We found that some of the proteins have an exceptionally higher number of amino acids at the interface and it was purely because of their elaborate interface or extended topology i.e. some of their secondary structure regions or loops were either inter-mixing or running parallel to one another or they were taking part in domain swapping. Residue networks were prepared for all the amino acids of the interacting proteins involved in different types of interactions (like van der Waals, hydrogen-bonding, electrostatic or intramolecular interactions) and were analysed between the query domain-interacting partner pair and its remote homologue-interacting partner pair. We found that, in exceptional cases, homologous proteins belonging to the same superfamily, but with remote sequence similarity, can share similar interfaces.

RAIN: RNA–protein Association and Interaction Networks

PubMed Central

Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan

2017-01-01

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain PMID:28077569

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

PubMed Central

Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

2014-01-01

The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881

Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource

PubMed Central

Koike, Asako; Kobayashi, Yoshiyuki; Takagi, Toshihisa

2003-01-01

Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein–protein, protein–gene, and protein–compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP).The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/. PMID:12799355

Tools & Services - SEER Registrars

Cancer.gov

View glossary for registrars. Access ICD conversion programs, SEER Abstracting Tool, SEER Data Viewer, SEER interactive drug database for coding oncology drugs, data documentation, variable recodes, and SEER Application Programming Interface for developers.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces

PubMed Central

Andreani, Jessica; Faure, Guilhem; Guerois, Raphaël

2012-01-01

Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity. Nonetheless, the elementary interactions which compose the interface are highly versatile throughout evolution. Understanding and characterizing interface plasticity across evolution is a fundamental issue which could provide new insights into protein-protein interaction prediction. Using a database of 1,024 couples of close and remote heteromeric structural interologs, we studied protein-protein interactions from a structural and evolutionary point of view. We systematically and quantitatively analyzed the conservation of different types of interface contacts. Our study highlights astonishing plasticity regarding polar contacts at complex interfaces. It also reveals that up to a quarter of the residues switch out of the interface when comparing two homologous complexes. Despite such versatility, we identify two important interface descriptors which correlate with an increased conservation in the evolution of interfaces: apolar patches and contacts surrounding anchor residues. These observations hold true even when restricting the dataset to transiently formed complexes. We show that a combination of six features related either to sequence or to geometric properties of interfaces can be used to rank positions likely to share similar contacts between two interologs. Altogether, our analysis provides important tracks for extracting meaningful information from multiple sequence alignments of conserved binding partners and for discriminating near-native interfaces using evolutionary information. PMID:22952442

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

PubMed

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

2008-01-01

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

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

HPIDB 2.0: a curated database for host–pathogen interactions

PubMed Central

Ammari, Mais G.; Gresham, Cathy R.; McCarthy, Fiona M.; Nanduri, Bindu

2016-01-01

Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html PMID:27374121

NASA Interactive Forms Type Interface - NIFTI

NASA Technical Reports Server (NTRS)

Jain, Bobby; Morris, Bill

2005-01-01

A flexible database query, update, modify, and delete tool was developed that provides an easy interface to Oracle forms. This tool - the NASA interactive forms type interface, or NIFTI - features on-the- fly forms creation, forms sharing among users, the capability to query the database from user-entered criteria on forms, traversal of query results, an ability to generate tab-delimited reports, viewing and downloading of reports to the user s workstation, and a hypertext-based help system. NIFTI is a very powerful ad hoc query tool that was developed using C++, X-Windows by a Motif application framework. A unique tool, NIFTI s capabilities appear in no other known commercial-off-the- shelf (COTS) tool, because NIFTI, which can be launched from the user s desktop, is a simple yet very powerful tool with a highly intuitive, easy-to-use graphical user interface (GUI) that will expedite the creation of database query/update forms. NIFTI, therefore, can be used in NASA s International Space Station (ISS) as well as within government and industry - indeed by all users of the widely disseminated Oracle base. And it will provide significant cost savings in the areas of user training and scalability while advancing the art over current COTS browsers. No COTS browser performs all the functions NIFTI does, and NIFTI is easier to use. NIFTI s cost savings are very significant considering the very large database with which it is used and the large user community with varying data requirements it will support. Its ease of use means that personnel unfamiliar with databases (e.g., managers, supervisors, clerks, and others) can develop their own personal reports. For NASA, a tool such as NIFTI was needed to query, update, modify, and make deletions within the ISS vehicle master database (VMDB), a repository of engineering data that includes an indentured parts list and associated resource data (power, thermal, volume, weight, and the like). Since the VMDB is used both as a collection point for data and as a common repository for engineering, integration, and operations teams, a tool such as NIFTI had to be designed that could expedite the creation of database query/update forms which could then be shared among users.

Research and realization of key technology in HILS interactive system

NASA Astrophysics Data System (ADS)

Liu, Che; Lu, Huiming; Wang, Fankai

2018-03-01

This paper designed HILS (Hardware In the Loop Simulation) interactive system based on xPC platform . Through the interface between C++ and MATLAB engine, establish the seamless data connection between Simulink and interactive system, complete data interaction between system and Simulink, realize the function development of model configuration, parameter modification and off line simulation. We establish the data communication between host and target machine through TCP/IP protocol to realize the model download and real-time simulation. Use database to store simulation data, implement real-time simulation monitoring and simulation data management. Realize system function integration by Qt graphic interface library and dynamic link library. At last, take the typical control system as an example to verify the feasibility of HILS interactive system.

Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases

PubMed Central

Lin, Chen; Mak, Wayne; Hong, Pengyu; Sepp, Katharine; Perrimon, Norbert

2010-01-01

Recently, High-content screening (HCS) has been combined with RNA interference (RNAi) to become an essential image-based high-throughput method for studying genes and biological networks through RNAi-induced cellular phenotype analyses. However, a genome-wide RNAi-HCS screen typically generates tens of thousands of images, most of which remain uncategorized due to the inadequacies of existing HCS image analysis tools. Until now, it still requires highly trained scientists to browse a prohibitively large RNAi-HCS image database and produce only a handful of qualitative results regarding cellular morphological phenotypes. For this reason we have developed intelligent interfaces to facilitate the application of the HCS technology in biomedical research. Our new interfaces empower biologists with computational power not only to effectively and efficiently explore large-scale RNAi-HCS image databases, but also to apply their knowledge and experience to interactive mining of cellular phenotypes using Content-Based Image Retrieval (CBIR) with Relevance Feedback (RF) techniques. PMID:21278820

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures.

PubMed

Ripoche, Hugues; Laine, Elodie; Ceres, Nicoletta; Carbone, Alessandra

2017-01-04

The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET 2 at large-scale on more than 20 000 chains. JET 2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET 2 analyses. Predictions were evaluated on more than 15 000 experimentally characterized protein interfaces. This is, to our knowledge, the largest evaluation of a protein binding site prediction method. The overall performance of JET 2 on all interfaces are: Sen = 52.52, PPV = 51.24, Spe = 80.05, Acc = 75.89. The data can be used to foster new strategies for protein-protein interactions modulation and interaction surface redesign. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The development of a dynamic software for the user interaction from the geographic information system environment with the database of the calibration site of the satellite remote electro-optic sensors

NASA Astrophysics Data System (ADS)

Zyelyk, Ya. I.; Semeniv, O. V.

2015-12-01

The state of the problem of the post-launch calibration of the satellite electro-optic remote sensors and its solutions in Ukraine is analyzed. The database is improved and dynamic services for user interaction with database from the environment of open geographical information system Quantum GIS for information support of calibration activities are created. A dynamic application under QGIS is developed, implementing these services in the direction of the possibility of data entering, editing and extraction from the database, using the technology of object-oriented programming and of modern complex program design patterns. The functional and algorithmic support of this dynamic software and its interface are developed.

Notre Dame Nuclear Database: A New Chart of Nuclides

NASA Astrophysics Data System (ADS)

Lee, Kevin; Khouw, Timothy; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

Nuclear data is critical to research fields from medicine to astrophysics. We are creating a database, the Notre Dame Nuclear Database, which can store theoretical and experimental datasets. We place emphasis on storing metadata and user interaction with the database. Users are able to search in addition to the specific nuclear datum, the author(s), the facility where the measurements were made, the institution of the facility, and device or method/technique used. We also allow users to interact with the database by providing online search, an interactive nuclide chart, and a command line interface. The nuclide chart is a more descriptive version of the periodic table that can be used to visualize nuclear properties such as half-lives and mass. We achieve this by using D3 (Data Driven Documents), HTML, and CSS3 to plot the nuclides and color them accordingly. Search capabilities can be applied dynamically to the chart by using Python to communicate with MySQL, allowing for customization. Users can save the customized chart they create to any image format. These features provide a unique approach for researchers to interface with nuclear data. We report on the current progress of this project and will present a working demo that highlights each aspect of the aforementioned features. This is the first time that all available technologies are put to use to make nuclear data more accessible than ever before in a manner that is much easier and fully detailed. This is a first and we will make it available as open source ware.

StarView: The object oriented design of the ST DADS user interface

NASA Technical Reports Server (NTRS)

Williams, J. D.; Pollizzi, J. A.

1992-01-01

StarView is the user interface being developed for the Hubble Space Telescope Data Archive and Distribution Service (ST DADS). ST DADS is the data archive for HST observations and a relational database catalog describing the archived data. Users will use StarView to query the catalog and select appropriate datasets for study. StarView sends requests for archived datasets to ST DADS which processes the requests and returns the database to the user. StarView is designed to be a powerful and extensible user interface. Unique features include an internal relational database to navigate query results, a form definition language that will work with both CRT and X interfaces, a data definition language that will allow StarView to work with any relational database, and the ability to generate adhoc queries without requiring the user to understand the structure of the ST DADS catalog. Ultimately, StarView will allow the user to refine queries in the local database for improved performance and merge in data from external sources for correlation with other query results. The user will be able to create a query from single or multiple forms, merging the selected attributes into a single query. Arbitrary selection of attributes for querying is supported. The user will be able to select how query results are viewed. A standard form or table-row format may be used. Navigation capabilities are provided to aid the user in viewing query results. Object oriented analysis and design techniques were used in the design of StarView to support the mechanisms and concepts required to implement these features. One such mechanism is the Model-View-Controller (MVC) paradigm. The MVC allows the user to have multiple views of the underlying database, while providing a consistent mechanism for interaction regardless of the view. This approach supports both CRT and X interfaces while providing a common mode of user interaction. Another powerful abstraction is the concept of a Query Model. This concept allows a single query to be built form a single or multiple forms before it is submitted to ST DADS. Supporting this concept is the adhoc query generator which allows the user to select and qualify an indeterminate number attributes from the database. The user does not need any knowledge of how the joins across various tables are to be resolved. The adhoc generator calculates the joins automatically and generates the correct SQL query.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

PubMed

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

PoMaMo--a comprehensive database for potato genome data.

PubMed

Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

2005-01-01

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes.

PoMaMo—a comprehensive database for potato genome data

PubMed Central

Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

2005-01-01

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes. PMID:15608284

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Integrating computer programs for engineering analysis and design

NASA Technical Reports Server (NTRS)

Wilhite, A. W.; Crisp, V. K.; Johnson, S. C.

1983-01-01

The design of a third-generation system for integrating computer programs for engineering and design has been developed for the Aerospace Vehicle Interactive Design (AVID) system. This system consists of an engineering data management system, program interface software, a user interface, and a geometry system. A relational information system (ARIS) was developed specifically for the computer-aided engineering system. It is used for a repository of design data that are communicated between analysis programs, for a dictionary that describes these design data, for a directory that describes the analysis programs, and for other system functions. A method is described for interfacing independent analysis programs into a loosely-coupled design system. This method emphasizes an interactive extension of analysis techniques and manipulation of design data. Also, integrity mechanisms exist to maintain database correctness for multidisciplinary design tasks by an individual or a team of specialists. Finally, a prototype user interface program has been developed to aid in system utilization.

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

NASA Astrophysics Data System (ADS)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs. PMID:20624715

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.

Merging in-silico and in vitro salivary protein complex partners using the STRING database: A tutorial.

PubMed

Crosara, Karla Tonelli Bicalho; Moffa, Eduardo Buozi; Xiao, Yizhi; Siqueira, Walter Luiz

2018-01-16

Protein-protein interaction is a common physiological mechanism for protection and actions of proteins in an organism. The identification and characterization of protein-protein interactions in different organisms is necessary to better understand their physiology and to determine their efficacy. In a previous in vitro study using mass spectrometry, we identified 43 proteins that interact with histatin 1. Six previously documented interactors were confirmed and 37 novel partners were identified. In this tutorial, we aimed to demonstrate the usefulness of the STRING database for studying protein-protein interactions. We used an in-silico approach along with the STRING database (http://string-db.org/) and successfully performed a fast simulation of a novel constructed histatin 1 protein-protein network, including both the previously known and the predicted interactors, along with our newly identified interactors. Our study highlights the advantages and importance of applying bioinformatics tools to merge in-silico tactics with experimental in vitro findings for rapid advancement of our knowledge about protein-protein interactions. Our findings also indicate that bioinformatics tools such as the STRING protein network database can help predict potential interactions between proteins and thus serve as a guide for future steps in our exploration of the Human Interactome. Our study highlights the usefulness of the STRING protein database for studying protein-protein interactions. The STRING database can collect and integrate data about known and predicted protein-protein associations from many organisms, including both direct (physical) and indirect (functional) interactions, in an easy-to-use interface. Copyright © 2017 Elsevier B.V. All rights reserved.

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

PubMed Central

Sagendorf, Jared M.

2017-01-01

Abstract Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. PMID:28431131

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

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.

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

The Auroral Planetary Imaging and Spectroscopy (APIS) service

NASA Astrophysics Data System (ADS)

Lamy, L.; Prangé, R.; Henry, F.; Le Sidaner, P.

2015-06-01

The Auroral Planetary Imaging and Spectroscopy (APIS) service, accessible online, provides an open and interactive access to processed auroral observations of the outer planets and their satellites. Such observations are of interest for a wide community at the interface between planetology, magnetospheric and heliospheric physics. APIS consists of (i) a high level database, built from planetary auroral observations acquired by the Hubble Space Telescope (HST) since 1997 with its mostly used Far-Ultraviolet spectro-imagers, (ii) a dedicated search interface aimed at browsing efficiently this database through relevant conditional search criteria and (iii) the ability to interactively work with the data online through plotting tools developed by the Virtual Observatory (VO) community, such as Aladin and Specview. This service is VO compliant and can therefore also been queried by external search tools of the VO community. The diversity of available data and the capability to sort them out by relevant physical criteria shall in particular facilitate statistical studies, on long-term scales and/or multi-instrumental multi-spectral combined analysis.

IAC - INTEGRATED ANALYSIS CAPABILITY

NASA Technical Reports Server (NTRS)

Frisch, H. P.

1994-01-01

The objective of the Integrated Analysis Capability (IAC) system is to provide a highly effective, interactive analysis tool for the integrated design of large structures. With the goal of supporting the unique needs of engineering analysis groups concerned with interdisciplinary problems, IAC was developed to interface programs from the fields of structures, thermodynamics, controls, and system dynamics with an executive system and database to yield a highly efficient multi-disciplinary system. Special attention is given to user requirements such as data handling and on-line assistance with operational features, and the ability to add new modules of the user's choice at a future date. IAC contains an executive system, a data base, general utilities, interfaces to various engineering programs, and a framework for building interfaces to other programs. IAC has shown itself to be effective in automatic data transfer among analysis programs. IAC 2.5, designed to be compatible as far as possible with Level 1.5, contains a major upgrade in executive and database management system capabilities, and includes interfaces to enable thermal, structures, optics, and control interaction dynamics analysis. The IAC system architecture is modular in design. 1) The executive module contains an input command processor, an extensive data management system, and driver code to execute the application modules. 2) Technical modules provide standalone computational capability as well as support for various solution paths or coupled analyses. 3) Graphics and model generation interfaces are supplied for building and viewing models. Advanced graphics capabilities are provided within particular analysis modules such as INCA and NASTRAN. 4) Interface modules provide for the required data flow between IAC and other modules. 5) User modules can be arbitrary executable programs or JCL procedures with no pre-defined relationship to IAC. 6) Special purpose modules are included, such as MIMIC (Model Integration via Mesh Interpolation Coefficients), which transforms field values from one model to another; LINK, which simplifies incorporation of user specific modules into IAC modules; and DATAPAC, the National Bureau of Standards statistical analysis package. The IAC database contains structured files which provide a common basis for communication between modules and the executive system, and can contain unstructured files such as NASTRAN checkpoint files, DISCOS plot files, object code, etc. The user can define groups of data and relations between them. A full data manipulation and query system operates with the database. The current interface modules comprise five groups: 1) Structural analysis - IAC contains a NASTRAN interface for standalone analysis or certain structural/control/thermal combinations. IAC provides enhanced structural capabilities for normal modes and static deformation analysis via special DMAP sequences. IAC 2.5 contains several specialized interfaces from NASTRAN in support of multidisciplinary analysis. 2) Thermal analysis - IAC supports finite element and finite difference techniques for steady state or transient analysis. There are interfaces for the NASTRAN thermal analyzer, SINDA/SINFLO, and TRASYS II. FEMNET, which converts finite element structural analysis models to finite difference thermal analysis models, is also interfaced with the IAC database. 3) System dynamics - The DISCOS simulation program which allows for either nonlinear time domain analysis or linear frequency domain analysis, is fully interfaced to the IAC database management capability. 4) Control analysis - Interfaces for the ORACLS, SAMSAN, NBOD2, and INCA programs allow a wide range of control system analyses and synthesis techniques. Level 2.5 includes EIGEN, which provides tools for large order system eigenanalysis, and BOPACE, which allows for geometric capabilities and finite element analysis with nonlinear material. Also included in IAC level 2.5 is SAMSAN 3.1, an engineering analysis program which contains a general purpose library of over 600 subroutin

The BioGRID Interaction Database: 2011 update

PubMed Central

Stark, Chris; Breitkreutz, Bobby-Joe; Chatr-aryamontri, Andrew; Boucher, Lorrie; Oughtred, Rose; Livstone, Michael S.; Nixon, Julie; Van Auken, Kimberly; Wang, Xiaodong; Shi, Xiaoqi; Reguly, Teresa; Rust, Jennifer M.; Winter, Andrew; Dolinski, Kara; Tyers, Mike

2011-01-01

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions. PMID:21071413

A PDB-wide, evolution-based assessment of protein-protein interfaces.

PubMed

Baskaran, Kumaran; Duarte, Jose M; Biyani, Nikhil; Bliven, Spencer; Capitani, Guido

2014-10-18

Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein-protein interfaces can be obtained by a comprehensive study of protein contacts in the PDB, their sequence conservation and geometric features. An automated computational pipeline was developed to run our Evolutionary Protein-Protein Interface Classifier (EPPIC) software on the entire PDB and store the results in a relational database, currently containing > 800,000 interfaces. This allows the analysis of interface data on a PDB-wide scale. Two large benchmark datasets of biological interfaces and crystal contacts, each containing about 3000 entries, were automatically generated based on criteria thought to be strong indicators of interface type. The BioMany set of biological interfaces includes NMR dimers solved as crystal structures and interfaces that are preserved across diverse crystal forms, as catalogued by the Protein Common Interface Database (ProtCID) from Xu and Dunbrack. The second dataset, XtalMany, is derived from interfaces that would lead to infinite assemblies and are therefore crystal contacts. BioMany and XtalMany were used to benchmark the EPPIC approach. The performance of EPPIC was also compared to classifications from the Protein Interfaces, Surfaces, and Assemblies (PISA) program on a PDB-wide scale, finding that the two approaches give the same call in about 88% of PDB interfaces. By comparing our safest predictions to the PDB author annotations, we provide a lower-bound estimate of the error rate of biological unit annotations in the PDB. Additionally, we developed a PyMOL plugin for direct download and easy visualization of EPPIC interfaces for any PDB entry. Both the datasets and the PyMOL plugin are available at http://www.eppic-web.org/ewui/\\#downloads. Our computational pipeline allows us to analyze protein-protein contacts and their sequence conservation across the entire PDB. Two new benchmark datasets are provided, which are over an order of magnitude larger than existing manually curated ones. These tools enable the comprehensive study of several aspects of protein-protein contacts in the PDB and represent a basis for future, even larger scale studies of protein-protein interactions.

HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species.

PubMed

López, Yosvany; Nakai, Kenta; Patil, Ashwini

2015-01-01

HitPredict is a consolidated resource of experimentally identified, physical protein-protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein-protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of physical, genetic and predicted interactions. Automated integration of interactions is further complicated by varying levels of accuracy of database content and lack of adherence to standard formats. To address these issues, the latest version of HitPredict provides a manually curated dataset of 398 696 physical associations between 70 808 proteins from 105 species. Manual confirmation was used to resolve all issues encountered during data integration. For improved reliability assessment, this version combines a new score derived from the experimental information of the interactions with the original score based on the features of the interacting proteins. The combined interaction score performs better than either of the individual scores in HitPredict as well as the reliability score of another similar database. HitPredict provides a web interface to search proteins and visualize their interactions, and the data can be downloaded for offline analysis. Data usability has been enhanced by mapping protein identifiers across multiple reference databases. Thus, the latest version of HitPredict provides a significantly larger, more reliable and usable dataset of protein-protein interactions from several species for the study of gene groups. Database URL: http://hintdb.hgc.jp/htp. © The Author(s) 2015. Published by Oxford University Press.

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

Chao, Tian-Jy; Kim, Younghun

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented thatmore » communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.« less

MapApp: A Java(TM) Applet for Accessing Geographic Databases

NASA Astrophysics Data System (ADS)

Haxby, W.; Carbotte, S.; Ryan, W. B.; OHara, S.

2001-12-01

MapApp (http://coast.ldeo.columbia.edu/help/MapApp.html) is a prototype Java(TM) applet that is intended to give easy and versatile access to geographic data sets through a web browser. It was developed initially to interface with the RIDGE Multibeam Synthesis. Subsequently, interfaces with other geophysical databases were added. At present, multibeam bathymetry grids, underway geophysics along ship tracks, and the LDEO Borehole Research Group's ODP well logging database are accessible through MapApp. We plan to add an interface with the Ridge Petrology Database in the near future. The central component of MapApp is a world physiographic map. Users may navigate around the map (zoom/pan) without waiting for HTTP requests to a remote server to be processed. A focus request loads image tiles from the server to compose a new map at the current viewing resolution. Areas in which multibeam grids are available may be focused to a pixel resolution of about 200 m. These areas may be identified by toggling a mask. Databases may be accessed through menus, and selected data objects may be loaded into MapApp by selecting items from tables. Once loaded, a bathymetry grid may be contoured or used to create bathymetric profiles; ship tracks and ODP sites may be overlain on the map and their geophysical data plotted in X-Y graphs. The advantage of applets over traditional web pages is that they permit dynamic interaction with data sets, while limiting time consuming interaction with a remote server. Users may customize the graphics display by modifying the scale, or the symbol or line characteristics of rendered data, contour interval, etc. The ease with which users can select areas, view the physiography of areas, and preview data sets and evaluate them for quality and applicability, makes MapApp a valuable tool for education and research.

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.

PubMed

Bordner, Andrew J; Gorin, Andrey A

2008-05-12

Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes can reveal the details of their function and provide a basis for many computational and experimental approaches. Differentiation between biological and non-biological contacts and reconstruction of the intact complex is a challenging computational problem. A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB). We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) combining these scores for each PDB entry in order to predict the complex structure. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions. These interfaces, as well as the predicted protein complexes, are available from the Protein Interface Server (PInS) website (see Availability and requirements section). Our method demonstrates an almost two-fold reduction of the annotation error rate as evaluated on a large benchmark set of complexes validated from the literature. We also estimate relative contributions of each interface property to the accurate discrimination of biologically relevant interfaces and discuss possible directions for further improving the prediction method.

Geographic information system/watershed model interface

USGS Publications Warehouse

Fisher, Gary T.

1989-01-01

Geographic information systems allow for the interactive analysis of spatial data related to water-resources investigations. A conceptual design for an interface between a geographic information system and a watershed model includes functions for the estimation of model parameter values. Design criteria include ease of use, minimal equipment requirements, a generic data-base management system, and use of a macro language. An application is demonstrated for a 90.1-square-kilometer subbasin of the Patuxent River near Unity, Maryland, that performs automated derivation of watershed parameters for hydrologic modeling.

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.

Interactive Scene Analysis Module - A sensor-database fusion system for telerobotic environments

NASA Technical Reports Server (NTRS)

Cooper, Eric G.; Vazquez, Sixto L.; Goode, Plesent W.

1992-01-01

Accomplishing a task with telerobotics typically involves a combination of operator control/supervision and a 'script' of preprogrammed commands. These commands usually assume that the location of various objects in the task space conform to some internal representation (database) of that task space. The ability to quickly and accurately verify the task environment against the internal database would improve the robustness of these preprogrammed commands. In addition, the on-line initialization and maintenance of a task space database is difficult for operators using Cartesian coordinates alone. This paper describes the Interactive Scene' Analysis Module (ISAM) developed to provide taskspace database initialization and verification utilizing 3-D graphic overlay modelling, video imaging, and laser radar based range imaging. Through the fusion of taskspace database information and image sensor data, a verifiable taskspace model is generated providing location and orientation data for objects in a task space. This paper also describes applications of the ISAM in the Intelligent Systems Research Laboratory (ISRL) at NASA Langley Research Center, and discusses its performance relative to representation accuracy and operator interface efficiency.

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.

MOOsburg: Multi-User Domain Support for a Community Network.

ERIC Educational Resources Information Center

Carroll, John M.; Rosson, Mary Beth; Isenhour, Philip L.; Van Metre, Christina; Schafer, Wendy A.; Ganoe, Craig H.

2001-01-01

Explains MOOsburg, a community-oriented MOO that models the geography of the town of Blacksburg, Virginia and is designed to be used by local residents. Highlights include the software architecture; client-server communication; spatial database; user interface; interaction; map-based navigation; application development; and future plans. (LRW)

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB(®) graphical user interface.

PubMed

Sridhar, Vishnu B; Tian, Peifang; Dale, Anders M; Devor, Anna; Saisan, Payam A

2014-01-01

We present a database client software-Neurovascular Network Explorer 1.0 (NNE 1.0)-that uses MATLAB(®) based Graphical User Interface (GUI) for interaction with a database of 2-photon single-vessel diameter measurements from our previous publication (Tian et al., 2010). These data are of particular interest for modeling the hemodynamic response. NNE 1.0 is downloaded by the user and then runs either as a MATLAB script or as a standalone program on a Windows platform. The GUI allows browsing the database according to parameters specified by the user, simple manipulation and visualization of the retrieved records (such as averaging and peak-normalization), and export of the results. Further, we provide NNE 1.0 source code. With this source code, the user can database their own experimental results, given the appropriate data structure and naming conventions, and thus share their data in a user-friendly format with other investigators. NNE 1.0 provides an example of seamless and low-cost solution for sharing of experimental data by a regular size neuroscience laboratory and may serve as a general template, facilitating dissemination of biological results and accelerating data-driven modeling approaches.

Resident database interfaces to the DAVID system, a heterogeneous distributed database management system

NASA Technical Reports Server (NTRS)

Moroh, Marsha

1988-01-01

A methodology for building interfaces of resident database management systems to a heterogeneous distributed database management system under development at NASA, the DAVID system, was developed. The feasibility of that methodology was demonstrated by construction of the software necessary to perform the interface task. The interface terminology developed in the course of this research is presented. The work performed and the results are summarized.

Spacecraft Orbit Design and Analysis (SODA), version 1.0 user's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.; Davis, John S.

1989-01-01

The Spacecraft Orbit Design and Analysis (SODA) computer program, Version 1.0 is described. SODA is a spaceflight mission planning system which consists of five program modules integrated around a common database and user interface. SODA runs on a VAX/VMS computer with an EVANS & SUTHERLAND PS300 graphics workstation. BOEING RIM-Version 7 relational database management system performs transparent database services. In the current version three program modules produce an interactive three dimensional (3D) animation of one or more satellites in planetary orbit. Satellite visibility and sensor coverage capabilities are also provided. One module produces an interactive 3D animation of the solar system. Another module calculates cumulative satellite sensor coverage and revisit time for one or more satellites. Currently Earth, Moon, and Mars systems are supported for all modules except the solar system module.

Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

ERIC Educational Resources Information Center

Fitzgibbons, Megan; Meert, Deborah

2010-01-01

The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

IAC - INTEGRATED ANALYSIS CAPABILITY

NASA Technical Reports Server (NTRS)

Frisch, H. P.

1994-01-01

The objective of the Integrated Analysis Capability (IAC) system is to provide a highly effective, interactive analysis tool for the integrated design of large structures. With the goal of supporting the unique needs of engineering analysis groups concerned with interdisciplinary problems, IAC was developed to interface programs from the fields of structures, thermodynamics, controls, and system dynamics with an executive system and database to yield a highly efficient multi-disciplinary system. Special attention is given to user requirements such as data handling and on-line assistance with operational features, and the ability to add new modules of the user's choice at a future date. IAC contains an executive system, a data base, general utilities, interfaces to various engineering programs, and a framework for building interfaces to other programs. IAC has shown itself to be effective in automatic data transfer among analysis programs. IAC 2.5, designed to be compatible as far as possible with Level 1.5, contains a major upgrade in executive and database management system capabilities, and includes interfaces to enable thermal, structures, optics, and control interaction dynamics analysis. The IAC system architecture is modular in design. 1) The executive module contains an input command processor, an extensive data management system, and driver code to execute the application modules. 2) Technical modules provide standalone computational capability as well as support for various solution paths or coupled analyses. 3) Graphics and model generation interfaces are supplied for building and viewing models. Advanced graphics capabilities are provided within particular analysis modules such as INCA and NASTRAN. 4) Interface modules provide for the required data flow between IAC and other modules. 5) User modules can be arbitrary executable programs or JCL procedures with no pre-defined relationship to IAC. 6) Special purpose modules are included, such as MIMIC (Model Integration via Mesh Interpolation Coefficients), which transforms field values from one model to another; LINK, which simplifies incorporation of user specific modules into IAC modules; and DATAPAC, the National Bureau of Standards statistical analysis package. The IAC database contains structured files which provide a common basis for communication between modules and the executive system, and can contain unstructured files such as NASTRAN checkpoint files, DISCOS plot files, object code, etc. The user can define groups of data and relations between them. A full data manipulation and query system operates with the database. The current interface modules comprise five groups: 1) Structural analysis - IAC contains a NASTRAN interface for standalone analysis or certain structural/control/thermal combinations. IAC provides enhanced structural capabilities for normal modes and static deformation analysis via special DMAP sequences. IAC 2.5 contains several specialized interfaces from NASTRAN in support of multidisciplinary analysis. 2) Thermal analysis - IAC supports finite element and finite difference techniques for steady state or transient analysis. There are interfaces for the NASTRAN thermal analyzer, SINDA/SINFLO, and TRASYS II. FEMNET, which converts finite element structural analysis models to finite difference thermal analysis models, is also interfaced with the IAC database. 3) System dynamics - The DISCOS simulation program which allows for either nonlinear time domain analysis or linear frequency domain analysis, is fully interfaced to the IAC database management capability. 4) Control analysis - Interfaces for the ORACLS, SAMSAN, NBOD2, and INCA programs allow a wide range of control system analyses and synthesis techniques. Level 2.5 includes EIGEN, which provides tools for large order system eigenanalysis, and BOPACE, which allows for geometric capabilities and finite element analysis with nonlinear material. Also included in IAC level 2.5 is SAMSAN 3.1, an engineering analysis program which contains a general purpose library of over 600 subroutines for numerical analysis. 5) Graphics - The graphics package IPLOT is included in IAC. IPLOT generates vector displays of tabular data in the form of curves, charts, correlation tables, etc. Either DI3000 or PLOT-10 graphics software is required for full graphic capability. In addition to these analysis tools, IAC 2.5 contains an IGES interface which allows the user to read arbitrary IGES files into an IAC database and to edit and output new IGES files. IAC is available by license for a period of 10 years to approved U.S. licensees. The licensed program product includes one set of supporting documentation. Additional copies may be purchased separately. IAC is written in FORTRAN 77 and has been implemented on a DEC VAX series computer operating under VMS. IAC can be executed by multiple concurrent users in batch or interactive mode. The program is structured to allow users to easily delete those program capabilities and "how to" examples they do not want in order to reduce the size of the package. The basic central memory requirement for IAC is approximately 750KB. The following programs are also available from COSMIC as separate packages: NASTRAN, SINDA/SINFLO, TRASYS II, DISCOS, ORACLS, SAMSAN, NBOD2, and INCA. The development of level 2.5 of IAC was completed in 1989.

End-to-end interoperability and workflows from building architecture design to one or more simulations

DOEpatents

Chao, Tian-Jy; Kim, Younghun

2015-02-10

An end-to-end interoperability and workflows from building architecture design to one or more simulations, in one aspect, may comprise establishing a BIM enablement platform architecture. A data model defines data entities and entity relationships for enabling the interoperability and workflows. A data definition language may be implemented that defines and creates a table schema of a database associated with the data model. Data management services and/or application programming interfaces may be implemented for interacting with the data model. Web services may also be provided for interacting with the data model via the Web. A user interface may be implemented that communicates with users and uses the BIM enablement platform architecture, the data model, the data definition language, data management services and application programming interfaces to provide functions to the users to perform work related to building information management.

Analysis of User Interaction with a Brain-Computer Interface Based on Steady-State Visually Evoked Potentials: Case Study of a Game

PubMed Central

de Carvalho, Sarah Negreiros; Costa, Thiago Bulhões da Silva; Attux, Romis; Hornung, Heiko Horst; Arantes, Dalton Soares

2018-01-01

This paper presents a systematic analysis of a game controlled by a Brain-Computer Interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEP). The objective is to understand BCI systems from the Human-Computer Interface (HCI) point of view, by observing how the users interact with the game and evaluating how the interface elements influence the system performance. The interactions of 30 volunteers with our computer game, named “Get Coins,” through a BCI based on SSVEP, have generated a database of brain signals and the corresponding responses to a questionnaire about various perceptual parameters, such as visual stimulation, acoustic feedback, background music, visual contrast, and visual fatigue. Each one of the volunteers played one match using the keyboard and four matches using the BCI, for comparison. In all matches using the BCI, the volunteers achieved the goals of the game. Eight of them achieved a perfect score in at least one of the four matches, showing the feasibility of the direct communication between the brain and the computer. Despite this successful experiment, adaptations and improvements should be implemented to make this innovative technology accessible to the end user. PMID:29849549

Analysis of User Interaction with a Brain-Computer Interface Based on Steady-State Visually Evoked Potentials: Case Study of a Game.

PubMed

Leite, Harlei Miguel de Arruda; de Carvalho, Sarah Negreiros; Costa, Thiago Bulhões da Silva; Attux, Romis; Hornung, Heiko Horst; Arantes, Dalton Soares

2018-01-01

This paper presents a systematic analysis of a game controlled by a Brain-Computer Interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEP). The objective is to understand BCI systems from the Human-Computer Interface (HCI) point of view, by observing how the users interact with the game and evaluating how the interface elements influence the system performance. The interactions of 30 volunteers with our computer game, named "Get Coins," through a BCI based on SSVEP, have generated a database of brain signals and the corresponding responses to a questionnaire about various perceptual parameters, such as visual stimulation, acoustic feedback, background music, visual contrast, and visual fatigue. Each one of the volunteers played one match using the keyboard and four matches using the BCI, for comparison. In all matches using the BCI, the volunteers achieved the goals of the game. Eight of them achieved a perfect score in at least one of the four matches, showing the feasibility of the direct communication between the brain and the computer. Despite this successful experiment, adaptations and improvements should be implemented to make this innovative technology accessible to the end user.

FunSimMat: a comprehensive functional similarity database

PubMed Central

Schlicker, Andreas; Albrecht, Mario

2008-01-01

Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML–RPC interface gives automatic online access to FunSimMat for programs and remote services. PMID:17932054

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.

FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues.

PubMed

El-Manzalawy, Yasser; Abbas, Mostafa; Malluhi, Qutaibah; Honavar, Vasant

2016-01-01

A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences. The computational efforts needed for generating PSSMs severely limits the practical utility of protein-RNA interface prediction servers. In this work, we experiment with two approaches, random sampling and sequence similarity reduction, for extracting a representative reference database of protein sequences from more than 50 million protein sequences in UniRef100. Our results suggest that random sampled databases produce better PSSM profiles (in terms of the number of hits used to generate the profile and the distance of the generated profile to the corresponding profile generated using the entire UniRef100 data as well as the accuracy of the machine learning classifier trained using these profiles). Based on our results, we developed FastRNABindR, an improved version of RNABindR for predicting protein-RNA interface residues using PSSM profiles generated using 1% of the UniRef100 sequences sampled uniformly at random. To the best of our knowledge, FastRNABindR is the only protein-RNA interface residue prediction online server that requires generation of PSSM profiles for query sequences and accepts hundreds of protein sequences per submission. Our approach for determining the optimal BLAST database for a protein-RNA interface residue classification task has the potential of substantially speeding up, and hence increasing the practical utility of, other amino acid sequence based predictors of protein-protein and protein-DNA interfaces.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

PubMed

Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

2003-11-01

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

A RESEARCH DATABASE FOR IMPROVED DATA MANAGEMENT AND ANALYSIS IN LONGITUDINAL STUDIES

PubMed Central

BIELEFELD, ROGER A.; YAMASHITA, TOYOKO S.; KEREKES, EDWARD F.; ERCANLI, EHAT; SINGER, LYNN T.

2014-01-01

We developed a research database for a five-year prospective investigation of the medical, social, and developmental correlates of chronic lung disease during the first three years of life. We used the Ingres database management system and the Statit statistical software package. The database includes records containing 1300 variables each, the results of 35 psychological tests, each repeated five times (providing longitudinal data on the child, the parents, and behavioral interactions), both raw and calculated variables, and both missing and deferred values. The four-layer menu-driven user interface incorporates automatic activation of complex functions to handle data verification, missing and deferred values, static and dynamic backup, determination of calculated values, display of database status, reports, bulk data extraction, and statistical analysis. PMID:7596250

Prediction of hot spots in protein interfaces using a random forest model with hybrid features.

PubMed

Wang, Lin; Liu, Zhi-Ping; Zhang, Xiang-Sun; Chen, Luonan

2012-03-01

Prediction of hot spots in protein interfaces provides crucial information for the research on protein-protein interaction and drug design. Existing machine learning methods generally judge whether a given residue is likely to be a hot spot by extracting features only from the target residue. However, hot spots usually form a small cluster of residues which are tightly packed together at the center of protein interface. With this in mind, we present a novel method to extract hybrid features which incorporate a wide range of information of the target residue and its spatially neighboring residues, i.e. the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). We provide a novel random forest (RF) model to effectively integrate these hybrid features for predicting hot spots in protein interfaces. Our method can achieve accuracy (ACC) of 82.4% and Matthew's correlation coefficient (MCC) of 0.482 in Alanine Scanning Energetics Database, and ACC of 77.6% and MCC of 0.429 in Binding Interface Database. In a comparison study, performance of our RF model exceeds other existing methods, such as Robetta, FOLDEF, KFC, KFC2, MINERVA and HotPoint. Of our hybrid features, three physicochemical features of target residues (mass, polarizability and isoelectric point), the relative side-chain accessible surface area and the average depth index of mirror-contact residues are found to be the main discriminative features in hot spots prediction. We also confirm that hot spots tend to form large contact surface areas between two interacting proteins. Source data and code are available at: http://www.aporc.org/doc/wiki/HotSpot.

Tibetan Magmatism Database

NASA Astrophysics Data System (ADS)

Chapman, James B.; Kapp, Paul

2017-11-01

A database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan-Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web-based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high-flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

Ioss IO Subsystem

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

Sjaardema, Gregory; Bauer, David; Erik, & Illescas

2017-01-06

The Ioss is a database-independent package for providing an object-oriented, abstract interface to IO capabilities for a finite element application; and concrete database interfaces which provided input and/or output to exodusII, xdmf, generated, and heartbeat database formats. The Ioss provides an object-oriented C++-based IO interface for a finite element application code. The application code can perform all IO operations through the Ioss interface which is typically at a higher abstraction level than the concrete database formats. The Ioss then performs the needed operations to translate the finite element data to the specific format required by the concrete database implementations. Themore » Ioss currently supports interfaces to exodusII, xdmf, generated, and heartbeat formats, but additional formats can be easily added.« less

FRED, a Front End for Databases.

ERIC Educational Resources Information Center

Crystal, Maurice I.; Jakobson, Gabriel E.

1982-01-01

FRED (a Front End for Databases) was conceived to alleviate data access difficulties posed by the heterogeneous nature of online databases. A hardware/software layer interposed between users and databases, it consists of three subsystems: user-interface, database-interface, and knowledge base. Architectural alternatives for this database machine…

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

Database interfaces on NASA's heterogeneous distributed database system

NASA Technical Reports Server (NTRS)

Huang, S. H. S.

1986-01-01

The purpose of the ORACLE interface is to enable the DAVID program to submit queries and transactions to databases running under the ORACLE DBMS. The interface package is made up of several modules. The progress of these modules is described below. The two approaches used in implementing the interface are also discussed. Detailed discussion of the design of the templates is shown and concluding remarks are presented.

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.

PubMed

Wang, Peng; Zhi, Hui; Zhang, Yunpeng; Liu, Yue; Zhang, Jizhou; Gao, Yue; Guo, Maoni; Ning, Shangwei; Li, Xia

2015-01-01

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or 'miRNA sponges' that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge. © The Author(s) 2015. Published by Oxford University Press.

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs

PubMed Central

Wang, Peng; Zhi, Hui; Zhang, Yunpeng; Liu, Yue; Zhang, Jizhou; Gao, Yue; Guo, Maoni; Ning, Shangwei; Li, Xia

2015-01-01

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or ‘miRNA sponges’ that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them interacting with their natural targets to play critical roles in various biological and pathological processes. It has become increasingly important to develop a high quality database to record and store ceRNA data to support future studies. To this end, we have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and 463 ceRNA relationships from 11 species following manual curating from nearly 1200 published articles. Database classes include endogenously generated molecules including coding genes, pseudogenes, long non-coding RNAs and circular RNAs, along with exogenously introduced molecules including viral RNAs and artificial engineered sponges. Approximately 70% of the interactions were identified experimentally in disease states. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading of dataset. A submission page is also included to allow researchers to submit newly validated miRNA sponge data. Database URL: http://www.bio-bigdata.net/miRSponge. PMID:26424084

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

PubMed

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

2014-01-01

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

CyBy(2): a structure-based data management tool for chemical and biological data.

PubMed

Höck, Stefan; Riedl, Rainer

2012-01-01

We report the development of a powerful data management tool for chemical and biological data: CyBy(2). CyBy(2) is a structure-based information management tool used to store and visualize structural data alongside additional information such as project assignment, physical information, spectroscopic data, biological activity, functional data and synthetic procedures. The application consists of a database, an application server, used to query and update the database, and a client application with a rich graphical user interface (GUI) used to interact with the server.

A Graphical Database Interface for Casual, Naive Users.

ERIC Educational Resources Information Center

Burgess, Clifford; Swigger, Kathleen

1986-01-01

Describes the design of a database interface for infrequent users of computers which consists of a graphical display of a model of a database and a natural language query language. This interface was designed for and tested with physicians at the University of Texas Health Science Center in Dallas. (LRW)

The BioGRID interaction database: 2013 update.

PubMed

Chatr-Aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heinicke, Sven; Boucher, Lorrie; Winter, Andrew; Stark, Chris; Nixon, Julie; Ramage, Lindsay; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Breitkreutz, Ashton; Sellam, Adnane; Chen, Daici; Chang, Christie; Rust, Jennifer; Livstone, Michael; Oughtred, Rose; Dolinski, Kara; Tyers, Mike

2013-01-01

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin.

Development and Dissemination of a Nationwide Helium Database for a National Assessment of Helium Resources.

NASA Astrophysics Data System (ADS)

Brennan, S. T.; East, J. A., II; Garrity, C. P.

2015-12-01

In 2013, Congress passed the Helium Stewardship Act requiring the U.S. Geological Survey (USGS) to undertake a national helium gas resource assessment to determine the nation's helium resources. An important initial component necessary to complete this assessment was the development of a comprehensive database of Helium (He) concentrations from petroleum exploration wells. Because Helium is often used as the carrier gas for compositional analyses for commercial and exploratory oil and gas wells, this limits the available helium concentration data. A literature search in peer-reviewed publications, state geologic survey databases, USGS energy geochemical databases, and the Bureau of Land Management databases provided approximately 16,000 data points from wells that had measurable He concentrations in the gas composition analyses. The data from these wells includes, date of sample collection, American Petroleum Institute well number, formation name, field name, depth of sample collection, and location. The gas compositional analyses, some performed as far back as 1934, do not all have the same level of precision and accuracy, therefore the date of the analysis is critical to the assessment as it indicates the relative amount of uncertainty in the analytical results. Non-proprietary data was used to create a GIS based interactive web interface that allows users to visualize, inspect, interact, and download our most current He data. The user can click on individual locations to see the available data at that location, as well as zoom in and out on a data density map. Concentrations on the map range from .04 mol% (lowest concentration of economic value) to 12% (highest naturally occurring values). This visual interface will allow users to develop a rapid appreciation of the areas with the highest potential for high helium concentrations within oil and gas fields.

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

PubMed Central

Hao, Yajing; Wu, Wei; Li, Hui; Yuan, Jiao; Luo, Jianjun; Zhao, Yi; Chen, Runsheng

2016-01-01

Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs’ functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA–miRNA interactions from in silico predictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available at http://www.bioinfo.org/NPInter/. Database URL: http://www.bioinfo.org/NPInter/ PMID:27087310

The strategies WDK: a graphical search interface and web development kit for functional genomics databases

PubMed Central

Fischer, Steve; Aurrecoechea, Cristina; Brunk, Brian P.; Gao, Xin; Harb, Omar S.; Kraemer, Eileen T.; Pennington, Cary; Treatman, Charles; Kissinger, Jessica C.; Roos, David S.; Stoeckert, Christian J.

2011-01-01

Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy’s flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org PMID:21705364

A Public-Use, Full-Screen Interface for SPIRES Databases.

ERIC Educational Resources Information Center

Kriz, Harry M.

This paper describes the techniques for implementing a full-screen, custom SPIRES interface for a public-use library database. The database-independent protocol that controls the system is described in detail. Source code for an entire working application using this interface is included. The protocol, with less than 170 lines of procedural code,…

Custom controls

NASA Astrophysics Data System (ADS)

Butell, Bart

1996-02-01

Microsoft's Visual Basic (VB) and Borland's Delphi provide an extremely robust programming environment for delivering multimedia solutions for interactive kiosks, games and titles. Their object oriented use of standard and custom controls enable a user to build extremely powerful applications. A multipurpose, database enabled programming environment that can provide an event driven interface functions as a multimedia kernel. This kernel can provide a variety of authoring solutions (e.g. a timeline based model similar to Macromedia Director or a node authoring model similar to Icon Author). At the heart of the kernel is a set of low level multimedia components providing object oriented interfaces for graphics, audio, video and imaging. Data preparation tools (e.g., layout, palette and Sprite Editors) could be built to manage the media database. The flexible interface for VB allows the construction of an infinite number of user models. The proliferation of these models within a popular, easy to use environment will allow the vast developer segment of 'producer' types to bring their ideas to the market. This is the key to building exciting, content rich multimedia solutions. Microsoft's VB and Borland's Delphi environments combined with multimedia components enable these possibilities.

Netlib services and resources

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

Browne, S.V.; Green, S.C.; Moore, K.

1994-04-01

The Netlib repository, maintained by the University of Tennessee and Oak Ridge National Laboratory, contains freely available software, documents, and databases of interest to the numerical, scientific computing, and other communities. This report includes both the Netlib User`s Guide and the Netlib System Manager`s Guide, and contains information about Netlib`s databases, interfaces, and system implementation. The Netlib repository`s databases include the Performance Database, the Conferences Database, and the NA-NET mail forwarding and Whitepages Databases. A variety of user interfaces enable users to access the Netlib repository in the manner most convenient and compatible with their networking capabilities. These interfaces includemore » the Netlib email interface, the Xnetlib X Windows client, the netlibget command-line TCP/IP client, anonymous FTP, anonymous RCP, and gopher.« less

Experiment Management System for the SND Detector

NASA Astrophysics Data System (ADS)

Pugachev, K.

2017-10-01

We present a new experiment management system for the SND detector at the VEPP-2000 collider (Novosibirsk). An important part to report about is access to experimental databases (configuration, conditions and metadata). The system is designed in client-server architecture. User interaction comes true using web-interface. The server side includes several logical layers: user interface templates; template variables description and initialization; implementation details. The templates are meant to involve as less IT knowledge as possible. Experiment configuration, conditions and metadata are stored in a database. To implement the server side Node.js, a modern JavaScript framework, has been chosen. A new template engine having an interesting feature is designed. A part of the system is put into production. It includes templates dealing with showing and editing first level trigger configuration and equipment configuration and also showing experiment metadata and experiment conditions data index.

Implementation of medical monitor system based on networks

NASA Astrophysics Data System (ADS)

Yu, Hui; Cao, Yuzhen; Zhang, Lixin; Ding, Mingshi

2006-11-01

In this paper, the development trend of medical monitor system is analyzed and portable trend and network function become more and more popular among all kinds of medical monitor devices. The architecture of medical network monitor system solution is provided and design and implementation details of medical monitor terminal, monitor center software, distributed medical database and two kind of medical information terminal are especially discussed. Rabbit3000 system is used in medical monitor terminal to implement security administration of data transfer on network, human-machine interface, power management and DSP interface while DSP chip TMS5402 is used in signal analysis and data compression. Distributed medical database is designed for hospital center according to DICOM information model and HL7 standard. Pocket medical information terminal based on ARM9 embedded platform is also developed to interactive with center database on networks. Two kernels based on WINCE are customized and corresponding terminal software are developed for nurse's routine care and doctor's auxiliary diagnosis. Now invention patent of the monitor terminal is approved and manufacture and clinic test plans are scheduled. Applications for invention patent are also arranged for two medical information terminals.

Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins.

PubMed

Sudarshan, Sanjana; Kodathala, Sasi B; Mahadik, Amruta C; Mehta, Isha; Beck, Brian W

2014-01-01

Specific protein interactions are responsible for most biological functions. Distinguishing Functionally Linked Interfaces of Proteins (FLIPs), from Functionally uncorrelated Contacts (FunCs), is therefore important to characterizing these interactions. To achieve this goal, we have created a database of protein structures called FLIPdb, containing proteins belonging to various functional sub-categories. Here, we use geometric features coupled with Kortemme and Baker's computational alanine scanning method to calculate the energetic sensitivity of each amino acid at the interface to substitution, identify hotspots, and identify other factors that may contribute towards an interface being FLIP or FunC. Using Principal Component Analysis and K-means clustering on a training set of 160 interfaces, we could distinguish FLIPs from FunCs with an accuracy of 76%. When these methods were applied to two test sets of 18 and 170 interfaces, we achieved similar accuracies of 78% and 80%. We have identified that FLIP interfaces have a stronger central organizing tendency than FunCs, due, we suggest, to greater specificity. We also observe that certain functional sub-categories, such as enzymes, antibody-heavy-light, antibody-antigen, and enzyme-inhibitors form distinct sub-clusters. The antibody-antigen and enzyme-inhibitors interfaces have patterns of physical characteristics similar to those of FunCs, which is in agreement with the fact that the selection pressures of these interfaces is differently evolutionarily driven. As such, our ECR model also successfully describes the impact of evolution and natural selection on protein-protein interfaces. Finally, we indicate how our ECR method may be of use in reducing the false positive rate of docking calculations.

Protein-Protein Interface Detection Using the Energy Centrality Relationship (ECR) Characteristic of Proteins

PubMed Central

Sudarshan, Sanjana; Kodathala, Sasi B.; Mahadik, Amruta C.; Mehta, Isha; Beck, Brian W.

2014-01-01

Specific protein interactions are responsible for most biological functions. Distinguishing Functionally Linked Interfaces of Proteins (FLIPs), from Functionally uncorrelated Contacts (FunCs), is therefore important to characterizing these interactions. To achieve this goal, we have created a database of protein structures called FLIPdb, containing proteins belonging to various functional sub-categories. Here, we use geometric features coupled with Kortemme and Baker's computational alanine scanning method to calculate the energetic sensitivity of each amino acid at the interface to substitution, identify hotspots, and identify other factors that may contribute towards an interface being FLIP or FunC. Using Principal Component Analysis and K-means clustering on a training set of 160 interfaces, we could distinguish FLIPs from FunCs with an accuracy of 76%. When these methods were applied to two test sets of 18 and 170 interfaces, we achieved similar accuracies of 78% and 80%. We have identified that FLIP interfaces have a stronger central organizing tendency than FunCs, due, we suggest, to greater specificity. We also observe that certain functional sub-categories, such as enzymes, antibody-heavy-light, antibody-antigen, and enzyme-inhibitors form distinct sub-clusters. The antibody-antigen and enzyme-inhibitors interfaces have patterns of physical characteristics similar to those of FunCs, which is in agreement with the fact that the selection pressures of these interfaces is differently evolutionarily driven. As such, our ECR model also successfully describes the impact of evolution and natural selection on protein-protein interfaces. Finally, we indicate how our ECR method may be of use in reducing the false positive rate of docking calculations. PMID:24830938

bioWidgets: data interaction components for genomics.

PubMed

Fischer, S; Crabtree, J; Brunk, B; Gibson, M; Overton, G C

1999-10-01

The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView.

Community-Supported Data Repositories in Paleobiology: A 'Middle Tail' Between the Geoscientific and Informatics Communities

NASA Astrophysics Data System (ADS)

Williams, J. W.; Ashworth, A. C.; Betancourt, J. L.; Bills, B.; Blois, J.; Booth, R.; Buckland, P.; Charles, D.; Curry, B. B.; Goring, S. J.; Davis, E.; Grimm, E. C.; Graham, R. W.; Smith, A. J.

2015-12-01

Community-supported data repositories (CSDRs) in paleoecology and paleoclimatology have a decades-long tradition and serve multiple critical scientific needs. CSDRs facilitate synthetic large-scale scientific research by providing open-access and curated data that employ community-supported metadata and data standards. CSDRs serve as a 'middle tail' or boundary organization between information scientists and the long-tail community of individual geoscientists collecting and analyzing paleoecological data. Over the past decades, a distributed network of CSDRs has emerged, each serving a particular suite of data and research communities, e.g. Neotoma Paleoecology Database, Paleobiology Database, International Tree Ring Database, NOAA NCEI for Paleoclimatology, Morphobank, iDigPaleo, and Integrated Earth Data Alliance. Recently, these groups have organized into a common Paleobiology Data Consortium dedicated to improving interoperability and sharing best practices and protocols. The Neotoma Paleoecology Database offers one example of an active and growing CSDR, designed to facilitate research into ecological and evolutionary dynamics during recent past global change. Neotoma combines a centralized database structure with distributed scientific governance via multiple virtual constituent data working groups. The Neotoma data model is flexible and can accommodate a variety of paleoecological proxies from many depositional contests. Data input into Neotoma is done by trained Data Stewards, drawn from their communities. Neotoma data can be searched, viewed, and returned to users through multiple interfaces, including the interactive Neotoma Explorer map interface, REST-ful Application Programming Interfaces (APIs), the neotoma R package, and the Tilia stratigraphic software. Neotoma is governed by geoscientists and provides community engagement through training workshops for data contributors, stewards, and users. Neotoma is engaged in the Paleobiological Data Consortium and other efforts to improve interoperability among cyberinfrastructure in the paleogeosciences.

Graphic Interfaces and Online Information.

ERIC Educational Resources Information Center

Percival, J. Mark

1990-01-01

Discusses the growing importance of the use of Graphic User Interfaces (GUIs) with microcomputers and online services. Highlights include the development of graphics interfacing with microcomputers; CD-ROM databases; an evaluation of HyperCard as a potential interface to electronic mail and online commercial databases; and future possibilities.…

Technical Aspects of Interfacing MUMPS to an External SQL Relational Database Management System

PubMed Central

Kuzmak, Peter M.; Walters, Richard F.; Penrod, Gail

1988-01-01

This paper describes an interface connecting InterSystems MUMPS (M/VX) to an external relational DBMS, the SYBASE Database Management System. The interface enables MUMPS to operate in a relational environment and gives the MUMPS language full access to a complete set of SQL commands. MUMPS generates SQL statements as ASCII text and sends them to the RDBMS. The RDBMS executes the statements and returns ASCII results to MUMPS. The interface suggests that the language features of MUMPS make it an attractive tool for use in the relational database environment. The approach described in this paper separates MUMPS from the relational database. Positioning the relational database outside of MUMPS promotes data sharing and permits a number of different options to be used for working with the data. Other languages like C, FORTRAN, and COBOL can access the RDBMS database. Advanced tools provided by the relational database vendor can also be used. SYBASE is an advanced high-performance transaction-oriented relational database management system for the VAX/VMS and UNIX operating systems. SYBASE is designed using a distributed open-systems architecture, and is relatively easy to interface with MUMPS.

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

PubMed

Xu, Huilei; Baroukh, Caroline; Dannenfelser, Ruth; Chen, Edward Y; Tan, Christopher M; Kou, Yan; Kim, Yujin E; Lemischka, Ihor R; Ma'ayan, Avi

2013-01-01

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE

The APIS service : a tool for accessing value-added HST planetary auroral observations over 1997-2015

NASA Astrophysics Data System (ADS)

Lamy, L.; Henry, F.; Prangé, R.; Le Sidaner, P.

2015-10-01

The Auroral Planetary Imaging and Spectroscopy (APIS) service http://obspm.fr/apis/ provides an open and interactive access to processed auroral observations of the outer planets and their satellites. Such observations are of interest for a wide community at the interface between planetology, magnetospheric and heliospheric physics. APIS consists of (i) a high level database, built from planetary auroral observations acquired by the Hubble Space Telescope (HST) since 1997 with its mostly used Far-Ultraviolet spectro- imagers, (ii) a dedicated search interface aimed at browsing efficiently this database through relevant conditional search criteria (Figure 1) and (iii) the ability to interactively work with the data online through plotting tools developed by the Virtual Observatory (VO) community, such as Aladin and Specview. This service is VO compliant and can therefore also been queried by external search tools of the VO community. The diversity of available data and the capability to sort them out by relevant physical criteria shall in particular facilitate statistical studies, on long-term scales and/or multi-instrumental multispectral combined analysis [1,2]. We will present the updated capabilities of APIS with several examples. Several tutorials are available online.

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes

PubMed Central

Ng, I-Man; Tsai, Shang-Chi

2017-01-01

Abstract Alternative splicing (AS), a mechanism by which different forms of mature messenger RNAs (mRNAs) are generated from the same gene, widely occurs in the metazoan genomes. Knowledge about isoform variants and abundance is crucial for understanding the functional context in the molecular diversity of the species. With increasing transcriptome data of model and non-model species, a database for visualization and comparison of AS events with up-to-date information is needed for further research. IsoPlot is a publicly available database with visualization tools for exploration of AS events, including three major species of mosquitoes, Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus, and fruit fly Drosophila melanogaster, the model insect species. IsoPlot includes not only 88,663 annotated transcripts but also 17,037 newly predicted transcripts from massive transcriptome data at different developmental stages of mosquitoes. The web interface enables users to explore the patterns and abundance of isoforms in different experimental conditions as well as cross-species sequence comparison of orthologous transcripts. IsoPlot provides a platform for researchers to access comprehensive information about AS events in mosquitoes and fruit fly. Our database is available on the web via an interactive user interface with an intuitive graphical design, which is applicable for the comparison of complex isoforms within or between species. Database URL: http://isoplot.iis.sinica.edu.tw/ PMID:29220459

IAC-1.5 - INTEGRATED ANALYSIS CAPABILITY

NASA Technical Reports Server (NTRS)

Vos, R. G.

1994-01-01

The objective of the Integrated Analysis Capability (IAC) system is to provide a highly effective, interactive analysis tool for the integrated design of large structures. IAC was developed to interface programs from the fields of structures, thermodynamics, controls, and system dynamics with an executive system and a database to yield a highly efficient multi-disciplinary system. Special attention is given to user requirements such as data handling and on-line assistance with operational features, and the ability to add new modules of the user's choice at a future date. IAC contains an executive system, a database, general utilities, interfaces to various engineering programs, and a framework for building interfaces to other programs. IAC has shown itself to be effective in automating data transfer among analysis programs. The IAC system architecture is modular in design. 1) The executive module contains an input command processor, an extensive data management system, and driver code to execute the application modules. 2) Technical modules provide standalone computational capability as well as support for various solution paths or coupled analyses. 3) Graphics and model generation modules are supplied for building and viewing models. 4) Interface modules provide for the required data flow between IAC and other modules. 5) User modules can be arbitrary executable programs or JCL procedures with no pre-defined relationship to IAC. 6) Special purpose modules are included, such as MIMIC (Model Integration via Mesh Interpolation Coefficients), which transforms field values from one model to another; LINK, which simplifies incorporation of user specific modules into IAC modules; and DATAPAC, the National Bureau of Standards statistical analysis package. The IAC database contains structured files which provide a common basis for communication between modules and the executive system, and can contain unstructured files such as NASTRAN checkpoint files, DISCOS plot files, object code, etc. The user can define groups of data and relations between them. A full data manipulation and query system operates with the database. The current interface modules comprise five groups: 1) Structural analysis - IAC contains a NASTRAN interface for standalone analysis or certain structural/control/thermal combinations. IAC provides enhanced structural capabilities for normal modes and static deformation analysis via special DMAP sequences. 2) Thermal analysis - IAC supports finite element and finite difference techniques for steady state or transient analysis. There are interfaces for the NASTRAN thermal analyzer, SINDA/SINFLO, and TRASYS II. 3) System dynamics - A DISCOS interface allows full use of this simulation program for either nonlinear time domain analysis or linear frequency domain analysis. 4) Control analysis - Interfaces for the ORACLS, SAMSAN, NBOD2, and INCA programs allow a wide range of control system analyses and synthesis techniques. 5) Graphics - The graphics packages PLOT and MOSAIC are included in IAC. PLOT generates vector displays of tabular data in the form of curves, charts, correlation tables, etc., while MOSAIC generates color raster displays of either tabular of array type data. Either DI3000 or PLOT-10 graphics software is required for full graphics capability. IAC is available by license for a period of 10 years to approved licensees. The licensed program product includes one complete set of supporting documentation. Additional copies of the documentation may be purchased separately. IAC is written in FORTRAN 77 and has been implemented on a DEC VAX series computer operating under VMS. IAC can be executed by multiple concurrent users in batch or interactive mode. The basic central memory requirement is approximately 750KB. IAC includes the executive system, graphics modules, a database, general utilities, and the interfaces to all analysis and controls programs described above. Source code is provided for the control programs ORACLS, SAMSAN, NBOD2, and DISCOS. The following programs are also available from COSMIC a

IAC-1.5 - INTEGRATED ANALYSIS CAPABILITY

NASA Technical Reports Server (NTRS)

Vos, R. G.

1994-01-01

The objective of the Integrated Analysis Capability (IAC) system is to provide a highly effective, interactive analysis tool for the integrated design of large structures. IAC was developed to interface programs from the fields of structures, thermodynamics, controls, and system dynamics with an executive system and a database to yield a highly efficient multi-disciplinary system. Special attention is given to user requirements such as data handling and on-line assistance with operational features, and the ability to add new modules of the user's choice at a future date. IAC contains an executive system, a database, general utilities, interfaces to various engineering programs, and a framework for building interfaces to other programs. IAC has shown itself to be effective in automating data transfer among analysis programs. The IAC system architecture is modular in design. 1) The executive module contains an input command processor, an extensive data management system, and driver code to execute the application modules. 2) Technical modules provide standalone computational capability as well as support for various solution paths or coupled analyses. 3) Graphics and model generation modules are supplied for building and viewing models. 4) Interface modules provide for the required data flow between IAC and other modules. 5) User modules can be arbitrary executable programs or JCL procedures with no pre-defined relationship to IAC. 6) Special purpose modules are included, such as MIMIC (Model Integration via Mesh Interpolation Coefficients), which transforms field values from one model to another; LINK, which simplifies incorporation of user specific modules into IAC modules; and DATAPAC, the National Bureau of Standards statistical analysis package. The IAC database contains structured files which provide a common basis for communication between modules and the executive system, and can contain unstructured files such as NASTRAN checkpoint files, DISCOS plot files, object code, etc. The user can define groups of data and relations between them. A full data manipulation and query system operates with the database. The current interface modules comprise five groups: 1) Structural analysis - IAC contains a NASTRAN interface for standalone analysis or certain structural/control/thermal combinations. IAC provides enhanced structural capabilities for normal modes and static deformation analysis via special DMAP sequences. 2) Thermal analysis - IAC supports finite element and finite difference techniques for steady state or transient analysis. There are interfaces for the NASTRAN thermal analyzer, SINDA/SINFLO, and TRASYS II. 3) System dynamics - A DISCOS interface allows full use of this simulation program for either nonlinear time domain analysis or linear frequency domain analysis. 4) Control analysis - Interfaces for the ORACLS, SAMSAN, NBOD2, and INCA programs allow a wide range of control system analyses and synthesis techniques. 5) Graphics - The graphics packages PLOT and MOSAIC are included in IAC. PLOT generates vector displays of tabular data in the form of curves, charts, correlation tables, etc., while MOSAIC generates color raster displays of either tabular of array type data. Either DI3000 or PLOT-10 graphics software is required for full graphics capability. IAC is available by license for a period of 10 years to approved licensees. The licensed program product includes one complete set of supporting documentation. Additional copies of the documentation may be purchased separately. IAC is written in FORTRAN 77 and has been implemented on a DEC VAX series computer operating under VMS. IAC can be executed by multiple concurrent users in batch or interactive mode. The basic central memory requirement is approximately 750KB. IAC includes the executive system, graphics modules, a database, general utilities, and the interfaces to all analysis and controls programs described above. Source code is provided for the control programs ORACLS, SAMSAN, NBOD2, and DISCOS. The following programs are also available from COSMIC as separate packages: NASTRAN, SINDA/SINFLO, TRASYS II, DISCOS, ORACLS, SAMSAN, NBOD2, and INCA. IAC was developed in 1985.

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.

Study of intermolecular contacts in proteins and oligomer interfaces and preliminary investigations into the design and production of nanomaterials from proteins

NASA Astrophysics Data System (ADS)

Iyer, Ganesh Hariharan

The first part of this research involved a study of the nature and extent of nonbonded interactions at crystal and oligomer interfaces. A survey was compiled of several characteristics of intersubunit contacts in 58 different oligomeric proteins, and of the intermolecular contacts in 223 protein crystal structures. Routines written in "S" language were utilized for the generation of the observed and expected contacts. The information in the Protein Data Bank (PDB) was extracted using the database management system, Protein Knowledge Base (PKB). Potentials of mean force for atom-atom contacts and residue-residue contacts were derived by comparison of the number of observed interactions with the number expected by mass action. Preference association matrices and log-linear analyses were applied to determine the different factors that could contribute to the overall interactions at the interfaces of oligomers and crystals. Surface patches at oligomer and crystal interfaces were also studied to further investigate the origin of the differences in their stabilities. Total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acid prominent in oligomer interfaces. Contact potentials indicate that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. The second part involved the development of a new class of biomaterials from two-dimensional arrays of ordered proteins. Point mutations were planned to introduce cysteine residues at appropriate locations to enable cross-linking at the molecular interface within given crystallographic planes. Crystallization and subsequent cross-linking of the modified protein would lead to the formation of arrays on subsequent dissociation of the crystal. Novel protein architectures can be generated from these cross-linked nanostructures. Experiments with model protein, maltose-binding protein (MBP) were performed to develop purification, cross-linking and crystallization techniques. The long-term goal of this project is to apply the experience gained with MBP to the fabrication of nanomaterials from other, application-specific proteins for ultrafiltration and microelectronic devices.

ECLSS evolution: Advanced instrumentation interface requirements. Volume 3: Appendix C

NASA Technical Reports Server (NTRS)

1991-01-01

An Advanced ECLSS (Environmental Control and Life Support System) Technology Interfaces Database was developed primarily to provide ECLSS analysts with a centralized and portable source of ECLSS technologies interface requirements data. The database contains 20 technologies which were previously identified in the MDSSC ECLSS Technologies database. The primary interfaces of interest in this database are fluid, electrical, data/control interfaces, and resupply requirements. Each record contains fields describing the function and operation of the technology. Fields include: an interface diagram, description applicable design points and operating ranges, and an explaination of data, as required. A complete set of data was entered for six of the twenty components including Solid Amine Water Desorbed (SAWD), Thermoelectric Integrated Membrane Evaporation System (TIMES), Electrochemical Carbon Dioxide Concentrator (EDC), Solid Polymer Electrolysis (SPE), Static Feed Electrolysis (SFE), and BOSCH. Additional data was collected for Reverse Osmosis Water Reclaimation-Potable (ROWRP), Reverse Osmosis Water Reclaimation-Hygiene (ROWRH), Static Feed Solid Polymer Electrolyte (SFSPE), Trace Contaminant Control System (TCCS), and Multifiltration Water Reclamation - Hygiene (MFWRH). A summary of the database contents is presented in this report.

Java RMI Software Technology for the Payload Planning System of the International Space Station

NASA Technical Reports Server (NTRS)

Bryant, Barrett R.

1999-01-01

The Payload Planning System is for experiment planning on the International Space Station. The planning process has a number of different aspects which need to be stored in a database which is then used to generate reports on the planning process in a variety of formats. This process is currently structured as a 3-tier client/server software architecture comprised of a Java applet at the front end, a Java server in the middle, and an Oracle database in the third tier. This system presently uses CGI, the Common Gateway Interface, to communicate between the user-interface and server tiers and Active Data Objects (ADO) to communicate between the server and database tiers. This project investigated other methods and tools for performing the communications between the three tiers of the current system so that both the system performance and software development time could be improved. We specifically found that for the hardware and software platforms that PPS is required to run on, the best solution is to use Java Remote Method Invocation (RMI) for communication between the client and server and SQLJ (Structured Query Language for Java) for server interaction with the database. Prototype implementations showed that RMI combined with SQLJ significantly improved performance and also greatly facilitated construction of the communication software.

Pharmit: interactive exploration of chemical space.

PubMed

Sunseri, Jocelyn; Koes, David Ryan

2016-07-08

Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

DBSecSys: a database of Burkholderia mallei secretion systems.

PubMed

Memišević, Vesna; Kumar, Kamal; Cheng, Li; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

2014-07-16

Bacterial pathogenicity represents a major public health concern worldwide. Secretion systems are a key component of bacterial pathogenicity, as they provide the means for bacterial proteins to penetrate host-cell membranes and insert themselves directly into the host cells' cytosol. Burkholderia mallei is a Gram-negative bacterium that uses multiple secretion systems during its host infection life cycle. To date, the identities of secretion system proteins for B. mallei are not well known, and their pathogenic mechanisms of action and host factors are largely uncharacterized. We present the Database of Burkholderia malleiSecretion Systems (DBSecSys), a compilation of manually curated and computationally predicted bacterial secretion system proteins and their host factors. Currently, DBSecSys contains comprehensive experimentally and computationally derived information about B. mallei strain ATCC 23344. The database includes 143 B. mallei proteins associated with five secretion systems, their 1,635 human and murine interacting targets, and the corresponding 2,400 host-B. mallei interactions. The database also includes information about 10 pathogenic mechanisms of action for B. mallei secretion system proteins inferred from the available literature. Additionally, DBSecSys provides details about 42 virulence attenuation experiments for 27 B. mallei secretion system proteins. Users interact with DBSecSys through a Web interface that allows for data browsing, querying, visualizing, and downloading. DBSecSys provides a comprehensive, systematically organized resource of experimental and computational data associated with B. mallei secretion systems. It provides the unique ability to study secretion systems not only through characterization of their corresponding pathogen proteins, but also through characterization of their host-interacting partners.The database is available at https://applications.bhsai.org/dbsecsys.

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

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

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

The use of haptic interfaces and web services in crystallography: an application for a `screen to beam' interface

DOE PAGES

Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.; ...

2016-11-11

Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. Our work illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from `point and click' to `touch and share', where results can be selected, annotated and discussed collaboratively. Furthermore, in the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting informationmore » can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient `screen to beam' approach. The application is not limited to the area of crystallization screening; `touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.« less

An Overview of ARL’s Multimodal Signatures Database and Web Interface

DTIC Science & Technology

2007-12-01

ActiveX components, which hindered distribution due to license agreements and run-time license software to use such components. g. Proprietary...Overview The database consists of multimodal signature data files in the HDF5 format. Generally, each signature file contains all the ancillary...only contains information in the database, Web interface, and signature files that is releasable to the public. The Web interface consists of static

Implementation and application of an interactive user-friendly validation software for RADIANCE

NASA Astrophysics Data System (ADS)

Sundaram, Anand; Boonn, William W.; Kim, Woojin; Cook, Tessa S.

2012-02-01

RADIANCE extracts CT dose parameters from dose sheets using optical character recognition and stores the data in a relational database. To facilitate validation of RADIANCE's performance, a simple user interface was initially implemented and about 300 records were evaluated. Here, we extend this interface to achieve a wider variety of functions and perform a larger-scale validation. The validator uses some data from the RADIANCE database to prepopulate quality-testing fields, such as correspondence between calculated and reported total dose-length product. The interface also displays relevant parameters from the DICOM headers. A total of 5,098 dose sheets were used to test the performance accuracy of RADIANCE in dose data extraction. Several search criteria were implemented. All records were searchable by accession number, study date, or dose parameters beyond chosen thresholds. Validated records were searchable according to additional criteria from validation inputs. An error rate of 0.303% was demonstrated in the validation. Dose monitoring is increasingly important and RADIANCE provides an open-source solution with a high level of accuracy. The RADIANCE validator has been updated to enable users to test the integrity of their installation and verify that their dose monitoring is accurate and effective.

Design and Implementation of an Interface Editor for the Amadeus Multi- Relational Database Front-end System

DTIC Science & Technology

1993-03-25

application of Object-Oriented Programming (OOP) and Human-Computer Interface (HCI) design principles. Knowledge gained from each topic has been incorporated...through the ap- plication of Object-Oriented Programming (OOP) and Human-Computer Interface (HCI) design principles. Knowledge gained from each topic has...programming and Human-Computer Interface (HCI) design. Knowledge gained from each is applied to the design of a Form-based interface for database data

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database.

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful AOP-DB user interface in...

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful user interface in the for...

Web based tools for data manipulation, visualisation and validation with interactive georeferenced graphs

NASA Astrophysics Data System (ADS)

Ivankovic, D.; Dadic, V.

2009-04-01

Some of oceanographic parameters have to be manually inserted into database; some (for example data from CTD probe) are inserted from various files. All this parameters requires visualization, validation and manipulation from research vessel or scientific institution, and also public presentation. For these purposes is developed web based system, containing dynamic sql procedures and java applets. Technology background is Oracle 10g relational database, and Oracle application server. Web interfaces are developed using PL/SQL stored database procedures (mod PL/SQL). Additional parts for data visualization include use of Java applets and JavaScript. Mapping tool is Google maps API (javascript) and as alternative java applet. Graph is realized as dynamically generated web page containing java applet. Mapping tool and graph are georeferenced. That means that click on some part of graph, automatically initiate zoom or marker onto location where parameter was measured. This feature is very useful for data validation. Code for data manipulation and visualization are partially realized with dynamic SQL and that allow as to separate data definition and code for data manipulation. Adding new parameter in system requires only data definition and description without programming interface for this kind of data.

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. PMID:29023571

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

Mewes, H. W.; Amid, C.; Arnold, R.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Münsterkötter, M.; Pagel, P.; Strack, N.; Stümpflen, V.; Warfsmann, J.; Ruepp, A.

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein–protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions.

PubMed

Cohen, Ariel; Rosenthal, Eran; Shifman, Julia M

2017-11-10

Ubiquitin is a small protein that enables one of the most common post-translational modifications, where the whole ubiquitin molecule is attached to various target proteins, forming mono- or polyubiquitin conjugations. As a prototypical multispecific protein, ubiquitin interacts non-covalently with a variety of proteins in the cell, including ubiquitin-modifying enzymes and ubiquitin receptors that recognize signals from ubiquitin-conjugated substrates. To enable recognition of multiple targets and to support fast dissociation from the ubiquitin modifying enzymes, ubiquitin/protein interactions are characterized with low affinities, frequently in the higher μM and lower mM range. To determine how structure encodes low binding affinity of ubiquitin/protein complexes, we analyzed structures of more than a hundred such complexes compiled in the Ubiquitin Structural Relational Database. We calculated various structure-based features of ubiquitin/protein binding interfaces and compared them to the same features of general protein-protein interactions (PPIs) with various functions and generally higher affinities. Our analysis shows that ubiquitin/protein binding interfaces on average do not differ in size and shape complementarity from interfaces of higher-affinity PPIs. However, they contain fewer favorable hydrogen bonds and more unfavorable hydrophobic/charge interactions. We further analyzed how binding interfaces change upon affinity maturation of ubiquitin toward its target proteins. We demonstrate that while different features are improved in different experiments, the majority of the evolved complexes exhibit better shape complementarity and hydrogen bond pattern compared to wild-type complexes. Our analysis helps to understand how low-affinity PPIs have evolved and how they could be converted into high-affinity PPIs. Copyright © 2017 Elsevier Ltd. All rights reserved.

The FRUITY database on AGB stars: past, present and future

NASA Astrophysics Data System (ADS)

Cristallo, S.; Piersanti, L.; Straniero, O.

2016-01-01

We present and show the features of the FRUITY database, an interactive web- based interface devoted to the nucleosynthesis in AGB stars. We describe the current available set of AGB models (largely expanded with respect to the original one) with masses in the range 1.3≤M/M⊙≤3.0 and metallicities -2.15 ≤[Fe/H]≤+0.15. We illustrate the details of our s-process surface distributions and we compare our results to observations. Moreover, we introduce a new set of models where the effects of rotation are taken into account. Finally, we shortly describe next planned upgrades.

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

Flight Planning in the Cloud

NASA Technical Reports Server (NTRS)

Flores, Sarah L.; Chapman, Bruce D.; Tung, Waye W.; Zheng, Yang

2011-01-01

This new interface will enable Principal Investigators (PIs), as well as UAVSAR (Uninhabited Aerial Vehicle Synthetic Aperture Radar) members to do their own flight planning and time estimation without having to request flight lines through the science coordinator. It uses an all-in-one Google Maps interface, a JPL hosted database, and PI flight requirements to design an airborne flight plan. The application will enable users to see their own flight plan being constructed interactively through a map interface, and then the flight planning software will generate all the files necessary for the flight. Afterward, the UAVSAR team can then complete the flight request, including calendaring and supplying requisite flight request files in the expected format for processing by NASA s airborne science program. Some of the main features of the interface include drawing flight lines on the map, nudging them, adding them to the current flight plan, and reordering them. The user can also search and select takeoff, landing, and intermediate airports. As the flight plan is constructed, all of its components are constantly being saved to the database, and the estimated flight times are updated. Another feature is the ability to import flight lines from previously saved flight plans. One of the main motivations was to make this Web application as simple and intuitive as possible, while also being dynamic and robust. This Web application can easily be extended to support other airborne instruments.

An Application Programming Interface for Synthetic Snowflake Particle Structure and Scattering Data

NASA Technical Reports Server (NTRS)

Lammers, Matthew; Kuo, Kwo-Sen

2017-01-01

The work by Kuo and colleagues on growing synthetic snowflakes and calculating their single-scattering properties has demonstrated great potential to improve the retrievals of snowfall. To grant colleagues flexible and targeted access to their large collection of sizes and shapes at fifteen (15) microwave frequencies, we have developed a web-based Application Programming Interface (API) integrated with NASA Goddard's Precipitation Processing System (PPS) Group. It is our hope that the API will enable convenient programmatic utilization of the database. To help users better understand the API's capabilities, we have developed an interactive web interface called the OpenSSP API Query Builder, which implements an intuitive system of mechanisms for selecting shapes, sizes, and frequencies to generate queries, with which the API can then extract and return data from the database. The Query Builder also allows for the specification of normalized particle size distributions by setting pertinent parameters, with which the API can also return mean geometric and scattering properties for each size bin. Additionally, the Query Builder interface enables downloading of raw scattering and particle structure data packages. This presentation will describe some of the challenges and successes associated with developing such an API. Examples of its usage will be shown both through downloading output and pulling it into a spreadsheet, as well as querying the API programmatically and working with the output in code.

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

Use of a Relational Database to Support Clinical Research: Application in a Diabetes Program

PubMed Central

Lomatch, Diane; Truax, Terry; Savage, Peter

1981-01-01

A database has been established to support conduct of clinical research and monitor delivery of medical care for 1200 diabetic patients as part of the Michigan Diabetes Research and Training Center (MDRTC). Use of an intelligent microcomputer to enter and retrieve the data and use of a relational database management system (DBMS) to store and manage data have provided a flexible, efficient method of achieving both support of small projects and monitoring overall activity of the Diabetes Center Unit (DCU). Simplicity of access to data, efficiency in providing data for unanticipated requests, ease of manipulations of relations, security and “logical data independence” were important factors in choosing a relational DBMS. The ability to interface with an interactive statistical program and a graphics program is a major advantage of this system. Out database currently provides support for the operation and analysis of several ongoing research projects.

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

Tags Extarction from Spatial Documents in Search Engines

NASA Astrophysics Data System (ADS)

Borhaninejad, S.; Hakimpour, F.; Hamzei, E.

2015-12-01

Nowadays the selective access to information on the Web is provided by search engines, but in the cases which the data includes spatial information the search task becomes more complex and search engines require special capabilities. The purpose of this study is to extract the information which lies in spatial documents. To that end, we implement and evaluate information extraction from GML documents and a retrieval method in an integrated approach. Our proposed system consists of three components: crawler, database and user interface. In crawler component, GML documents are discovered and their text is parsed for information extraction; storage. The database component is responsible for indexing of information which is collected by crawlers. Finally the user interface component provides the interaction between system and user. We have implemented this system as a pilot system on an Application Server as a simulation of Web. Our system as a spatial search engine provided searching capability throughout the GML documents and thus an important step to improve the efficiency of search engines has been taken.

Active Exploration of Large 3D Model Repositories.

PubMed

Gao, Lin; Cao, Yan-Pei; Lai, Yu-Kun; Huang, Hao-Zhi; Kobbelt, Leif; Hu, Shi-Min

2015-12-01

With broader availability of large-scale 3D model repositories, the need for efficient and effective exploration becomes more and more urgent. Existing model retrieval techniques do not scale well with the size of the database since often a large number of very similar objects are returned for a query, and the possibilities to refine the search are quite limited. We propose an interactive approach where the user feeds an active learning procedure by labeling either entire models or parts of them as "like" or "dislike" such that the system can automatically update an active set of recommended models. To provide an intuitive user interface, candidate models are presented based on their estimated relevance for the current query. From the methodological point of view, our main contribution is to exploit not only the similarity between a query and the database models but also the similarities among the database models themselves. We achieve this by an offline pre-processing stage, where global and local shape descriptors are computed for each model and a sparse distance metric is derived that can be evaluated efficiently even for very large databases. We demonstrate the effectiveness of our method by interactively exploring a repository containing over 100 K models.

DITOP: drug-induced toxicity related protein database.

PubMed

Zhang, Jing-Xian; Huang, Wei-Juan; Zeng, Jing-Hua; Huang, Wen-Hui; Wang, Yi; Zhao, Rui; Han, Bu-Cong; Liu, Qing-Feng; Chen, Yu-Zong; Ji, Zhi-Liang

2007-07-01

Drug-induced toxicity related proteins (DITRPs) are proteins that mediate adverse drug reactions (ADRs) or toxicities through their binding to drugs or reactive metabolites. Collection of these proteins facilitates better understanding of the molecular mechanisms of drug-induced toxicity and the rational drug discovery. Drug-induced toxicity related protein database (DITOP) is such a database that is intending to provide comprehensive information of DITRPs. Currently, DITOP contains 1501 records, covering 618 distinct literature-reported DITRPs, 529 drugs/ligands and 418 distinct toxicity terms. These proteins were confirmed experimentally to interact with drugs or their reactive metabolites, thus directly or indirectly cause adverse effects or toxicities. Five major types of drug-induced toxicities or ADRs are included in DITOP, which are the idiosyncratic adverse drug reactions, the dose-dependent toxicities, the drug-drug interactions, the immune-mediated adverse drug effects (IMADEs) and the toxicities caused by genetic susceptibility. Molecular mechanisms underlying the toxicity and cross-links to related resources are also provided while available. Moreover, a series of user-friendly interfaces were designed for flexible retrieval of DITRPs-related information. The DITOP can be accessed freely at http://bioinf.xmu.edu.cn/databases/ADR/index.html. Supplementary data are available at Bioinformatics online.

AFTOMS Technology Issues and Alternatives Report

DTIC Science & Technology

1989-12-01

color , resolu- power requirements, physi- tion; memory , processor speed; cal and weather rugged- IAN interfaces, etc,) f,: these ness. display...Telephone and Telegraph 3 CD-I Compact Disk - Interactive CD-ROM Compact Disk-Read Only Memory CGM Computer Graphics Metafile CNWDI Critical Nuclear...Database Management System RFP Request For Proposal 3 RFS Remote File System ROM Read Only Memory 3 S SA-ALC San Antonio Air Logistics Center 3 SAC

Collaborative Interactive Visualization Exploratory Concept

DTIC Science & Technology

2015-06-01

the FIAC concepts. It consists of various DRDC-RDDC-2015-N004 intelligence analysis web services build of top of big data technologies exploited...sits on the UDS where validated common knowledge is stored. Based on the Lumify software2, this important component exploits big data technologies such...interfaces. Above this database resides the Big Data Manager responsible for transparent data transmission between the UDS and the rest of the S3

Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis.

PubMed

Journet, Etienne-Pascal; van Tuinen, Diederik; Gouzy, Jérome; Crespeau, Hervé; Carreau, Véronique; Farmer, Mary-Jo; Niebel, Andreas; Schiex, Thomas; Jaillon, Olivier; Chatagnier, Odile; Godiard, Laurence; Micheli, Fabienne; Kahn, Daniel; Gianinazzi-Pearson, Vivienne; Gamas, Pascal

2002-12-15

We report on a large-scale expressed sequence tag (EST) sequencing and analysis program aimed at characterizing the sets of genes expressed in roots of the model legume Medicago truncatula during interactions with either of two microsymbionts, the nitrogen-fixing bacterium Sinorhizobium meliloti or the arbuscular mycorrhizal fungus Glomus intraradices. We have designed specific tools for in silico analysis of EST data, in relation to chimeric cDNA detection, EST clustering, encoded protein prediction, and detection of differential expression. Our 21 473 5'- and 3'-ESTs could be grouped into 6359 EST clusters, corresponding to distinct virtual genes, along with 52 498 other M.truncatula ESTs available in the dbEST (NCBI) database that were recruited in the process. These clusters were manually annotated, using a specifically developed annotation interface. Analysis of EST cluster distribution in various M.truncatula cDNA libraries, supported by a refined R test to evaluate statistical significance and by 'electronic northern' representation, enabled us to identify a large number of novel genes predicted to be up- or down-regulated during either symbiotic root interaction. These in silico analyses provide a first global view of the genetic programs for root symbioses in M.truncatula. A searchable database has been built and can be accessed through a public interface.

An expert system shell for inferring vegetation characteristics: Changes to the historical cover type database (Task F)

NASA Technical Reports Server (NTRS)

1993-01-01

All the options in the NASA VEGetation Workbench (VEG) make use of a database of historical cover types. This database contains results from experiments by scientists on a wide variety of different cover types. The learning system uses the database to provide positive and negative training examples of classes that enable it to learn distinguishing features between classes of vegetation. All the other VEG options use the database to estimate the error bounds involved in the results obtained when various analysis techniques are applied to the sample of cover type data that is being studied. In the previous version of VEG, the historical cover type database was stored as part of the VEG knowledge base. This database was removed from the knowledge base. It is now stored as a series of flat files that are external to VEG. An interface between VEG and these files was provided. The interface allows the user to select which files of historical data to use. The files are then read, and the data are stored in Knowledge Engineering Environment (KEE) units using the same organization of units as in the previous version of VEG. The interface also allows the user to delete some or all of the historical database units from VEG and load new historical data from a file. This report summarizes the use of the historical cover type database in VEG. It then describes the new interface to the files containing the historical data. It describes minor changes that were made to VEG to enable the externally stored database to be used. Test runs to test the operation of the new interface and also to test the operation of VEG using historical data loaded from external files are described. Task F was completed. A Sun cartridge tape containing the KEE and Common Lisp code for the new interface and the modified version of the VEG knowledge base was delivered to the NASA GSFC technical representative.

iDrug: a web-accessible and interactive drug discovery and design platform

PubMed Central

2014-01-01

Background The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. As programs are developed by various research groups, a consistent user-friendly online graphical working environment, combining computational techniques such as pharmacophore mapping, similarity calculation, scoring, and target identification is needed. Results We presented a versatile, user-friendly, and efficient online tool for computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing. All the customized configurations of the functional modules can be accessed through featured session files provided, which can be saved to the local disk and uploaded to resume or update the history work. Conclusions iDrug is easy to use, and provides a novel, fast and reliable tool for conducting drug design experiments. By using iDrug, various molecular design processing tasks can be submitted and visualized simply in one browser without installing locally any standalone modeling softwares. iDrug is accessible free of charge at http://lilab.ecust.edu.cn/idrug. PMID:24955134

An online database for informing ecological network models: http://kelpforest.ucsc.edu.

PubMed

Beas-Luna, Rodrigo; Novak, Mark; Carr, Mark H; Tinker, Martin T; Black, August; Caselle, Jennifer E; Hoban, Michael; Malone, Dan; Iles, Alison

2014-01-01

Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/databaseui).

An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu

PubMed Central

Beas-Luna, Rodrigo; Novak, Mark; Carr, Mark H.; Tinker, Martin T.; Black, August; Caselle, Jennifer E.; Hoban, Michael; Malone, Dan; Iles, Alison

2014-01-01

Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/databaseui). PMID:25343723

An online database for informing ecological network models: http://kelpforest.ucsc.edu

USGS Publications Warehouse

Beas-Luna, Rodrigo; Tinker, M. Tim; Novak, Mark; Carr, Mark H.; Black, August; Caselle, Jennifer E.; Hoban, Michael; Malone, Dan; Iles, Alison C.

2014-01-01

Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/data​baseui).

The Protein-DNA Interface database

PubMed Central

2010-01-01

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. PMID:20482798

The Protein-DNA Interface database.

PubMed

Norambuena, Tomás; Melo, Francisco

2010-05-18

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 A or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface.We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.

Microcomputer Database Management Systems that Interface with Online Public Access Catalogs.

ERIC Educational Resources Information Center

Rice, James

1988-01-01

Describes a study that assessed the availability and use of microcomputer database management interfaces to online public access catalogs. The software capabilities needed to effect such an interface are identified, and available software packages are evaluated by these criteria. A directory of software vendors is provided. (4 notes with…

TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

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

Gu, Shengyin; Anderson, Iain; Kunin, Victor

2007-05-07

Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

A personal digital assistant application (MobilDent) for dental fieldwork data collection, information management and database handling.

PubMed

Forsell, M; Häggström, M; Johansson, O; Sjögren, P

2008-11-08

To develop a personal digital assistant (PDA) application for oral health assessment fieldwork, including back-office and database systems (MobilDent). System design, construction and implementation of PDA, back-office and database systems. System requirements for MobilDent were collected, analysed and translated into system functions. User interfaces were implemented and system architecture was outlined. MobilDent was based on a platform with. NET (Microsoft) components, using an SQL Server 2005 (Microsoft) for data storage with Windows Mobile (Microsoft) operating system. The PDA devices were Dell Axim. System functions and user interfaces were specified for MobilDent. User interfaces for PDA, back-office and database systems were based on. NET programming. The PDA user interface was based on Windows suitable to a PDA display, whereas the back-office interface was designed for a normal-sized computer screen. A synchronisation module (MS Active Sync, Microsoft) was used to enable download of field data from PDA to the database. MobilDent is a feasible application for oral health assessment fieldwork, and the oral health assessment database may prove a valuable source for care planning, educational and research purposes. Further development of the MobilDent system will include wireless connectivity with download-on-demand technology.

The development of a prototype intelligent user interface subsystem for NASA's scientific database systems

NASA Technical Reports Server (NTRS)

Campbell, William J.; Roelofs, Larry H.; Short, Nicholas M., Jr.

1987-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has as one of its components the development of an Intelligent User Interface (IUI).The intent of the latter is to develop a friendly and intelligent user interface service that is based on expert systems and natural language processing technologies. The purpose is to support the large number of potential scientific and engineering users presently having need of space and land related research and technical data but who have little or no experience in query languages or understanding of the information content or architecture of the databases involved. This technical memorandum presents prototype Intelligent User Interface Subsystem (IUIS) using the Crustal Dynamics Project Database as a test bed for the implementation of the CRUDDES (Crustal Dynamics Expert System). The knowledge base has more than 200 rules and represents a single application view and the architectural view. Operational performance using CRUDDES has allowed nondatabase users to obtain useful information from the database previously accessible only to an expert database user or the database designer.

ChemProt-2.0: visual navigation in a disease chemical biology database

PubMed Central

Kim Kjærulff, Sonny; Wich, Louis; Kringelum, Jens; Jacobsen, Ulrik P.; Kouskoumvekaki, Irene; Audouze, Karine; Lund, Ole; Brunak, Søren; Oprea, Tudor I.; Taboureau, Olivier

2013-01-01

ChemProt-2.0 (http://www.cbs.dtu.dk/services/ChemProt-2.0) is a public available compilation of multiple chemical–protein annotation resources integrated with diseases and clinical outcomes information. The database has been updated to >1.15 million compounds with 5.32 millions bioactivity measurements for 15 290 proteins. Each protein is linked to quality-scored human protein–protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO terms) through protein complexes. In ChemProt-2.0, therapeutic effects as well as adverse drug reactions have been integrated allowing for suggesting proteins associated to clinical outcomes. New chemical structure fingerprints were computed based on the similarity ensemble approach. Protein sequence similarity search was also integrated to evaluate the promiscuity of proteins, which can help in the prediction of off-target effects. Finally, the database was integrated into a visual interface that enables navigation of the pharmacological space for small molecules. Filtering options were included in order to facilitate and to guide dynamic search of specific queries. PMID:23185041

The Chandra Source Catalog: Storage and Interfaces

NASA Astrophysics Data System (ADS)

van Stone, David; Harbo, Peter N.; Tibbetts, Michael S.; Zografou, Panagoula; Evans, Ian N.; Primini, Francis A.; Glotfelty, Kenny J.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Hain, Roger; Hall, Diane M.; He, Xiang Qun (Helen); Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph B.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Plummer, David A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta L.; Sundheim, Beth A.; Winkelman, Sherry L.

2009-09-01

The Chandra Source Catalog (CSC) is part of the Chandra Data Archive (CDA) at the Chandra X-ray Center. The catalog contains source properties and associated data objects such as images, spectra, and lightcurves. The source properties are stored in relational databases and the data objects are stored in files with their metadata stored in databases. The CDA supports different versions of the catalog: multiple fixed release versions and a live database version. There are several interfaces to the catalog: CSCview, a graphical interface for building and submitting queries and for retrieving data objects; a command-line interface for property and source searches using ADQL; and VO-compliant services discoverable though the VO registry. This poster describes the structure of the catalog and provides an overview of the interfaces.

DiscoverySpace: an interactive data analysis application

PubMed Central

Robertson, Neil; Oveisi-Fordorei, Mehrdad; Zuyderduyn, Scott D; Varhol, Richard J; Fjell, Christopher; Marra, Marco; Jones, Steven; Siddiqui, Asim

2007-01-01

DiscoverySpace is a graphical application for bioinformatics data analysis. Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface. Datasets can be compared using a suite of novel tools to aid in the identification of significant patterns. DiscoverySpace is of broad utility and its particular strength is in the analysis of serial analysis of gene expression (SAGE) data. The application is freely available online. PMID:17210078

PCACE-Personal-Computer-Aided Cabling Engineering

NASA Technical Reports Server (NTRS)

Billitti, Joseph W.

1987-01-01

PCACE computer program developed to provide inexpensive, interactive system for learning and using engineering approach to interconnection systems. Basically database system that stores information as files of individual connectors and handles wiring information in circuit groups stored as records. Directly emulates typical manual engineering methods of handling data, thus making interface between user and program very natural. Apple version written in P-Code Pascal and IBM PC version of PCACE written in TURBO Pascal 3.0

[Construction and application of the tissue bank and database of oral mucosa precancerous lesions in the Yangtze delta].

PubMed

Huang, Ji-yan; Zhao, Hou-ming; Zhou, Hai-wen

2014-04-01

To construct a database and a tissue bank of oral mucosa precancerous lesions and to estimate the application values. Patients in the Yangtze delta suffering oral mucosa precancerous lesions were enrolled into this study. The patients' clinical data and samples of oral precancerous mucosa, salivary and blood were collected to create a tissue bank, based on which a database was constructed using Microsoft Access software, Brower/Server structure and ASP language. The tissue bank and database of oral mucosa precancerous lesions were successfully built. The procedure to harvest, store and transport the samples had been standardized. The database showed good interactive interface, convenient for data collection, query and share in the internet. We constructed the tissue bank and database of oral mucosa precancerous lesions for the first time, which not only help preserve the biological resource of oral mucosa precancerous lesions, but also provide enormous convenience in clinical work, researching and teaching. Supported by Research Fund of Science and Technology Committee of Shanghai Municipality (08ZR1416700).

SoyFN: a knowledge database of soybean functional networks.

PubMed

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

Discovery of multiple interacting partners of gankyrin, a proteasomal chaperone and an oncoprotein--evidence for a common hot spot site at the interface and its functional relevance.

PubMed

Nanaware, Padma P; Ramteke, Manoj P; Somavarapu, Arun K; Venkatraman, Prasanna

2014-07-01

Gankyrin, a non-ATPase component of the proteasome and a chaperone of proteasome assembly, is also an oncoprotein. Gankyrin regulates a variety of oncogenic signaling pathways in cancer cells and accelerates degradation of tumor suppressor proteins p53 and Rb. Therefore gankyrin may be a unique hub integrating signaling networks with the degradation pathway. To identify new interactions that may be crucial in consolidating its role as an oncogenic hub, crystal structure of gankyrin-proteasome ATPase complex was used to predict novel interacting partners. EEVD, a four amino acid linear sequence seems a hot spot site at this interface. By searching for EEVD in exposed regions of human proteins in PDB database, we predicted 34 novel interactions. Eight proteins were tested and seven of them were found to interact with gankyrin. Affinity of four interactions is high enough for endogenous detection. Others require gankyrin overexpression in HEK 293 cells or occur endogenously in breast cancer cell line- MDA-MB-435, reflecting lower affinity or presence of a deregulated network. Mutagenesis and peptide inhibition confirm that EEVD is the common hot spot site at these interfaces and therefore a potential polypharmacological drug target. In MDA-MB-231 cells in which the endogenous CLIC1 is silenced, trans-expression of Wt protein (CLIC1_EEVD) and not the hot spot site mutant (CLIC1_AAVA) resulted in significant rescue of the migratory potential. Our approach can be extended to identify novel functionally relevant protein-protein interactions, in expansion of oncogenic networks and in identifying potential therapeutic targets. © 2013 Wiley Periodicals, Inc.

MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action.

PubMed

Nelson, Justin; Simpkins, Scott W; Safizadeh, Hamid; Li, Sheena C; Piotrowski, Jeff S; Hirano, Hiroyuki; Yashiroda, Yoko; Osada, Hiroyuki; Yoshida, Minoru; Boone, Charles; Myers, Chad L

2018-04-01

Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13 000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs. To facilitate future analysis of these valuable data, we developed a public database and web interface named MOSAIC. The website provides a convenient interface for querying compounds, bioprocesses (Gene Ontology terms) and genes for CG information including direct CG interactions, bioprocesses and gene-level target predictions. MOSAIC also provides access to chemical structure information of screened molecules, chemical-genomic profiles and the ability to search for compounds sharing structural and functional similarity. This resource will be of interest to chemical biologists for discovering new small molecule probes with specific modes-of-action as well as computational biologists interested in analysing CG interaction networks. MOSAIC is available at http://mosaic.cs.umn.edu. hisyo@riken.jp, yoshidam@riken.jp, charlie.boone@utoronto.ca or chadm@umn.edu. Supplementary data are available at Bioinformatics online.

The LatHyS database for planetary plasma environment investigations: Overview and a case study of data/model comparisons

NASA Astrophysics Data System (ADS)

Modolo, R.; Hess, S.; Génot, V.; Leclercq, L.; Leblanc, F.; Chaufray, J.-Y.; Weill, P.; Gangloff, M.; Fedorov, A.; Budnik, E.; Bouchemit, M.; Steckiewicz, M.; André, N.; Beigbeder, L.; Popescu, D.; Toniutti, J.-P.; Al-Ubaidi, T.; Khodachenko, M.; Brain, D.; Curry, S.; Jakosky, B.; Holmström, M.

2018-01-01

We present the Latmos Hybrid Simulation (LatHyS) database, which is dedicated to the investigations of planetary plasma environment. Simulation results of several planetary objects (Mars, Mercury, Ganymede) are available in an online catalogue. The full description of the simulations and their results is compliant with a data model developped in the framework of the FP7 IMPEx project. The catalogue is interfaced with VO-visualization tools such AMDA, 3DView, TOPCAT, CLweb or the IMPEx portal. Web services ensure the possibilities of accessing and extracting simulated quantities/data. We illustrate the interoperability between the simulation database and VO-tools using a detailed science case that focuses on a three-dimensional representation of the solar wind interaction with the Martian upper atmosphere, combining MAVEN and Mars Express observations and simulation results.

5SRNAdb: an information resource for 5S ribosomal RNAs.

PubMed

Szymanski, Maciej; Zielezinski, Andrzej; Barciszewski, Jan; Erdmann, Volker A; Karlowski, Wojciech M

2016-01-04

Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Common Database Interface for Heterogeneous Software Engineering Tools.

DTIC Science & Technology

1987-12-01

SUB-GROUP Database Management Systems ;Programming(Comuters); 1e 05 Computer Files;Information Transfer;Interfaces; 19. ABSTRACT (Continue on reverse...Air Force Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Information Systems ...Literature ..... 8 System 690 Configuration ......... 8 Database Functionis ............ 14 Software Engineering Environments ... 14 Data Manager

Argo: an integrative, interactive, text mining-based workbench supporting curation

PubMed Central

Rak, Rafal; Rowley, Andrew; Black, William; Ananiadou, Sophia

2012-01-01

Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in-built manual annotation editor that is well suited for in-text corpus annotation tasks. Database URL: http://www.nactem.ac.uk/Argo PMID:22434844

Version 1.00 programmer`s tools used in constructing the INEL RML/analytical radiochemistry sample tracking database and its user interface

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

Femec, D.A.

This report describes two code-generating tools used to speed design and implementation of relational databases and user interfaces: CREATE-SCHEMA and BUILD-SCREEN. CREATE-SCHEMA produces the SQL commands that actually create and define the database. BUILD-SCREEN takes templates for data entry screens and generates the screen management system routine calls to display the desired screen. Both tools also generate the related FORTRAN declaration statements and precompiled SQL calls. Included with this report is the source code for a number of FORTRAN routines and functions used by the user interface. This code is broadly applicable to a number of different databases.

The online Tabloid Proteome: an annotated database of protein associations

PubMed Central

Turan, Demet; Tavernier, Jan

2018-01-01

Abstract A complete knowledge of the proteome can only be attained by determining the associations between proteins, along with the nature of these associations (e.g. physical contact in protein–protein interactions, participation in complex formation or different roles in the same pathway). Despite extensive efforts in elucidating direct protein interactions, our knowledge on the complete spectrum of protein associations remains limited. We therefore developed a new approach that detects protein associations from identifications obtained after re-processing of large-scale, public mass spectrometry-based proteomics data. Our approach infers protein association based on the co-occurrence of proteins across many different proteomics experiments, and provides information that is almost completely complementary to traditional direct protein interaction studies. We here present a web interface to query and explore the associations derived from this method, called the online Tabloid Proteome. The online Tabloid Proteome also integrates biological knowledge from several existing resources to annotate our derived protein associations. The online Tabloid Proteome is freely available through a user-friendly web interface, which provides intuitive navigation and data exploration options for the user at http://iomics.ugent.be/tabloidproteome. PMID:29040688

Analysis and modeling of heat-labile enterotoxins of Escherichia coli suggests a novel space with insights into receptor preference.

PubMed

Krishna Raja, M; Ghosh, Asit Ranjan; Vino, S; Sajitha Lulu, S

2015-01-01

Features of heat-labile enterotoxins of Escherichia coli which make them fit to use as novel receptors for antidiarrheals are not completely explored. Data-set of 14 different serovars of enterotoxigenic Escherichia coli producing heat-labile toxins were taken from NCBI Genbank database and used in the study. Sequence analysis showed mutations in different subunits and also at their interface residues. As these toxins lack crystallography structures, homology modeling using Modeller 9.11 led to the structural approximation for the E. coli producing heat-labile toxins. Interaction of modeled toxin subunits with proanthocyanidin, an antidiarrheal showed several strong hydrogen bonding interactions at the cost of minimized energy. The hits were subsequently characterized by molecular dynamics simulation studies to monitor their binding stabilities. This study looks into novel space where the ligand can choose the receptor preference not as a whole but as an individual subunit. Mutation at interface residues and interaction among subunits along with the binding of ligand to individual subunits would help to design a non-toxic labile toxin and also to improve the therapeutics.

Atlas - a data warehouse for integrative bioinformatics.

PubMed

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

2005-02-21

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Atlas – a data warehouse for integrative bioinformatics

PubMed Central

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

2005-01-01

Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

WOVOdat, A Worldwide Volcano Unrest Database, to Improve Eruption Forecasts

NASA Astrophysics Data System (ADS)

Widiwijayanti, C.; Costa, F.; Win, N. T. Z.; Tan, K.; Newhall, C. G.; Ratdomopurbo, A.

2015-12-01

WOVOdat is the World Organization of Volcano Observatories' Database of Volcanic Unrest. An international effort to develop common standards for compiling and storing data on volcanic unrests in a centralized database and freely web-accessible for reference during volcanic crises, comparative studies, and basic research on pre-eruption processes. WOVOdat will be to volcanology as an epidemiological database is to medicine. Despite the large spectrum of monitoring techniques, the interpretation of monitoring data throughout the evolution of the unrest and making timely forecasts remain the most challenging tasks for volcanologists. The field of eruption forecasting is becoming more quantitative, based on the understanding of the pre-eruptive magmatic processes and dynamic interaction between variables that are at play in a volcanic system. Such forecasts must also acknowledge and express the uncertainties, therefore most of current research in this field focused on the application of event tree analysis to reflect multiple possible scenarios and the probability of each scenario. Such forecasts are critically dependent on comprehensive and authoritative global volcano unrest data sets - the very information currently collected in WOVOdat. As the database becomes more complete, Boolean searches, side-by-side digital and thus scalable comparisons of unrest, pattern recognition, will generate reliable results. Statistical distribution obtained from WOVOdat can be then used to estimate the probabilities of each scenario after specific patterns of unrest. We established main web interface for data submission and visualizations, and have now incorporated ~20% of worldwide unrest data into the database, covering more than 100 eruptive episodes. In the upcoming years we will concentrate in acquiring data from volcano observatories develop a robust data query interface, optimizing data mining, and creating tools by which WOVOdat can be used for probabilistic eruption forecasting. The more data in WOVOdat, the more useful it will be.

A natural language interface plug-in for cooperative query answering in biological databases.

PubMed

Jamil, Hasan M

2012-06-11

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed using sophisticated tools. In such highly interpretive environments, rigidly structured databases do not always perform well. In this paper, our goal is to propose a semantic correspondence plug-in to aid natural language query processing over arbitrary biological database schema with an aim to providing cooperative responses to queries tailored to users' interpretations. Natural language interfaces for databases are generally effective when they are tuned to the underlying database schema and its semantics. Therefore, changes in database schema become impossible to support, or a substantial reorganization cost must be absorbed to reflect any change. We leverage developments in natural language parsing, rule languages and ontologies, and data integration technologies to assemble a prototype query processor that is able to transform a natural language query into a semantically equivalent structured query over the database. We allow knowledge rules and their frequent modifications as part of the underlying database schema. The approach we adopt in our plug-in overcomes some of the serious limitations of many contemporary natural language interfaces, including support for schema modifications and independence from underlying database schema. The plug-in introduced in this paper is generic and facilitates connecting user selected natural language interfaces to arbitrary databases using a semantic description of the intended application. We demonstrate the feasibility of our approach with a practical example.

CodeSlinger: a case study in domain-driven interactive tool design for biomedical coding scheme exploration and use.

PubMed

Flowers, Natalie L

2010-01-01

CodeSlinger is a desktop application that was developed to aid medical professionals in the intertranslation, exploration, and use of biomedical coding schemes. The application was designed to provide a highly intuitive, easy-to-use interface that simplifies a complex business problem: a set of time-consuming, laborious tasks that were regularly performed by a group of medical professionals involving manually searching coding books, searching the Internet, and checking documentation references. A workplace observation session with a target user revealed the details of the current process and a clear understanding of the business goals of the target user group. These goals drove the design of the application's interface, which centers on searches for medical conditions and displays the codes found in the application's database that represent those conditions. The interface also allows the exploration of complex conceptual relationships across multiple coding schemes.

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs.

PubMed

Disney, Matthew D; Winkelsas, Audrey M; Velagapudi, Sai Pradeep; Southern, Mark; Fallahi, Mohammad; Childs-Disney, Jessica L

2016-06-17

The development of small molecules that target RNA is challenging yet, if successful, could advance the development of chemical probes to study RNA function or precision therapeutics to treat RNA-mediated disease. Previously, we described Inforna, an approach that can mine motifs (secondary structures) within target RNAs, which is deduced from the RNA sequence, and compare them to a database of known RNA motif-small molecule binding partners. Output generated by Inforna includes the motif found in both the database and the desired RNA target, lead small molecules for that target, and other related meta-data. Lead small molecules can then be tested for binding and affecting cellular (dys)function. Herein, we describe Inforna 2.0, which incorporates all known RNA motif-small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. By incorporation of interactions identified by other laboratories, the database has been doubled, containing 1936 RNA motif-small molecule interactions, including 244 unique small molecules and 1331 motifs. Interestingly, chemotype analysis of the compounds that bind RNA in the database reveals features in small molecule chemotypes that are privileged for binding. Further, this updated database expanded the number of cellular RNAs to which lead compounds can be identified.

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

User`s and reference guide to the INEL RML/analytical radiochemistry sample tracking database version 1.00

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

Femec, D.A.

This report discusses the sample tracking database in use at the Idaho National Engineering Laboratory (INEL) by the Radiation Measurements Laboratory (RML) and Analytical Radiochemistry. The database was designed in-house to meet the specific needs of the RML and Analytical Radiochemistry. The report consists of two parts, a user`s guide and a reference guide. The user`s guide presents some of the fundamentals needed by anyone who will be using the database via its user interface. The reference guide describes the design of both the database and the user interface. Briefly mentioned in the reference guide are the code-generating tools, CREATE-SCHEMAmore » and BUILD-SCREEN, written to automatically generate code for the database and its user interface. The appendices contain the input files used by the these tools to create code for the sample tracking database. The output files generated by these tools are also included in the appendices.« less

PGSB PlantsDB: updates to the database framework for comparative plant genome research.

PubMed

Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai C; Martis, Mihaela M; Seidel, Michael; Kugler, Karl G; Gundlach, Heidrun; Mayer, Klaus F X

2016-01-04

PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/). © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

New design and facilities for the International Database for Absolute Gravity Measurements (AGrav): A support for the Establishment of a new Global Absolute Gravity Reference System

NASA Astrophysics Data System (ADS)

Wziontek, Hartmut; Falk, Reinhard; Bonvalot, Sylvain; Rülke, Axel

2017-04-01

After about 10 years of successful joint operation by BGI and BKG, the International Database for Absolute Gravity Measurements "AGrav" (see references hereafter) was under a major revision. The outdated web interface was replaced by a responsive, high level web application framework based on Python and built on top of Pyramid. Functionality was added, like interactive time series plots or a report generator and the interactive map-based station overview was updated completely, comprising now clustering and the classification of stations. Furthermore, the database backend was migrated to PostgreSQL for better support of the application framework and long-term availability. As comparisons of absolute gravimeters (AG) become essential to realize a precise and uniform gravity standard, the database was extended to document the results on international and regional level, including those performed at monitoring stations equipped with SGs. By this it will be possible to link different AGs and to trace their equivalence back to the key comparisons under the auspices of International Committee for Weights and Measures (CIPM) as the best metrological realization of the absolute gravity standard. In this way the new AGrav database accommodates the demands of the new Global Absolute Gravity Reference System as recommended by the IAG Resolution No. 2 adopted in Prague 2015. The new database will be presented with focus on the new user interface and new functionality, calling all institutions involved in absolute gravimetry to participate and contribute with their information to built up a most complete picture of high precision absolute gravimetry and improve its visibility. A Digital Object Identifier (DOI) will be provided by BGI to contributors to give a better traceability and facilitate the referencing of their gravity surveys. Links and references: BGI mirror site : http://bgi.obs-mip.fr/data-products/Gravity-Databases/Absolute-Gravity-data/ BKG mirror site: http://agrav.bkg.bund.de/agrav-meta/ Wilmes, H., H. Wziontek, R. Falk, S. Bonvalot (2009). AGrav - the New Absolute Gravity Database and a Proposed Cooperation with the GGP Project. J. of Geodynamics, 48, pp. 305-309. doi:10.1016/j.jog.2009.09.035. Wziontek, H., H. Wilmes, S. Bonvalot (2011). AGrav: An international database for absolute gravity measurements. In Geodesy for Planet Earth (S. Kenyon at al. eds). IAG Symposia, 136, 1035-1040, Springer, Berlin. 2011. doi:10.1007/978-3-642-20338-1_130.

The development of an intelligent user interface for NASA's scientific databases

NASA Technical Reports Server (NTRS)

Campbell, William J.; Roelofs, Larry H.

1986-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has as one of its components, the development of an Intelligent User Interface (IUI). The intent of the IUI effort is to develop a friendly and intelligent user interface service that is based on expert systems and natural language processing technologies. This paper presents the design concepts, development approach and evaluation of performance of a prototype Intelligent User Interface Subsystem (IUIS) supporting an operational database.

FDDI information management system for centralizing interactive, computerized multimedia clinical experiences in pediatric rheumatology/Immunology.

PubMed

Rouhani, R; Cronenberger, H; Stein, L; Hannum, W; Reed, A M; Wilhelm, C; Hsiao, H

1995-01-01

This paper describes the design, authoring, and development of interactive, computerized, multimedia clinical simulations in pediatric rheumatology/immunology and related musculoskeletal diseases, the development and implementation of a high speed information management system for their centralized storage and distribution, and analytical methods for evaluating the total system's educational impact on medical students and pediatric residents. An FDDI fiber optic network with client/server/host architecture is the core. The server houses digitized audio, still-image video clips and text files. A host station houses the DB2/2 database containing case-associated labels and information. Cases can be accessed from any workstation via a customized interface in AVA/2 written specifically for this application. OS/2 Presentation Manager controls, written in C, are incorporated into the interface. This interface allows SQL searches and retrievals of cases and case materials. In addition to providing user-directed clinical experiences, this centralized information management system provides designated faculty with the ability to add audio notes and visual pointers to image files. Users may browse through case materials, mark selected ones and download them for utilization in lectures or for editing and converting into 35mm slides.

HAEdb: a novel interactive, locus-specific mutation database for the C1 inhibitor gene.

PubMed

Kalmár, Lajos; Hegedüs, Tamás; Farkas, Henriette; Nagy, Melinda; Tordai, Attila

2005-01-01

Hereditary angioneurotic edema (HAE) is an autosomal dominant disorder characterized by episodic local subcutaneous and submucosal edema and is caused by the deficiency of the activated C1 esterase inhibitor protein (C1-INH or C1INH; approved gene symbol SERPING1). Published C1-INH mutations are represented in large universal databases (e.g., OMIM, HGMD), but these databases update their data rather infrequently, they are not interactive, and they do not allow searches according to different criteria. The HAEdb, a C1-INH gene mutation database (http://hae.biomembrane.hu) was created to contribute to the following expectations: 1) help the comprehensive collection of information on genetic alterations of the C1-INH gene; 2) create a database in which data can be searched and compared according to several flexible criteria; and 3) provide additional help in new mutation identification. The website uses MySQL, an open-source, multithreaded, relational database management system. The user-friendly graphical interface was written in the PHP web programming language. The website consists of two main parts, the freely browsable search function, and the password-protected data deposition function. Mutations of the C1-INH gene are divided in two parts: gross mutations involving DNA fragments >1 kb, and micro mutations encompassing all non-gross mutations. Several attributes (e.g., affected exon, molecular consequence, family history) are collected for each mutation in a standardized form. This database may facilitate future comprehensive analyses of C1-INH mutations and also provide regular help for molecular diagnostic testing of HAE patients in different centers.

SuperTarget goes quantitative: update on drug–target interactions

PubMed Central

Hecker, Nikolai; Ahmed, Jessica; von Eichborn, Joachim; Dunkel, Mathias; Macha, Karel; Eckert, Andreas; Gilson, Michael K.; Bourne, Philip E.; Preissner, Robert

2012-01-01

There are at least two good reasons for the on-going interest in drug–target interactions: first, drug-effects can only be fully understood by considering a complex network of interactions to multiple targets (so-called off-target effects) including metabolic and signaling pathways; second, it is crucial to consider drug-target-pathway relations for the identification of novel targets for drug development. To address this on-going need, we have developed a web-based data warehouse named SuperTarget, which integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present, the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. SuperTarget is available at http://bioinformatics.charite.de/supertarget. PMID:22067455

Plasma Interactions With Spacecraft (I)

DTIC Science & Technology

2009-04-01

with the Windows, Red hat LINUX, and MacOS X environments. We wrote N2kScriptRunner, a C++ code that runs a Nascap-2k script outside of the Java ...console-based and with a Java interface), a stand alone program that reads and writes Nascap-2k database files. This program has proved invaluable...surface currents for DSX and prototyped it in Java . A description of the algorithm and the prototype implementation is in Section 3. 1.5. DSX

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

Grote, D. P.

Forthon generates links between Fortran and Python. Python is a high level, object oriented, interactive and scripting language that allows a flexible and versatile interface to computational tools. The Forthon package generates the necessary wrapping code which allows access to the Fortran database and to the Fortran subroutines and functions. This provides a development package where the computationally intensive parts of a code can be written in efficient Fortran, and the high level controlling code can be written in the much more versatile Python language.

Student Research Projects

NASA Technical Reports Server (NTRS)

Yeske, Lanny A.

1998-01-01

Numerous FY1998 student research projects were sponsored by the Mississippi State University Center for Air Sea Technology. This technical note describes these projects which include research on: (1) Graphical User Interfaces, (2) Master Environmental Library, (3) Database Management Systems, (4) Naval Interactive Data Analysis System, (5) Relocatable Modeling Environment, (6) Tidal Models, (7) Book Inventories, (8) System Analysis, (9) World Wide Web Development, (10) Virtual Data Warehouse, (11) Enterprise Information Explorer, (12) Equipment Inventories, (13) COADS, and (14) JavaScript Technology.

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

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.

Legal assessment tool (LAT): an interactive tool to address privacy and data protection issues for data sharing.

PubMed

Kuchinke, Wolfgang; Krauth, Christian; Bergmann, René; Karakoyun, Töresin; Woollard, Astrid; Schluender, Irene; Braasch, Benjamin; Eckert, Martin; Ohmann, Christian

2016-07-07

In an unprecedented rate data in the life sciences is generated and stored in many different databases. An ever increasing part of this data is human health data and therefore falls under data protected by legal regulations. As part of the BioMedBridges project, which created infrastructures that connect more than 10 ESFRI research infrastructures (RI), the legal and ethical prerequisites of data sharing were examined employing a novel and pragmatic approach. We employed concepts from computer science to create legal requirement clusters that enable legal interoperability between databases for the areas of data protection, data security, Intellectual Property (IP) and security of biosample data. We analysed and extracted access rules and constraints from all data providers (databases) involved in the building of data bridges covering many of Europe's most important databases. These requirement clusters were applied to five usage scenarios representing the data flow in different data bridges: Image bridge, Phenotype data bridge, Personalised medicine data bridge, Structural data bridge, and Biosample data bridge. A matrix was built to relate the important concepts from data protection regulations (e.g. pseudonymisation, identifyability, access control, consent management) with the results of the requirement clusters. An interactive user interface for querying the matrix for requirements necessary for compliant data sharing was created. To guide researchers without the need for legal expert knowledge through legal requirements, an interactive tool, the Legal Assessment Tool (LAT), was developed. LAT provides researchers interactively with a selection process to characterise the involved types of data and databases and provides suitable requirements and recommendations for concrete data access and sharing situations. The results provided by LAT are based on an analysis of the data access and sharing conditions for different kinds of data of major databases in Europe. Data sharing for research purposes must be opened for human health data and LAT is one of the means to achieve this aim. In summary, LAT provides requirements in an interactive way for compliant data access and sharing with appropriate safeguards, restrictions and responsibilities by introducing a culture of responsibility and data governance when dealing with human data.

Comprehensive Reconstruction and Visualization of Non-Coding Regulatory Networks in Human

PubMed Central

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape. PMID:25540777

Comprehensive reconstruction and visualization of non-coding regulatory networks in human.

PubMed

Bonnici, Vincenzo; Russo, Francesco; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba

2014-01-01

Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By accessing only one resource, users can search for ncRNAs and their interactions, build a network annotated with all known ncRNAs and associated diseases, and use all visual and mining features available in Cytoscape.

The Degradome database: expanding roles of mammalian proteases in life and disease

PubMed Central

Pérez-Silva, José G.; Español, Yaiza; Velasco, Gloria; Quesada, Víctor

2016-01-01

Since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology and pathology. Once the genomic sequences of several important model organisms were made available, we presented the Degradome database containing the curated sets of known protease genes in human, chimpanzee, mouse and rat. Here, we describe the updated Degradome database, featuring 81 new protease genes and 7 new protease families. Notably, in this short time span, the number of known hereditary diseases caused by mutations in protease genes has increased from 77 to 119. This increase reflects the growing interest on the roles of the degradome in multiple diseases, including cancer and ageing. Finally, we have leveraged the widespread adoption of new webtools to provide interactive graphic views that show information about proteases in the global context of the degradome. The Degradome database can be accessed through its web interface at http://degradome.uniovi.es. PMID:26553809

SeqDepot: streamlined database of biological sequences and precomputed features.

PubMed

Ulrich, Luke E; Zhulin, Igor B

2014-01-15

Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot-a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to >28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines. Freely available on the web at http://seqdepot.net/. RESTaccess via http://seqdepot.net/api/v1. Database files and scripts maybe downloaded from http://seqdepot.net/download.

Evolution of the NASA/IPAC Extragalactic Database (NED) into a Data Mining Discovery Engine

NASA Astrophysics Data System (ADS)

Mazzarella, Joseph M.; NED Team

2017-06-01

We review recent advances and ongoing work in evolving the NASA/IPAC Extragalactic Database (NED) beyond an object reference database into a data mining discovery engine. Updates to the infrastructure and data integration techniques are enabling more than a 10-fold expansion; NED will soon contain over a billion objects with their fundamental attributes fused across the spectrum via cross-identifications among the largest sky surveys (e.g., GALEX, SDSS, 2MASS, AllWISE, EMU), and over 100,000 smaller but scientifically important catalogs and journal articles. The recent discovery of super-luminous spiral galaxies exemplifies the opportunities for data mining and science discovery directly from NED's rich data synthesis. Enhancements to the user interface, including new APIs, VO protocols, and queries involving derived physical quantities, are opening new pathways for panchromatic studies of large galaxy samples. Examples are shown of graphics characterizing the content of NED, as well as initial steps in exploring the database via interactive statistical visualizations.

Open Geoscience Database

NASA Astrophysics Data System (ADS)

Bashev, A.

2012-04-01

Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data treatment could be conducted in other programs after extraction the filtered data into *.csv file. It makes the database understandable for non-experts. The database employs open data format (*.csv) and wide spread tools: PHP as the program language, MySQL as database management system, JavaScript for interaction with GoogleMaps and JQueryUI for create user interface. The database is multilingual: there are association tables, which connect with elements of the database. In total the development required about 150 hours. The database still has several problems. The main problem is the reliability of the data. Actually it needs an expert system for estimation the reliability, but the elaboration of such a system would take more resources than the database itself. The second problem is the problem of stream selection - how to select the stations that are connected with each other (for example, belong to one water stream) and indicate their sequence. Currently the interface is English and Russian. However it can be easily translated to your language. But some problems we decided. For example problem "the problem of the same station" (sometimes the distance between stations is smaller, than the error of position): when you adding new station to the database our application automatically find station near this place. Also we decided problem of object and parameter type (how to regard "EC" and "electrical conductivity" as the same parameter). This problem has been solved using "associative tables". If you would like to see the interface on your language, just contact us. We should send you the list of terms and phrases for translation on your language. The main advantage of the database is that it is totally open: everybody can see, extract the data from the database and use them for non-commercial purposes with no charge. Registered users can contribute to the database without getting paid. We hope, that it will be widely used first of all for education purposes, but professional scientists could use it also.

Digital hand atlas for web-based bone age assessment: system design and implementation

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

2000-04-01

A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.

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.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

NASA Astrophysics Data System (ADS)

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/˜knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

PubMed Central

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407

PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

PubMed Central

2011-01-01

Background Renewed interest in plant × environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community. Description PHENOPSIS DB is a publicly available (URL: http://bioweb.supagro.inra.fr/phenopsis/) information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i) the visualisation of environmental data of an experiment, (ii) the visualisation and statistical analysis of phenotypic data, and (iii) the analysis of Arabidopsis thaliana plant images. Conclusions Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development of other similar databases related to genotype × environment interactions. PMID:21554668

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

mESAdb: microRNA Expression and Sequence Analysis Database

PubMed Central

Kaya, Koray D.; Karakülah, Gökhan; Yakıcıer, Cengiz M.; Acar, Aybar C.; Konu, Özlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data. PMID:21177657

mESAdb: microRNA expression and sequence analysis database.

PubMed

Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

Integrating a local database into the StarView distributed user interface

NASA Technical Reports Server (NTRS)

Silberberg, D. P.

1992-01-01

A distributed user interface to the Space Telescope Data Archive and Distribution Service (DADS) known as StarView is being developed. The DADS architecture consists of the data archive as well as a relational database catalog describing the archive. StarView is a client/server system in which the user interface is the front-end client to the DADS catalog and archive servers. Users query the DADS catalog from the StarView interface. Query commands are transmitted via a network and evaluated by the database. The results are returned via the network and are displayed on StarView forms. Based on the results, users decide which data sets to retrieve from the DADS archive. Archive requests are packaged by StarView and sent to DADS, which returns the requested data sets to the users. The advantages of distributed client/server user interfaces over traditional one-machine systems are well known. Since users run software on machines separate from the database, the overall client response time is much faster. Also, since the server is free to process only database requests, the database response time is much faster. Disadvantages inherent in this architecture are slow overall database access time due to the network delays, lack of a 'get previous row' command, and that refinements of a previously issued query must be submitted to the database server, even though the domain of values have already been returned by the previous query. This architecture also does not allow users to cross correlate DADS catalog data with other catalogs. Clearly, a distributed user interface would be more powerful if it overcame these disadvantages. A local database is being integrated into StarView to overcome these disadvantages. When a query is made through a StarView form, which is often composed of fields from multiple tables, it is translated to an SQL query and issued to the DADS catalog. At the same time, a local database table is created to contain the resulting rows of the query. The returned rows are displayed on the form as well as inserted into the local database table. Identical results are produced by reissuing the query to either the DADS catalog or to the local table. Relational databases do not provide a 'get previous row' function because of the inherent complexity of retrieving previous rows of multiple-table joins. However, since this function is easily implemented on a single table, StarView uses the local table to retrieve the previous row. Also, StarView issues subsequent query refinements to the local table instead of the DADS catalog, eliminating the network transmission overhead. Finally, other catalogs can be imported into the local database for cross correlation with local tables. Overall, it is believe that this is a more powerful architecture for distributed, database user interfaces.

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems.

PubMed

Memišević, Vesna; Kumar, Kamal; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

2016-09-20

Burkholderia mallei and B. pseudomallei are the causative agents of glanders and melioidosis, respectively, diseases with high morbidity and mortality rates. B. mallei and B. pseudomallei are closely related genetically; B. mallei evolved from an ancestral strain of B. pseudomallei by genome reduction and adaptation to an obligate intracellular lifestyle. Although these two bacteria cause different diseases, they share multiple virulence factors, including bacterial secretion systems, which represent key components of bacterial pathogenicity. Despite recent progress, the secretion system proteins for B. mallei and B. pseudomallei, their pathogenic mechanisms of action, and host factors are not well characterized. We previously developed a manually curated database, DBSecSys, of bacterial secretion system proteins for B. mallei. Here, we report an expansion of the database with corresponding information about B. pseudomallei. DBSecSys 2.0 contains comprehensive literature-based and computationally derived information about B. mallei ATCC 23344 and literature-based and computationally derived information about B. pseudomallei K96243. The database contains updated information for 163 B. mallei proteins from the previous database and 61 additional B. mallei proteins, and new information for 281 B. pseudomallei proteins associated with 5 secretion systems, their 1,633 human- and murine-interacting targets, and 2,400 host-B. mallei interactions and 2,286 host-B. pseudomallei interactions. The database also includes information about 13 pathogenic mechanisms of action for B. mallei and B. pseudomallei secretion system proteins inferred from the available literature or computationally. Additionally, DBSecSys 2.0 provides details about 82 virulence attenuation experiments for 52 B. mallei secretion system proteins and 98 virulence attenuation experiments for 61 B. pseudomallei secretion system proteins. We updated the Web interface and data access layer to speed-up users' search of detailed information for orthologous proteins related to secretion systems of the two pathogens. The updates of DBSecSys 2.0 provide unique capabilities to access comprehensive information about secretion systems of B. mallei and B. pseudomallei. They enable studies and comparisons of corresponding proteins of these two closely related pathogens and their host-interacting partners. The database is available at http://dbsecsys.bhsai.org .

SCOWLP classification: Structural comparison and analysis of protein binding regions

PubMed Central

Teyra, Joan; Paszkowski-Rogacz, Maciej; Anders, Gerd; Pisabarro, M Teresa

2008-01-01

Background Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Description Protein binding regions (PBRs) might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed. We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions. The hierarchical classification of PBRs is implemented into the SCOWLP database and extends the SCOP classification with three additional family sub-levels: Binding Region, Interface and Contacting Domains. SCOWLP contains 9,334 binding regions distributed within 2,561 families. In 65% of the cases we observe families containing more than one binding region. Besides, 22% of the regions are forming complex with more than one different protein family. Conclusion The current SCOWLP classification and its web application represent a framework for the study of protein interfaces and comparative analysis of protein family binding regions. This comparison can be performed at atomic level and allows the user to study interactome conservation and variability. The new SCOWLP classification may be of great utility for reconstruction of protein complexes, understanding protein networks and ligand design. SCOWLP will be updated with every SCOP release. The web application is available at . PMID:18182098

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

Human/Computer Interfacing in Educational Environments.

ERIC Educational Resources Information Center

Sarti, Luigi

1992-01-01

This discussion of educational applications of user interfaces covers the benefits of adopting database techniques in organizing multimedia materials; the evolution of user interface technology, including teletype interfaces, analogic overlay graphics, window interfaces, and adaptive systems; application design problems, including the…

Database interfaces on NASA's heterogeneous distributed database system

NASA Technical Reports Server (NTRS)

Huang, Shou-Hsuan Stephen

1987-01-01

The purpose of Distributed Access View Integrated Database (DAVID) interface module (Module 9: Resident Primitive Processing Package) is to provide data transfer between local DAVID systems and resident Data Base Management Systems (DBMSs). The result of current research is summarized. A detailed description of the interface module is provided. Several Pascal templates were constructed. The Resident Processor program was also developed. Even though it is designed for the Pascal templates, it can be modified for templates in other languages, such as C, without much difficulty. The Resident Processor itself can be written in any programming language. Since Module 5 routines are not ready yet, there is no way to test the interface module. However, simulation shows that the data base access programs produced by the Resident Processor do work according to the specifications.

A new relational database structure and online interface for the HITRAN database

NASA Astrophysics Data System (ADS)

Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

2013-11-01

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Universal Index System

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

1993-01-01

The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

Hierarchical data security in a Query-By-Example interface for a shared database.

PubMed

Taylor, Merwyn

2002-06-01

Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security module that limits access to the data. The security module ensures that researchers working in one clinic do not get access to data from another clinic. The security can be based on a flexible taxonomy structure that allows ordinary users to access data from individual clinics and super users to access data from all clinics. All researchers submit queries through the same interface and the security module processes the taxonomy and user identifiers to limit access. Using this system, two different users with different access rights can submit the same query and get different results thus reducing the need to create different interfaces for different clinics and access rights.

HC Forum®: a web site based on an international human cytogenetic database

PubMed Central

Cohen, Olivier; Mermet, Marie-Ange; Demongeot, Jacques

2001-01-01

Familial structural rearrangements of chromosomes represent a factor of malformation risk that could vary over a large range, making genetic counseling difficult. However, they also represent a powerful tool for increasing knowledge of the genome, particularly by studying breakpoints and viable imbalances of the genome. We have developed a collaborative database that now includes data on more than 4100 families, from which we have developed a web site called HC Forum® (http://HCForum.imag.fr). It offers geneticists assistance in diagnosis and in genetic counseling by assessing the malformation risk with statistical models. For researchers, interactive interfaces exhibit the distribution of chromosomal breakpoints and of the genome regions observed at birth in trisomy or in monosomy. Dedicated tools including an interactive pedigree allow electronic submission of data, which will be anonymously shown in a forum for discussions. After validation, data are definitively registered in the database with the email of the sender, allowing direct location of biological material. Thus HC Forum® constitutes a link between diagnosis laboratories and genome research centers, and after 1 year, more than 700 users from about 40 different countries already exist. PMID:11125121

Analysis and Development of a Web-Enabled Planning and Scheduling Database Application

DTIC Science & Technology

2013-09-01

establishes an entity—relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web- enabled interface for...development, develop, design, process, re- engineering, reengineering, MySQL , structured query language, SQL, myPHPadmin. 15. NUMBER OF PAGES 107 16...relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web-enabled interface for the population of

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

PubMed

Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

2016-10-01

We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct aggregate data analysis that will inform the next generation of epilepsy self-management studies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

HITRANonline: a New Structure and Interface for HITRAN Line Lists and Cross Sections

NASA Astrophysics Data System (ADS)

Hill, Christian; Rothman, Laurence S.; Gordon, Iouli E.; Kochanov, Roman V.; Wcislo, Piotr; Wilzewski, Jonas

2015-06-01

We present HITRANonline, an online interface to the internationally-recognised HITRAN molecular spectroscopic database[1], and describe the structure of its relational database backend[2]. As the amount and complexity of spectroscopic data on molecules used in atmospheric modelling has increased, the existing 160-character, text-based format has become inadequate for its description. For example, line shapes such as the Hartmann-Tran profile[3] require up to six parameters for their full description (each with uncertainties and references), data is available on line-broadening by species other than ``air'' and ``self'' and more than the current maximum of 10 isotopologues of some molecules (for example, CO_2) can be important for accurate radiative-transfer modelling. The new relational database structure overcomes all of these limitations as well as allowing for better data provenance through ``timestamping'' of transitions and a direct link between items of data and their literature sources. To take full advantage of this new database structure, the online interface HITRANonline, available at www.hitran.org, provides a user-friendly way to make queries of HITRAN data with the option of returning it in a customizable format with user-defined fields and precisions. Binary formats such as HDF-5 are also supported. In addition to the data, each query also produces its own bibliography (in HTML and BibTeX formats), ``README'' documentation and interactive graph for easy visualization. L. S. Rothman et al., JSQRT 130, 4-50 (2013). C. Hill, I. E. Gordon, L. S. Rothman, J. Tennyson, JQSRT130, 51-61 (2013). N. H. Ngo, D. Lisak, H. Tran, J.-M. Hartmann, JQSRT 129, 89--100, (2013); erratum: JQSRT 134, 105 (2014). This work has been supported by NASA Aura Science Team Grant NNX14AI55G and NASA Planetary Atmospheres Grant NNX13AI59G.

DFACS - DATABASE, FORMS AND APPLICATIONS FOR CABLING AND SYSTEMS, VERSION 3.30

NASA Technical Reports Server (NTRS)

Billitti, J. W.

1994-01-01

DFACS is an interactive multi-user computer-aided engineering tool for system level electrical integration and cabling engineering. The purpose of the program is to provide the engineering community with a centralized database for entering and accessing system functional definitions, subsystem and instrument-end circuit pinout details, and harnessing data. The primary objective is to provide an instantaneous single point of information interchange, thus avoiding error-prone, time-consuming, and costly multiple-path data shuttling. The DFACS program, which is centered around a single database, has built-in menus that provide easy data input and access for all involved system, subsystem, and cabling personnel. The DFACS program allows parallel design of circuit data sheets and harness drawings. It also recombines raw information to automatically generate various project documents and drawings including the Circuit Data Sheet Index, the Electrical Interface Circuits List, Assembly and Equipment Lists, Electrical Ground Tree, Connector List, Cable Tree, Cabling Electrical Interface and Harness Drawings, Circuit Data Sheets, and ECR List of Affected Interfaces/Assemblies. Real time automatic production of harness drawings and circuit data sheets from the same data reservoir ensures instant system and cabling engineering design harmony. DFACS also contains automatic wire routing procedures and extensive error checking routines designed to minimize the possibility of engineering error. DFACS is designed to run on DEC VAX series computers under VMS using Version 6.3/01 of INGRES QUEL/OSL, a relational database system which is available through Relational Technology, Inc. The program is available in VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard media) or a TK50 tape cartridge. DFACS was developed in 1987 and last updated in 1990. DFACS is a copyrighted work with all copyright vested in NASA. DEC, VAX and VMS are trademarks of Digital Equipment Corporation. INGRES QUEL/OSL is a trademark of Relational Technology, Inc.

Co-PylotDB - A Python-Based Single-Window User Interface for Transmitting Information to a Database

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

Barnette, Daniel W.

2012-01-05

Co-PylotDB, written completely in Python, provides a user interface (UI) with which to select user and data file(s), directories, and file content, and provide or capture various other information for sending data collected from running any computer program to a pre-formatted database table for persistent storage. The interface allows the user to select input, output, make, source, executable, and qsub files. It also provides fields for specifying the machine name on which the software was run, capturing compile and execution lines, and listing relevant user comments. Data automatically captured by Co-PylotDB and sent to the database are user, current directory,more » local hostname, current date, and time of send. The UI provides fields for logging into a local or remote database server, specifying a database and a table, and sending the information to the selected database table. If a server is not available, the UI provides for saving the command that would have saved the information to a database table for either later submission or for sending via email to a collaborator who has access to the desired database.« less

The design and implementation of the immune epitope database and analysis resource

PubMed Central

Peters, Bjoern; Sidney, John; Bourne, Phil; Bui, Huynh-Hoa; Buus, Soeren; Doh, Grace; Fleri, Ward; Kronenberg, Mitch; Kubo, Ralph; Lund, Ole; Nemazee, David; Ponomarenko, Julia V.; Sathiamurthy, Muthu; Schoenberger, Stephen P.; Stewart, Scott; Surko, Pamela; Way, Scott; Wilson, Steve; Sette, Alessandro

2016-01-01

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, “The Immune Epitope Database and Analysis Resource.” We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide. PMID:15895191

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

PubMed Central

Castagnetto, Jesus M.; Hennessy, Sean W.; Roberts, Victoria A.; Getzoff, Elizabeth D.; Tainer, John A.; Pique, Michael E.

2002-01-01

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB. PMID:11752342

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.

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

ClearedLeavesDB: an online database of cleared plant leaf images

PubMed Central

2014-01-01

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

ClearedLeavesDB: an online database of cleared plant leaf images.

PubMed

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

2014-03-28

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

AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data

PubMed Central

Toseland, Christopher P; Clayton, Debra J; McSparron, Helen; Hemsley, Shelley L; Blythe, Martin J; Paine, Kelly; Doytchinova, Irini A; Guan, Pingping; Hattotuwagama, Channa K; Flower, Darren R

2005-01-01

AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology. Compared to its progenitor JenPep, the interface has been completely rewritten and redesigned and now offers a wider variety of search methods, including a nucleotide and a peptide BLAST search. In terms of data archived, AntiJen has a richer and more complete breadth, depth, and scope, and this has seen the database increase to over 31,000 entries. AntiJen provides the most complete and up-to-date dataset of its kind. While AntiJen v2.0 retains a focus on both T cell and B cell epitopes, its greatest novelty is the archiving of continuous quantitative data on a variety of immunological molecular interactions. This includes thermodynamic and kinetic measures of peptide binding to TAP and the Major Histocompatibility Complex (MHC), peptide-MHC complexes binding to T cell receptors, antibodies binding to protein antigens and general immunological protein-protein interactions. The database also contains quantitative specificity data from position-specific peptide libraries and biophysical data, in the form of diffusion co-efficients and cell surface copy numbers, on MHCs and other immunological molecules. The uses of AntiJen include the design of vaccines and diagnostics, such as tetramers, and other laboratory reagents, as well as helping parameterize the bioinformatic or mathematical in silico modeling of the immune system. The database is accessible from the URL: . PMID:16305757

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

Development of the geometry database for the CBM experiment

NASA Astrophysics Data System (ADS)

Akishina, E. P.; Alexandrov, E. I.; Alexandrov, I. N.; Filozova, I. A.; Friese, V.; Ivanov, V. V.

2018-01-01

The paper describes the current state of the Geometry Database (Geometry DB) for the CBM experiment. The main purpose of this database is to provide convenient tools for: (1) managing the geometry modules; (2) assembling various versions of the CBM setup as a combination of geometry modules and additional files. The CBM users of the Geometry DB may use both GUI (Graphical User Interface) and API (Application Programming Interface) tools for working with it.

A generalized strategy for building resident database interfaces

NASA Technical Reports Server (NTRS)

Moroh, Marsha; Wanderman, Ken

1990-01-01

A strategy for building resident interfaces to host heterogeneous distributed data base management systems is developed. The strategy is used to construct several interfaces. A set of guidelines is developed for users to construct their own interfaces.

YM500: a small RNA sequencing (smRNA-seq) database for microRNA research

PubMed Central

Cheng, Wei-Chung; Chung, I-Fang; Huang, Tse-Shun; Chang, Shih-Ting; Sun, Hsing-Jen; Tsai, Cheng-Fong; Liang, Muh-Lii; Wong, Tai-Tong; Wang, Hsei-Wei

2013-01-01

MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database, the YM500 (http://ngs.ym.edu.tw/ym500/), containing analysis pipelines and analysis results for 609 human and mice smRNA-seq results, including public data from the Gene Expression Omnibus (GEO) and some private sources. YM500 collects analysis results for miRNA quantification, for isomiR identification (incl. RNA editing), for arm switching discovery, and, more importantly, for novel miRNA predictions. Wetlab validation on >100 miRNAs confirmed high correlation between miRNA profiling and RT-qPCR results (R = 0.84). This database allows researchers to search these four different types of analysis results via our interactive web interface. YM500 allows researchers to define the criteria of isomiRs, and also integrates the information of dbSNP to help researchers distinguish isomiRs from SNPs. A user-friendly interface is provided to integrate miRNA-related information and existing evidence from hundreds of sequencing datasets. The identified novel miRNAs and isomiRs hold the potential for both basic research and biotech applications. PMID:23203880

A service-based framework for pharmacogenomics data integration

NASA Astrophysics Data System (ADS)

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

2010-08-01

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

IAIMS Architecture

PubMed Central

Hripcsak, George

1997-01-01

Abstract An information system architecture defines the components of a system and the interfaces among the components. A good architecture is essential for creating an Integrated Advanced Information Management System (IAIMS) that works as an integrated whole yet is flexible enough to accommodate many users and roles, multiple applications, changing vendors, evolving user needs, and advancing technology. Modularity and layering promote flexibility by reducing the complexity of a system and by restricting the ways in which components may interact. Enterprise-wide mediation promotes integration by providing message routing, support for standards, dictionary-based code translation, a centralized conceptual data schema, business rule implementation, and consistent access to databases. Several IAIMS sites have adopted a client-server architecture, and some have adopted a three-tiered approach, separating user interface functions, application logic, and repositories. PMID:9067884

Software Tools to Support Research on Airport Departure Planning

NASA Technical Reports Server (NTRS)

Carr, Francis; Evans, Antony; Feron, Eric; Clarke, John-Paul

2003-01-01

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

Planform: an application and database of graph-encoded planarian regenerative experiments.

PubMed

Lobo, Daniel; Malone, Taylor J; Levin, Michael

2013-04-15

Understanding the mechanisms governing the regeneration capabilities of many organisms is a fundamental interest in biology and medicine. An ever-increasing number of manipulation and molecular experiments are attempting to discover a comprehensive model for regeneration, with the planarian flatworm being one of the most important model species. Despite much effort, no comprehensive, constructive, mechanistic models exist yet, and it is now clear that computational tools are needed to mine this huge dataset. However, until now, there is no database of regenerative experiments, and the current genotype-phenotype ontologies and databases are based on textual descriptions, which are not understandable by computers. To overcome these difficulties, we present here Planform (Planarian formalization), a manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. The database contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset. The database and software tool are freely available at http://planform.daniel-lobo.com.

ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins

PubMed Central

Krassowski, Michal; Paczkowska, Marta; Cullion, Kim; Huang, Tina; Dzneladze, Irakli; Ouellette, B F Francis; Yamada, Joseph T; Fradet-Turcotte, Amelie

2018-01-01

Abstract Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs. We integrated >385,000 published PTM sites with ∼3.6 million substitutions from The Cancer Genome Atlas (TCGA), the ClinVar database of disease genes, and human genome sequencing projects. The database includes site-specific interaction networks of proteins, upstream enzymes such as kinases, and drugs targeting these enzymes. We also predicted network-rewiring impact of mutations by analyzing gains and losses of kinase-bound sequence motifs. ActiveDriverDB provides detailed visualization, filtering, browsing and searching options for studying PTM-associated mutations. Users can upload mutation datasets interactively and use our application programming interface in pipelines. Integrative analysis of mutations and PTMs may help decipher molecular mechanisms of phenotypes and disease, as exemplified by case studies of TP53, BRCA2 and VHL. The open-source database is available at https://www.ActiveDriverDB.org. PMID:29126202

Development of a real-time clinical decision support system upon the web mvc-based architecture for prostate cancer treatment

PubMed Central

2011-01-01

Background A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. Methods We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. Results The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Conclusions Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases. PMID:21385459

Development of a real-time clinical decision support system upon the Web MVC-based architecture for prostate cancer treatment.

PubMed

Lin, Hsueh-Chun; Wu, Hsi-Chin; Chang, Chih-Hung; Li, Tsai-Chung; Liang, Wen-Miin; Wang, Jong-Yi Wang

2011-03-08

A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases.

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model

PubMed Central

Xia, Kai; Dong, Dong; Han, Jing-Dong J

2006-01-01

Background Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking. Results By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs. Conclusion IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at . Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer. PMID:17112386

Hierarchthis: An Interactive Interface for Identifying Mission-Relevant Components of the Advanced Multi-Mission Operations System

NASA Technical Reports Server (NTRS)

Litomisky, Krystof

2012-01-01

Even though NASA's space missions are many and varied, there are some tasks that are common to all of them. For example, all spacecraft need to communicate with other entities, and all spacecraft need to know where they are. These tasks use tools and services that can be inherited and reused between missions, reducing systems engineering effort and therefore reducing cost.The Advanced Multi-Mission Operations System, or AMMOS, is a collection of multimission tools and services, whose development and maintenance are funded by NASA. I created HierarchThis, a plugin designed to provide an interactive interface to help customers identify mission-relevant tools and services. HierarchThis automatically creates diagrams of the AMMOS database, and then allows users to show/hide specific details through a graphical interface. Once customers identify tools and services they want for a specific mission, HierarchThis can automatically generate a contract between the Multimission Ground Systems and Services Office, which manages AMMOS, and the customer. The document contains the selected AMMOS components, along with their capabilities and satisfied requirements. HierarchThis reduces the time needed for the process from service selections to having a mission-specific contract from the order of days to the order of minutes.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

JASPAR RESTful API: accessing JASPAR data from any programming language.

PubMed

Khan, Aziz; Mathelier, Anthony

2018-05-01

JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers. This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license. aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no. Supplementary data are available at Bioinformatics online.

Connecting the Library's Patron Database to Campus Administrative Software: Simplifying the Library's Accounts Receivable Process

ERIC Educational Resources Information Center

Oliver, Astrid; Dahlquist, Janet; Tankersley, Jan; Emrich, Beth

2010-01-01

This article discusses the processes that occurred when the Library, Controller's Office, and Information Technology Department agreed to create an interface between the Library's Innovative Interfaces patron database and campus administrative software, Banner, using file transfer protocol, in an effort to streamline the Library's accounts…

[Tumor Data Interacted System Design Based on Grid Platform].

PubMed

Liu, Ying; Cao, Jiaji; Zhang, Haowei; Zhang, Ke

2016-06-01

In order to satisfy demands of massive and heterogeneous tumor clinical data processing and the multi-center collaborative diagnosis and treatment for tumor diseases,a Tumor Data Interacted System(TDIS)was established based on grid platform,so that an implementing virtualization platform of tumor diagnosis service was realized,sharing tumor information in real time and carrying on standardized management.The system adopts Globus Toolkit 4.0tools to build the open grid service framework and encapsulats data resources based on Web Services Resource Framework(WSRF).The system uses the middleware technology to provide unified access interface for heterogeneous data interaction,which could optimize interactive process with virtualized service to query and call tumor information resources flexibly.For massive amounts of heterogeneous tumor data,the federated stored and multiple authorized mode is selected as security services mechanism,real-time monitoring and balancing load.The system can cooperatively manage multi-center heterogeneous tumor data to realize the tumor patient data query,sharing and analysis,and compare and match resources in typical clinical database or clinical information database in other service node,thus it can assist doctors in consulting similar case and making up multidisciplinary treatment plan for tumors.Consequently,the system can improve efficiency of diagnosis and treatment for tumor,and promote the development of collaborative tumor diagnosis model.

A COSTAR interface using WWW technology.

PubMed Central

Rabbani, U.; Morgan, M.; Barnett, O.

1998-01-01

The concentration of industry on modern relational databases has left many nonrelational and proprietary databases without support for integration with new technologies. Emerging interface tools and data-access methodologies can be applied with difficulty to medical record systems which have proprietary data representation. Users of such medical record systems usually must access the clinical content of such record systems with keyboard-intensive and time-consuming interfaces. COSTAR is a legacy ambulatory medical record system developed over 25 years ago that is still popular and extensively used at the Massachusetts General Hospital. We define a model for using middle layer services to extract and cache data from non-relational databases, and present an intuitive World-Wide Web interface to COSTAR. This model has been implemented and successfully piloted in the Internal Medicine Associates at Massachusetts General Hospital. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:9929310

Vanderbilt University Institute of Imaging Science Center for Computational Imaging XNAT: A multimodal data archive and processing environment.

PubMed

Harrigan, Robert L; Yvernault, Benjamin C; Boyd, Brian D; Damon, Stephen M; Gibney, Kyla David; Conrad, Benjamin N; Phillips, Nicholas S; Rogers, Baxter P; Gao, Yurui; Landman, Bennett A

2016-01-01

The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has developed a database built on XNAT housing over a quarter of a million scans. The database provides framework for (1) rapid prototyping, (2) large scale batch processing of images and (3) scalable project management. The system uses the web-based interfaces of XNAT and REDCap to allow for graphical interaction. A python middleware layer, the Distributed Automation for XNAT (DAX) package, distributes computation across the Vanderbilt Advanced Computing Center for Research and Education high performance computing center. All software are made available in open source for use in combining portable batch scripting (PBS) grids and XNAT servers. Copyright © 2015 Elsevier Inc. All rights reserved.

A collaborative platform for consensus sessions in pathology over Internet.

PubMed

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

2003-01-01

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

RefPrimeCouch—a reference gene primer CouchApp

PubMed Central

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html PMID:24368831

RefPrimeCouch--a reference gene primer CouchApp.

PubMed

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html.

Exponential 6 parameterization for the JCZ3-EOS

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

McGee, B.C.; Hobbs, M.L.; Baer, M.R.

1998-07-01

A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium for detonation and expansion states of energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. All product species are characterized by r*, the radius of the minimum pair potential energy, and {var_epsilon}/k, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) EOS database describing 750 gases (including all the gases in the JANNAF tables), and have been obtained by using Lennard-Jones potential parameters, a corresponding states theory, pure liquid shockmore » Hugoniot data, and fit values using an empirical EOS. This database can be used with the CHEETAH 1.40 or CHEETAH 2.0 interface to the TIGER computer program that predicts the equilibrium state of gas- and condensed-phase product species. The large JCZS-EOS database permits intermolecular potential based equilibrium calculations of energetic materials with complex elemental composition.« less

MGDB: a comprehensive database of genes involved in melanoma.

PubMed

Zhang, Di; Zhu, Rongrong; Zhang, Hanqian; Zheng, Chun-Hou; Xia, Junfeng

2015-01-01

The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL: http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp. © The Author(s) 2015. Published by Oxford University Press.

MScanner: a classifier for retrieving Medline citations

PubMed Central

Poulter, Graham L; Rubin, Daniel L; Altman, Russ B; Seoighe, Cathal

2008-01-01

Background Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains. Results MScanner is an implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by decreasing probability of relevance. For maximum speed it uses the Medical Subject Headings (MeSH) and journal of publication as a concise document representation, and takes roughly 90 seconds to return results against the 16 million records in Medline. The web interface provides interactive exploration of the results, and cross validated performance evaluation on the relevant input against a random subset of Medline. We describe the classifier implementation, cross validate it on three domain-specific topics, and compare its performance to that of an expert PubMed query for a complex topic. In cross validation on the three sample topics against 100,000 random articles, the classifier achieved excellent separation of relevant and irrelevant article score distributions, ROC areas between 0.97 and 0.99, and averaged precision between 0.69 and 0.92. Conclusion MScanner is an effective non-domain-specific classifier that operates on the entire Medline database, and is suited to retrieving topics for which many features may indicate relevance. Its web interface simplifies the task of classifying Medline citations, compared to building a pre-filter and classifier specific to the topic. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material, and the web interface may be accessed at . PMID:18284683

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

PubMed

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

1998-07-15

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

Using Geocoded Databases in Teaching Urban Historical Geography.

ERIC Educational Resources Information Center

Miller, Roger P.

1986-01-01

Provides information regarding hardware and software requirements for using geocoded databases in urban historical geography. Reviews 11 IBM and Apple Macintosh database programs and describes the pen plotter and digitizing table interface used with the databases. (JDH)

A Visual Interface for Querying Heterogeneous Phylogenetic Databases.

PubMed

Jamil, Hasan M

2017-01-01

Despite the recent growth in the number of phylogenetic databases, access to these wealth of resources remain largely tool or form-based interface driven. It is our thesis that the flexibility afforded by declarative query languages may offer the opportunity to access these repositories in a better way, and to use such a language to pose truly powerful queries in unprecedented ways. In this paper, we propose a substantially enhanced closed visual query language, called PhyQL, that can be used to query phylogenetic databases represented in a canonical form. The canonical representation presented helps capture most phylogenetic tree formats in a convenient way, and is used as the storage model for our PhyloBase database for which PhyQL serves as the query language. We have implemented a visual interface for the end users to pose PhyQL queries using visual icons, and drag and drop operations defined over them. Once a query is posed, the interface translates the visual query into a Datalog query for execution over the canonical database. Responses are returned as hyperlinks to phylogenies that can be viewed in several formats using the tree viewers supported by PhyloBase. Results cached in PhyQL buffer allows secondary querying on the computed results making it a truly powerful querying architecture.

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

PubMed Central

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E.

2017-01-01

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. PMID:27915230

When is a search not a search? A comparison of searching the AMED complementary health database via EBSCOhost, OVID and DIALOG.

PubMed

Younger, Paula; Boddy, Kate

2009-06-01

The researchers involved in this study work at Exeter Health library and at the Complementary Medicine Unit, Peninsula School of Medicine and Dentistry (PCMD). Within this collaborative environment it is possible to access the electronic resources of three institutions. This includes access to AMED and other databases using different interfaces. The aim of this study was to investigate whether searching different interfaces to the AMED allied health and complementary medicine database produced the same results when using identical search terms. The following Internet-based AMED interfaces were searched: DIALOG DataStar; EBSCOhost and OVID SP_UI01.00.02. Search results from all three databases were saved in an endnote database to facilitate analysis. A checklist was also compiled comparing interface features. In our initial search, DIALOG returned 29 hits, OVID 14 and Ebsco 8. If we assume that DIALOG returned 100% of potential hits, OVID initially returned only 48% of hits and EBSCOhost only 28%. In our search, a researcher using the Ebsco interface to carry out a simple search on AMED would miss over 70% of possible search hits. Subsequent EBSCOhost searches on different subjects failed to find between 21 and 86% of the hits retrieved using the same keywords via DIALOG DataStar. In two cases, the simple EBSCOhost search failed to find any of the results found via DIALOG DataStar. Depending on the interface, the number of hits retrieved from the same database with the same simple search can vary dramatically. Some simple searches fail to retrieve a substantial percentage of citations. This may result in an uninformed literature review, research funding application or treatment intervention. In addition to ensuring that keywords, spelling and medical subject headings (MeSH) accurately reflect the nature of the search, database users should include wildcards and truncation and adapt their search strategy substantially to retrieve the maximum number of appropriate citations possible. Librarians should be aware of these differences when making purchasing decisions, carrying out literature searches and planning user education.

MetPetDB: A database for metamorphic geochemistry

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

The article describes the developed database designed as comprehensive data storage of the fixed target experiment BM@N [1] at Joint Institute for Nuclear Research (JINR) in Dubna. The structure and purposes of the BM@N facility will be briefly presented. The scheme of the unified database and its parameters will be described in detail. The use of the BM@N database implemented on the PostgreSQL database management system (DBMS) allows one to provide user access to the actual information of the experiment. Also the interfaces developed for the access to the database will be presented. One was implemented as the set of C++ classes to access the data without SQL statements, the other-Web-interface being available on the Web page of the BM@N experiment.

The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

PubMed Central

Bagger, Frederik Otzen; Sasivarevic, Damir; Sohi, Sina Hadi; Laursen, Linea Gøricke; Pundhir, Sachin; Sønderby, Casper Kaae; Winther, Ole; Rapin, Nicolas; Porse, Bo T.

2016-01-01

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. PMID:26507857

Tox-Database.net: a curated resource for data describing chemical triggered in vitro cardiac ion channels inhibition

PubMed Central

2012-01-01

Background Drugs safety issues are now recognized as being factors generating the most reasons for drug withdrawals at various levels of development and at the post-approval stage. Among them cardiotoxicity remains the main reason, despite the substantial effort put into in vitro and in vivo testing, with the main focus put on hERG channel inhibition as the hypothesized surrogate of drug proarrhythmic potency. The large interest in the IKr current has resulted in the development of predictive tools and informative databases describing a drug's susceptibility to interactions with the hERG channel, although there are no similar, publicly available sets of data describing other ionic currents driven by the human cardiomyocyte ionic channels, which are recognized as an overlooked drug safety target. Discussion The aim of this database development and publication was to provide a scientifically useful, easily usable and clearly verifiable set of information describing not only IKr (hERG), but also other human cardiomyocyte specific ionic channels inhibition data (IKs, INa, ICa). Summary The broad range of data (chemical space and in vitro settings) and the easy to use user interface makes tox-database.net a useful tool for interested scientists. Database URL http://tox-database.net. PMID:22947121

Monitoring and controlling ATLAS data management: The Rucio web user interface

NASA Astrophysics Data System (ADS)

Lassnig, M.; Beermann, T.; Vigne, R.; Barisits, M.; Garonne, V.; Serfon, C.

2015-12-01

The monitoring and controlling interfaces of the previous data management system DQ2 followed the evolutionary requirements and needs of the ATLAS collaboration. The new data management system, Rucio, has put in place a redesigned web-based interface based upon the lessons learnt from DQ2, and the increased volume of managed information. This interface encompasses both a monitoring and controlling component, and allows easy integration for usergenerated views. The interface follows three design principles. First, the collection and storage of data from internal and external systems is asynchronous to reduce latency. This includes the use of technologies like ActiveMQ or Nagios. Second, analysis of the data into information is done massively parallel due to its volume, using a combined approach with an Oracle database and Hadoop MapReduce. Third, sharing of the information does not distinguish between human or programmatic access, making it easy to access selective parts of the information both in constrained frontends like web-browsers as well as remote services. This contribution will detail the reasons for these principles and the design choices taken. Additionally, the implementation, the interactions with external systems, and an evaluation of the system in production, both from a technological and user perspective, conclude this contribution.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

PubMed Central

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas

2018-01-01

Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. PMID:29149270

WheatGenome.info: an integrated database and portal for wheat genome information.

PubMed

Lai, Kaitao; Berkman, Paul J; Lorenc, Michal Tadeusz; Duran, Chris; Smits, Lars; Manoli, Sahana; Stiller, Jiri; Edwards, David

2012-02-01

Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.

Design and development of a web-based application for diabetes patient data management.

PubMed

Deo, S S; Deobagkar, D N; Deobagkar, Deepti D

2005-01-01

A web-based database management system developed for collecting, managing and analysing information of diabetes patients is described here. It is a searchable, client-server, relational database application, developed on the Windows platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script. The software is menu-driven and allows authorized healthcare providers to access, enter, update and analyse patient information. Graphical representation of data can be generated by the system using bar charts and pie charts. An interactive web interface allows users to query the database and generate reports. Alpha- and beta-testing of the system was carried out and the system at present holds records of 500 diabetes patients and is found useful in diagnosis and treatment. In addition to providing patient data on a continuous basis in a simple format, the system is used in population and comparative analysis. It has proved to be of significant advantage to the healthcare provider as compared to the paper-based system.

Intelligent data management

NASA Technical Reports Server (NTRS)

Campbell, William J.

1985-01-01

Intelligent data management is the concept of interfacing a user to a database management system with a value added service that will allow a full range of data management operations at a high level of abstraction using human written language. The development of such a system will be based on expert systems and related artificial intelligence technologies, and will allow the capturing of procedural and relational knowledge about data management operations and the support of a user with such knowledge in an on-line, interactive manner. Such a system will have the following capabilities: (1) the ability to construct a model of the users view of the database, based on the query syntax; (2) the ability to transform English queries and commands into database instructions and processes; (3) the ability to use heuristic knowledge to rapidly prune the data space in search processes; and (4) the ability to use an on-line explanation system to allow the user to understand what the system is doing and why it is doing it. Additional information is given in outline form.

The Molecule Pages database

PubMed Central

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community. PMID:17965093

The Molecule Pages database.

PubMed

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar; Vadivelu, Ilango

2008-01-01

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

Protein-protein interface analysis and hot spots identification for chemical ligand design.

PubMed

Chen, Jing; Ma, Xiaomin; Yuan, Yaxia; Pei, Jianfeng; Lai, Luhua

2014-01-01

Rational design for chemical compounds targeting protein-protein interactions has grown from a dream to reality after a decade of efforts. There are an increasing number of successful examples, though major challenges remain in the field. In this paper, we will first give a brief review of the available methods that can be used to analyze protein-protein interface and predict hot spots for chemical ligand design. New developments of binding sites detection, ligandability and hot spots prediction from the author's group will also be described. Pocket V.3 is an improved program for identifying hot spots in protein-protein interface using only an apo protein structure. It has been developed based on Pocket V.2 that can derive receptor-based pharmacophore model for ligand binding cavity. Given similarities and differences between the essence of pharmacophore and hot spots for guiding design of chemical compounds, not only energetic but also spatial properties of protein-protein interface are used in Pocket V.3 for dealing with protein-protein interface. In order to illustrate the capability of Pocket V.3, two datasets have been used. One is taken from ASEdb and BID having experimental alanine scanning results for testing hot spots prediction. The other is taken from the 2P2I database containing complex structures of protein-ligand binding at the original protein-protein interface for testing hot spots application in ligand design.

Tangible interactive system for document browsing and visualisation of multimedia data

NASA Astrophysics Data System (ADS)

Rytsar, Yuriy; Voloshynovskiy, Sviatoslav; Koval, Oleksiy; Deguillaume, Frederic; Topak, Emre; Startchik, Sergei; Pun, Thierry

2006-01-01

In this paper we introduce and develop a framework for document interactive navigation in multimodal databases. First, we analyze the main open issues of existing multimodal interfaces and then discuss two applications that include interaction with documents in several human environments, i.e., the so-called smart rooms. Second, we propose a system set-up dedicated to the efficient navigation in the printed documents. This set-up is based on the fusion of data from several modalities that include images and text. Both modalities can be used as cover data for hidden indexes using data-hiding technologies as well as source data for robust visual hashing. The particularities of the proposed robust visual hashing are described in the paper. Finally, we address two practical applications of smart rooms for tourism and education and demonstrate the advantages of the proposed solution.

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.

DrugBank 5.0: a major update to the DrugBank database for 2018.

PubMed

Wishart, David S; Feunang, Yannick D; Guo, An C; Lo, Elvis J; Marcu, Ana; Grant, Jason R; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Sayeeda, Zinat; Assempour, Nazanin; Iynkkaran, Ithayavani; Liu, Yifeng; Maciejewski, Adam; Gale, Nicola; Wilson, Alex; Chin, Lucy; Cummings, Ryan; Le, Diana; Pon, Allison; Knox, Craig; Wilson, Michael

2018-01-04

DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development. This year's update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years. In many cases, existing data content has grown by 100% or more over the last update. For instance, the total number of investigational drugs in the database has grown by almost 300%, the number of drug-drug interactions has grown by nearly 600% and the number of SNP-associated drug effects has grown more than 3000%. Significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions. A great deal of brand new data have also been added to DrugBank 5.0. This includes information on the influence of hundreds of drugs on metabolite levels (pharmacometabolomics), gene expression levels (pharmacotranscriptomics) and protein expression levels (pharmacoprotoemics). New data have also been added on the status of hundreds of new drug clinical trials and existing drug repurposing trials. Many other important improvements in the content, interface and performance of the DrugBank website have been made and these should greatly enhance its ease of use, utility and potential applications in many areas of pharmacological research, pharmaceutical science and drug education. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

bioDBnet - Biological Database Network

Cancer.gov

bioDBnet is a comprehensive resource of most of the biological databases available from different sites like NCBI, Uniprot, EMBL, Ensembl, Affymetrix. It provides a queryable interface to all the databases available, converts identifiers from one database into another and generates comprehensive reports.

MAGIC database and interfaces: an integrated package for gene discovery and expression.

PubMed

Cordonnier-Pratt, Marie-Michèle; Liang, Chun; Wang, Haiming; Kolychev, Dmitri S; Sun, Feng; Freeman, Robert; Sullivan, Robert; Pratt, Lee H

2004-01-01

The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.

Mobile object retrieval in server-based image databases

NASA Astrophysics Data System (ADS)

Manger, D.; Pagel, F.; Widak, H.

2013-05-01

The increasing number of mobile phones equipped with powerful cameras leads to huge collections of user-generated images. To utilize the information of the images on site, image retrieval systems are becoming more and more popular to search for similar objects in an own image database. As the computational performance and the memory capacity of mobile devices are constantly increasing, this search can often be performed on the device itself. This is feasible, for example, if the images are represented with global image features or if the search is done using EXIF or textual metadata. However, for larger image databases, if multiple users are meant to contribute to a growing image database or if powerful content-based image retrieval methods with local features are required, a server-based image retrieval backend is needed. In this work, we present a content-based image retrieval system with a client server architecture working with local features. On the server side, the scalability to large image databases is addressed with the popular bag-of-word model with state-of-the-art extensions. The client end of the system focuses on a lightweight user interface presenting the most similar images of the database highlighting the visual information which is common with the query image. Additionally, new images can be added to the database making it a powerful and interactive tool for mobile contentbased image retrieval.

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

T-LECS: The Control Software System for MOIRCS

NASA Astrophysics Data System (ADS)

Yoshikawa, T.; Omata, K.; Konishi, M.; Ichikawa, T.; Suzuki, R.; Tokoku, C.; Katsuno, Y.; Nishimura, T.

2006-07-01

MOIRCS (Multi-Object Infrared Camera and Spectrograph) is a new instrument for the Subaru Telescope. We present the system design of the control software system for MOIRCS, named T-LECS (Tohoku University - Layered Electronic Control System). T-LECS is a PC-Linux based network distributed system. Two PCs equipped with the focal plane array system operate two HAWAII2 detectors, respectively, and another PC is used for user interfaces and a database server. Moreover, these PCs control various devices for observations distributed on a TCP/IP network. T-LECS has three interfaces; interfaces to the devices and two user interfaces. One of the user interfaces is to the integrated observation control system (Subaru Observation Software System) for observers, and another one provides the system developers the direct access to the devices of MOIRCS. In order to help the communication between these interfaces, we employ an SQL database system.

The One Universal Graph — a free and open graph database

NASA Astrophysics Data System (ADS)

Ng, Liang S.; Champion, Corbin

2016-02-01

Recent developments in graph database mostly are huge projects involving big organizations, big operations and big capital, as the name Big Data attests. We proposed the concept of One Universal Graph (OUG) which states that all observable and known objects and concepts (physical, conceptual or digitally represented) can be connected with only one single graph; furthermore the OUG can be implemented with a very simple text file format with free software, capable of being executed on Android or smaller devices. As such the One Universal Graph Data Exchange (GOUDEX) modules can potentially be installed on hundreds of millions of Android devices and Intel compatible computers shipped annually. Coupled with its open nature and ability to connect to existing leading search engines and databases currently in operation, GOUDEX has the potential to become the largest and a better interface for users and programmers to interact with the data on the Internet. With a Web User Interface for users to use and program in native Linux environment, Free Crowdware implemented in GOUDEX can help inexperienced users learn programming with better organized documentation for free software, and is able to manage programmer's contribution down to a single line of code or a single variable in software projects. It can become the first practically realizable “Internet brain” on which a global artificial intelligence system can be implemented. Being practically free and open, One Universal Graph can have significant applications in robotics, artificial intelligence as well as social networks.

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

Social media based NPL system to find and retrieve ARM data: Concept paper

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

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

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

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

Relational databases: a transparent framework for encouraging biology students to think informatically.

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically

PubMed Central

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. PMID:15592597

PceRBase: a database of plant competing endogenous RNA.

PubMed

Yuan, Chunhui; Meng, Xianwen; Li, Xue; Illing, Nicola; Ingle, Robert A; Wang, Jingjing; Chen, Ming

2017-01-04

Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

PubMed Central

Wilbur, W. John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical–gene interactions, chemical–disease relationships and gene–disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein–protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

Access to Space Interactive Design Web Site

NASA Technical Reports Server (NTRS)

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.

PubMed

Kumar, Pankaj; Halama, Anna; Hayat, Shahina; Billing, Anja M; Gupta, Manish; Yousri, Noha A; Smith, Gregory M; Suhre, Karsten

2015-01-01

The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO). Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe "MetaRNA-Seq," a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.

PubMed

De Oliveira, T; Miller, R; Tarin, M; Cassol, S

2003-01-01

Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors.

PubMed

Sable, Rushikesh; Jois, Seetharama

2015-06-23

Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.

Web-based metabolic network visualization with a zooming user interface

PubMed Central

2011-01-01

Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu. PMID:21595965

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

Freva - Freie Univ Evaluation System Framework for Scientific Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Schartner, Thomas; Kirchner, Ingo; Rust, Henning W.; Cubasch, Ulrich; Ulbrich, Uwe

2016-04-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science. Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins 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. Facilitation of the provision and usage of tools and climate data automatically increases the number of scientists working with the data sets and identifying discrepancies. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Therefore, plugged-in tools benefit from transparency and reproducibility. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

Freva - Freie Univ Evaluation System Framework for Scientific HPC Infrastructures in Earth System Modeling

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Schartner, T.; Grieger, J.; Kirchner, I.; Rust, H.; Cubasch, U.; Ulbrich, U.

2017-12-01

The Freie Univ Evaluation System Framework (Freva - freva.met.fu-berlin.de) is a software infrastructure for standardized data and tool solutions in Earth system science (e.g. www-miklip.dkrz.de, cmip-eval.dkrz.de). Freva runs on high performance computers to handle customizable evaluation systems of research projects, institutes or universities. It combines different software technologies into one common hybrid infrastructure, including all features present in the shell and web environment. The database interface satisfies the international standards provided by the Earth System Grid Federation (ESGF). Freva indexes different data projects into one common search environment by storing the meta data information of the self-describing model, reanalysis and observational data sets in a database. This implemented meta data system with its advanced but easy-to-handle search tool supports users, developers and their plugins 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. The integrated web-shell (shellinabox) adds a degree of freedom in the choice of the working environment and can be used as a gate to the research projects HPC. Plugins are able to integrate their e.g. post-processed results into the database of the user. This allows e.g. post-processing plugins to feed statistical analysis plugins, which fosters an active exchange between plugin developers of a research project. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a database. Configurations and results of the tools can be shared among scientists via shell or web system. Furthermore, if configurations match while starting an evaluation plugin, the system suggests to use results already produced by other users - saving CPU/h, I/O, disk space and time. The efficient interaction between different technologies improves the Earth system modeling science framed by Freva.

apART: system for the acquisition, processing, archiving, and retrieval of digital images in an open, distributed imaging environment

NASA Astrophysics Data System (ADS)

Schneider, Uwe; Strack, Ruediger

1992-04-01

apART reflects the structure of an open, distributed environment. According to the general trend in the area of imaging, network-capable, general purpose workstations with capabilities of open system image communication and image input are used. Several heterogeneous components like CCD cameras, slide scanners, and image archives can be accessed. The system is driven by an object-oriented user interface where devices (image sources and destinations), operators (derived from a commercial image processing library), and images (of different data types) are managed and presented uniformly to the user. Browsing mechanisms are used to traverse devices, operators, and images. An audit trail mechanism is offered to record interactive operations on low-resolution image derivatives. These operations are processed off-line on the original image. Thus, the processing of extremely high-resolution raster images is possible, and the performance of resolution dependent operations is enhanced significantly during interaction. An object-oriented database system (APRIL), which can be browsed, is integrated into the system. Attribute retrieval is supported by the user interface. Other essential features of the system include: implementation on top of the X Window System (X11R4) and the OSF/Motif widget set; a SUN4 general purpose workstation, inclusive ethernet, magneto optical disc, etc., as the hardware platform for the user interface; complete graphical-interactive parametrization of all operators; support of different image interchange formats (GIF, TIFF, IIF, etc.); consideration of current IPI standard activities within ISO/IEC for further refinement and extensions.

CNVinspector: a web-based tool for the interactive evaluation of copy number variations in single patients and in cohorts.

PubMed

Knierim, Ellen; Schwarz, Jana Marie; Schuelke, Markus; Seelow, Dominik

2013-08-01

Many genetic disorders are caused by copy number variations (CNVs) in the human genome. However, the large number of benign CNV polymorphisms makes it difficult to delineate causative variants for a certain disease phenotype. Hence, we set out to create software that accumulates and visualises locus-specific knowledge and enables clinicians to study their own CNVs in the context of known polymorphisms and disease variants. CNV data from healthy cohorts (Database of Genomic Variants) and from disease-related databases (DECIPHER) were integrated into a joint resource. Data are presented in an interactive web-based application that allows inspection, evaluation and filtering of CNVs in single individuals or in entire cohorts. CNVinspector provides simple interfaces to upload CNV data, compare them with own or published control data and visualise the results in graphical interfaces. Beyond choosing control data from different public studies, platforms and methods, dedicated filter options allow the detection of CNVs that are either enriched in patients or depleted in controls. Alternatively, a search can be restricted to those CNVs that appear in individuals of similar clinical phenotype. For each gene of interest within a CNV, we provide a link to NCBI, ENSEMBL and the GeneDistiller search engine to browse for potential disease-associated genes. With its user-friendly handling, the integration of control data and the filtering options, CNVinspector will facilitate the daily work of clinical geneticists and accelerate the delineation of new syndromes and gene functions. CNVinspector is freely accessible under http://www.cnvinspector.org.

IT-CARES: an interactive tool for case-crossover analyses of electronic medical records for patient safety.

PubMed

Caron, Alexandre; Chazard, Emmanuel; Muller, Joris; Perichon, Renaud; Ferret, Laurie; Koutkias, Vassilis; Beuscart, Régis; Beuscart, Jean-Baptiste; Ficheur, Grégoire

2017-03-01

The significant risk of adverse events following medical procedures supports a clinical epidemiological approach based on the analyses of collections of electronic medical records. Data analytical tools might help clinical epidemiologists develop more appropriate case-crossover designs for monitoring patient safety. To develop and assess the methodological quality of an interactive tool for use by clinical epidemiologists to systematically design case-crossover analyses of large electronic medical records databases. We developed IT-CARES, an analytical tool implementing case-crossover design, to explore the association between exposures and outcomes. The exposures and outcomes are defined by clinical epidemiologists via lists of codes entered via a user interface screen. We tested IT-CARES on data from the French national inpatient stay database, which documents diagnoses and medical procedures for 170 million inpatient stays between 2007 and 2013. We compared the results of our analysis with reference data from the literature on thromboembolic risk after delivery and bleeding risk after total hip replacement. IT-CARES provides a user interface with 3 columns: (i) the outcome criteria in the left-hand column, (ii) the exposure criteria in the right-hand column, and (iii) the estimated risk (odds ratios, presented in both graphical and tabular formats) in the middle column. The estimated odds ratios were consistent with the reference literature data. IT-CARES may enhance patient safety by facilitating clinical epidemiological studies of adverse events following medical procedures. The tool's usability must be evaluated and improved in further research. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association.

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.

InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface.

PubMed

Hoeck, W G

1994-06-01

InfoTrac TFD provides a graphical user interface (GUI) for viewing and manipulating datasets in the Transcription Factor Database, TFD. The interface was developed in Filemaker Pro 2.0 by Claris Corporation, which provides cross platform compatibility between Apple Macintosh computers running System 7.0 and higher and IBM-compatibles running Microsoft Windows 3.0 and higher. TFD ASCII-tables were formatted to fit data into several custom data tables using Add/Strip, a shareware utility and Filemaker Pro's lookup feature. The lookup feature was also put to use to allow TFD data tables to become linked within a flat-file database management system. The 'Navigator', consisting of several pop-up menus listing transcription factor abbreviations, facilitates the search for transcription factor entries. Data are presented onscreen in several layouts, that can be further customized by the user. InfoTrac TFD makes the transcription factor database accessible to a much wider community of scientists by making it available on two popular microcomputer platforms.

NASA Access Mechanism: Lessons learned document

NASA Technical Reports Server (NTRS)

Burdick, Lisa; Dunbar, Rick; Duncan, Denise; Generous, Curtis; Hunter, Judy; Lycas, John; Taber-Dudas, Ardeth

1994-01-01

The six-month beta test of the NASA Access Mechanism (NAM) prototype was completed on June 30, 1993. This report documents the lessons learned from the use of this Graphical User Interface to NASA databases such as the NASA STI Database, outside databases, Internet resources, and peers in the NASA R&D community. Design decisions, such as the use of XWindows software, a client-server distributed architecture, and use of the NASA Science Internet, are explained. Users' reactions to the interface and suggestions for design changes are reported, as are the changes made by the software developers based on new technology for information discovery and retrieval. The lessons learned section also reports reactions from the public, both at demonstrations and in response to articles in the trade press and journals. Recommendations are included for future versions, such as a World Wide Web (WWW) and Mosaic based interface to heterogeneous databases, and NAM-Lite, a version which allows customization to include utilities provided locally at NASA Centers.

MONA – Interactive manipulation of molecule collections

PubMed Central

2013-01-01

Working with small‐molecule datasets is a routine task for cheminformaticians and chemists. The analysis and comparison of vendor catalogues and the compilation of promising candidates as starting points for screening campaigns are but a few very common applications. The workflows applied for this purpose usually consist of multiple basic cheminformatics tasks such as checking for duplicates or filtering by physico‐chemical properties. Pipelining tools allow to create and change such workflows without much effort, but usually do not support interventions once the pipeline has been started. In many contexts, however, the best suited workflow is not known in advance, thus making it necessary to take the results of the previous steps into consideration before proceeding. To support intuition‐driven processing of compound collections, we developed MONA, an interactive tool that has been designed to prepare and visualize large small‐molecule datasets. Using an SQL database common cheminformatics tasks such as analysis and filtering can be performed interactively with various methods for visual support. Great care was taken in creating a simple, intuitive user interface which can be instantly used without any setup steps. MONA combines the interactivity of molecule database systems with the simplicity of pipelining tools, thus enabling the case‐to‐case application of chemistry expert knowledge. The current version is available free of charge for academic use and can be downloaded at http://www.zbh.uni‐hamburg.de/mona. PMID:23985157

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

CEBS: a comprehensive annotated database of toxicological data

PubMed Central

Lea, Isabel A.; Gong, Hui; Paleja, Anand; Rashid, Asif; Fostel, Jennifer

2017-01-01

The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/databases/cebs/. PMID:27899660

Design and implementation of the NPOI database and website

NASA Astrophysics Data System (ADS)

Newman, K.; Jorgensen, A. M.; Landavazo, M.; Sun, B.; Hutter, D. J.; Armstrong, J. T.; Mozurkewich, David; Elias, N.; van Belle, G. T.; Schmitt, H. R.; Baines, E. K.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) has been recording astronomical observations for nearly two decades, at this point with hundreds of thousands of individual observations recorded to date for a total data volume of many terabytes. To make maximum use of the NPOI data it is necessary to organize them in an easily searchable manner and be able to extract essential diagnostic information from the data to allow users to quickly gauge data quality and suitability for a specific science investigation. This sets the motivation for creating a comprehensive database of observation metadata as well as, at least, reduced data products. The NPOI database is implemented in MySQL using standard database tools and interfaces. The use of standard database tools allows us to focus on top-level database and interface implementation and take advantage of standard features such as backup, remote access, mirroring, and complex queries which would otherwise be time-consuming to implement. A website was created in order to give scientists a user friendly interface for searching the database. It allows the user to select various metadata to search for and also allows them to decide how and what results are displayed. This streamlines the searches, making it easier and quicker for scientists to find the information they are looking for. The website has multiple browser and device support. In this paper we present the design of the NPOI database and website, and give examples of its use.

Virtual Diagnostic Interface: Aerospace Experimentation in the Synthetic Environment

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; McCrea, Andrew C.

2009-01-01

The Virtual Diagnostics Interface (ViDI) methodology combines two-dimensional image processing and three-dimensional computer modeling to provide comprehensive in-situ visualizations commonly utilized for in-depth planning of wind tunnel and flight testing, real time data visualization of experimental data, and unique merging of experimental and computational data sets in both real-time and post-test analysis. The preparation of such visualizations encompasses the realm of interactive three-dimensional environments, traditional and state of the art image processing techniques, database management and development of toolsets with user friendly graphical user interfaces. ViDI has been under development at the NASA Langley Research Center for over 15 years, and has a long track record of providing unique and insightful solutions to a wide variety of experimental testing techniques and validation of computational simulations. This report will address the various aspects of ViDI and how it has been applied to test programs as varied as NASCAR race car testing in NASA wind tunnels to real-time operations concerning Space Shuttle aerodynamic flight testing. In addition, future trends and applications will be outlined in the paper.

Virtual Diagnostic Interface: Aerospace Experimentation in the Synthetic Environment

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; McCrea, Andrew C.

2010-01-01

The Virtual Diagnostics Interface (ViDI) methodology combines two-dimensional image processing and three-dimensional computer modeling to provide comprehensive in-situ visualizations commonly utilized for in-depth planning of wind tunnel and flight testing, real time data visualization of experimental data, and unique merging of experimental and computational data sets in both real-time and post-test analysis. The preparation of such visualizations encompasses the realm of interactive three-dimensional environments, traditional and state of the art image processing techniques, database management and development of toolsets with user friendly graphical user interfaces. ViDI has been under development at the NASA Langley Research Center for over 15 years, and has a long track record of providing unique and insightful solutions to a wide variety of experimental testing techniques and validation of computational simulations. This report will address the various aspects of ViDI and how it has been applied to test programs as varied as NASCAR race car testing in NASA wind tunnels to real-time operations concerning Space Shuttle aerodynamic flight testing. In addition, future trends and applications will be outlined in the paper.

PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

PubMed

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E

2017-01-04

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

PubMed

Vlachos, Ioannis S; Paraskevopoulou, Maria D; Karagkouni, Dimitra; Georgakilas, Georgios; Vergoulis, Thanasis; Kanellos, Ilias; Anastasopoulos, Ioannis-Laertis; Maniou, Sofia; Karathanou, Konstantina; Kalfakakou, Despina; Fevgas, Athanasios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

2015-01-01

microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Oceans of Data: In what ways can learning research inform the development of electronic interfaces and tools for use by students accessing large scientific databases?

NASA Astrophysics Data System (ADS)

Krumhansl, R. A.; Foster, J.; Peach, C. L.; Busey, A.; Baker, I.

2012-12-01

The practice of science and engineering is being revolutionized by the development of cyberinfrastructure for accessing near real-time and archived observatory data. Large cyberinfrastructure projects have the potential to transform the way science is taught in high school classrooms, making enormous quantities of scientific data available, giving students opportunities to analyze and draw conclusions from many kinds of complex data, and providing students with experiences using state-of-the-art resources and techniques for scientific investigations. However, online interfaces to scientific data are built by scientists for scientists, and their design can significantly impede broad use by novices. Knowledge relevant to the design of student interfaces to complex scientific databases is broadly dispersed among disciplines ranging from cognitive science to computer science and cartography and is not easily accessible to designers of educational interfaces. To inform efforts at bridging scientific cyberinfrastructure to the high school classroom, Education Development Center, Inc. and the Scripps Institution of Oceanography conducted an NSF-funded 2-year interdisciplinary review of literature and expert opinion pertinent to making interfaces to large scientific databases accessible to and usable by precollege learners and their teachers. Project findings are grounded in the fundamentals of Cognitive Load Theory, Visual Perception, Schemata formation and Universal Design for Learning. The Knowledge Status Report (KSR) presents cross-cutting and visualization-specific guidelines that highlight how interface design features can address/ ameliorate challenges novice high school students face as they navigate complex databases to find data, and construct and look for patterns in maps, graphs, animations and other data visualizations. The guidelines present ways to make scientific databases more broadly accessible by: 1) adjusting the cognitive load imposed by the user interface and visualizations so that it doesn't exceed the amount of information the learner can actively process; 2) drawing attention to important features and patterns; and 3) enabling customization of visualizations and tools to meet the needs of diverse learners.

Design and implementation of a portal for the medical equipment market: MEDICOM.

PubMed

Palamas, S; Kalivas, D; Panou-Diamandi, O; Zeelenberg, C; van Nimwegen, C

2001-01-01

The MEDICOM (Medical Products Electronic Commerce) Portal provides the electronic means for medical-equipment manufacturers to communicate online with their customers while supporting the Purchasing Process and Post Market Surveillance. The Portal offers a powerful Internet-based search tool for finding medical products and manufacturers. Its main advantage is the fast, reliable and up-to-date retrieval of information while eliminating all unrelated content that a general-purpose search engine would retrieve. The Universal Medical Device Nomenclature System (UMDNS) registers all products. The Portal accepts end-user requests and generates a list of results containing text descriptions of devices, UMDNS attribute values, and links to manufacturer Web pages and online catalogues for access to more-detailed information. Device short descriptions are provided by the corresponding manufacturer. The Portal offers technical support for integration of the manufacturers Web sites with itself. The network of the Portal and the connected manufacturers sites is called the MEDICOM system. To establish an environment hosting all the interactions of consumers (health care organizations and professionals) and providers (manufacturers, distributors, and resellers of medical devices). The Portal provides the end-user interface, implements system management, and supports database compatibility. The Portal hosts information about the whole MEDICOM system (Common Database) and summarized descriptions of medical devices (Short Description Database); the manufacturers servers present extended descriptions. The Portal provides end-user profiling and registration, an efficient product-searching mechanism, bulletin boards, links to on-line libraries and standards, on-line information for the MEDICOM system, and special messages or advertisements from manufacturers. Platform independence and interoperability characterize the system design. Relational Database Management Systems are used for the system s databases. The end-user interface is implemented using HTML, Javascript, Java applets, and XML documents. Communication between the Portal and the manufacturers servers is implemented using a CORBA interface. Remote administration of the Portal is enabled by dynamically-generated HTML interfaces based on XML documents. A representative group of users evaluated the system. The aim of the evaluation was validation of the usability of all of MEDICOM s functionality. The evaluation procedure was based on ISO/IEC 9126 Information technology - Software product evaluation - Quality characteristics and guidelines for their use. The overall user evaluation of the MEDICOM system was very positive. The MEDICOM system was characterized as an innovative concept that brings significant added value to medical-equipment commerce. The eventual benefits of the MEDICOM system are (a) establishment of a worldwide-accessible marketplace between manufacturers and health care professionals that provides up-to-date and high-quality product information in an easy and friendly way and (b) enhancement of the efficiency of marketing procedures and after-sales support.

Design and Implementation of a Portal for the Medical Equipment Market: MEDICOM

PubMed Central

Kalivas, Dimitris; Panou-Diamandi, Ourania; Zeelenberg, Cees; van Nimwegen, Chris

2001-01-01

Background The MEDICOM (Medical Products Electronic Commerce) Portal provides the electronic means for medical-equipment manufacturers to communicate online with their customers while supporting the Purchasing Process and Post Market Surveillance. The Portal offers a powerful Internet-based search tool for finding medical products and manufacturers. Its main advantage is the fast, reliable and up-to-date retrieval of information while eliminating all unrelated content that a general-purpose search engine would retrieve. The Universal Medical Device Nomenclature System (UMDNS) registers all products. The Portal accepts end-user requests and generates a list of results containing text descriptions of devices, UMDNS attribute values, and links to manufacturer Web pages and online catalogues for access to more-detailed information. Device short descriptions are provided by the corresponding manufacturer. The Portal offers technical support for integration of the manufacturers' Web sites with itself. The network of the Portal and the connected manufacturers' sites is called the MEDICOM system. Objective To establish an environment hosting all the interactions of consumers (health care organizations and professionals) and providers (manufacturers, distributors, and resellers of medical devices). Methods The Portal provides the end-user interface, implements system management, and supports database compatibility. The Portal hosts information about the whole MEDICOM system (Common Database) and summarized descriptions of medical devices (Short Description Database); the manufacturers' servers present extended descriptions. The Portal provides end-user profiling and registration, an efficient product-searching mechanism, bulletin boards, links to on-line libraries and standards, on-line information for the MEDICOM system, and special messages or advertisements from manufacturers. Platform independence and interoperability characterize the system design. Relational Database Management Systems are used for the system's databases. The end-user interface is implemented using HTML, Javascript, Java applets, and XML documents. Communication between the Portal and the manufacturers' servers is implemented using a CORBA interface. Remote administration of the Portal is enabled by dynamically-generated HTML interfaces based on XML documents. A representative group of users evaluated the system. The aim of the evaluation was validation of the usability of all of MEDICOM's functionality. The evaluation procedure was based on ISO/IEC 9126 Information technology - Software product evaluation - Quality characteristics and guidelines for their use. Results The overall user evaluation of the MEDICOM system was very positive. The MEDICOM system was characterized as an innovative concept that brings significant added value to medical-equipment commerce. Conclusions The eventual benefits of the MEDICOM system are (a) establishment of a worldwide-accessible marketplace between manufacturers and health care professionals that provides up-to-date and high-quality product information in an easy and friendly way and (b) enhancement of the efficiency of marketing procedures and after-sales support. PMID:11772547

yStreX: yeast stress expression database

PubMed Central

Wanichthanarak, Kwanjeera; Nookaew, Intawat; Petranovic, Dina

2014-01-01

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

MIPS: curated databases and comprehensive secondary data resources in 2010.

PubMed

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

MIPS: curated databases and comprehensive secondary data resources in 2010

PubMed Central

Mewes, H. Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F.X.; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de). PMID:21109531

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

New method for identifying features of an image on a digital video display

NASA Astrophysics Data System (ADS)

Doyle, Michael D.

1991-04-01

The MetaMap process extends the concept of direct manipulation human-computer interfaces to new limits. Its specific capabilities include the correlation of discrete image elements to relevant text information and the correlation of these image features to other images as well as to program control mechanisms. The correlation is accomplished through reprogramming of both the color map and the image so that discrete image elements comprise unique sets of color indices. This process allows the correlation to be accomplished with very efficient data storage and program execution times. Image databases adapted to this process become object-oriented as a result. Very sophisticated interrelationships can be set up between images text and program control mechanisms using this process. An application of this interfacing process to the design of an interactive atlas of medical histology as well as other possible applications are described. The MetaMap process is protected by U. S. patent #4

Educational and Scientific Applications of the \\itTime Navigator}

NASA Astrophysics Data System (ADS)

Cole, M.; Snow, J. T.; Slatt, R. M.

2001-05-01

Several recent conferences have noted the need to focus on the evolving interface between research and education at all levels of science, mathematics, engineering, and technology education. This interface, which is a distinguishing feature of graduate education in the U.S., is increasingly in demand at the undergraduate and K-12 levels, particularly in the earth sciences. In this talk, we present a new database for earth systems science and will explore applications to K-12 and undergraduate education, as well as the scientific and graduate role. The University of Oklahoma, College of Geosciences is in the process of acquiring the \\itTime Navigator}, a multi-disciplinary, multimedia database, which will form the core asset of the Center for Earth Systems Science. The Center, whose mission is to further the understanding of the dynamic Earth within both the academic and the general public communities, will serve as a portal for research, information, and education for scientists and educators. \\itTime Navigator} was developed over a period of some twenty years by the noted British geoscience author, Ron Redfern, in connection with the recently published, \\itOrigins, the evolution of continents, oceans and life}, the third in a series of books for the educated layperson. Over the years \\itTime Navigator} has evolved into an interactive, multimedia database displaying much of the significant geological, paleontological, climatological, and tectonic events from the latest Proterozoic (750 MYA) through to the present. The focus is mainly on the Western Hemisphere and events associated with the coalescence and breakup of Pangea and the evolution of the earth into its present form. \\itOrigins} will be available as early as Fall 2001 as an interactive electronic book for the general, scientifically-literate public. While electronic books are unlikely to replace traditional print books, the format does allow non-linear exploration of content. We believe that the electronic version of \\itOrigins} can be a demonstration project for delivering multimedia content to a variety of audiences. In the first half of this presentation, we give a brief overview of \\itTime Navigator}, including a demonstration of the content and sophistication of the database, We will focus on layered, multimedia features, ease of use, and interactivity. The second half of the presentation will feature undergraduate and 9-12 applications which are built around a series of "research projects" emphasizing application of the Scientific Method, analyzing scientific data, and how scientists achieve consensus on theories.

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.

78 FR 58545 - Global Unique Device Identification Database; Draft Guidance for Industry; Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-24

...] Global Unique Device Identification Database; Draft Guidance for Industry; Availability AGENCY: Food and... the availability of the draft guidance entitled ``Global Unique Device Identification Database (GUDID... manufacturer) will interface with the GUDID, as well as information on the database elements that must be...

FIREMON Database

Treesearch

John F. Caratti

2006-01-01

The FIREMON database software allows users to enter data, store, analyze, and summarize plot data, photos, and related documents. The FIREMON database software consists of a Java application and a Microsoft® Access database. The Java application provides the user interface with FIREMON data through data entry forms, data summary reports, and other data management tools...

Mission and Assets Database

NASA Technical Reports Server (NTRS)

Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

2009-01-01

Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

3DNALandscapes: a database for exploring the conformational features of DNA.

PubMed

Zheng, Guohui; Colasanti, Andrew V; Lu, Xiang-Jun; Olson, Wilma K

2010-01-01

3DNALandscapes, located at: http://3DNAscapes.rutgers.edu, is a new database for exploring the conformational features of DNA. In contrast to most structural databases, which archive the Cartesian coordinates and/or derived parameters and images for individual structures, 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures--both free and bound to proteins, drugs and other ligands--currently available in the Protein Data Bank. The web interface allows the user to link, report, plot and analyze this information from numerous perspectives and thereby gain insight into DNA conformation, deformability and interactions in different sequence and structural contexts. The data accumulated from known, well-resolved DNA structures can serve as useful benchmarks for the analysis and simulation of new structures. The collective data can also help to understand how DNA deforms in response to proteins and other molecules and undergoes conformational rearrangements.

Image

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

Marsh, Amber; Harsch, Tim; Pitt, Julie

2007-08-31

The computer side of the IMAGE project consists of a collection of Perl scripts that perform a variety of tasks; scripts are available to insert, update and delete data from the underlying Oracle database, download data from NCBI's Genbank and other sources, and generate data files for download by interested parties. Web scripts make up the tracking interface, and various tools available on the project web-site (image.llnl.gov) that provide a search interface to the database.

Open Clients for Distributed Databases

NASA Astrophysics Data System (ADS)

Chayes, D. N.; Arko, R. A.

2001-12-01

We are actively developing a collection of open source example clients that demonstrate use of our "back end" data management infrastructure. The data management system is reported elsewhere at this meeting (Arko and Chayes: A Scaleable Database Infrastructure). In addition to their primary goal of being examples for others to build upon, some of these clients may have limited utility in them selves. More information about the clients and the data infrastructure is available on line at http://data.ldeo.columbia.edu. The available examples to be demonstrated include several web-based clients including those developed for the Community Review System of the Digital Library for Earth System Education, a real-time watch standers log book, an offline interface to use log book entries, a simple client to search on multibeam metadata and others are Internet enabled and generally web-based front ends that support searches against one or more relational databases using industry standard SQL queries. In addition to the web based clients, simple SQL searches from within Excel and similar applications will be demonstrated. By defining, documenting and publishing a clear interface to the fully searchable databases, it becomes relatively easy to construct client interfaces that are optimized for specific applications in comparison to building a monolithic data and user interface system.

A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake).

PubMed

Yamamoto, Naoki; Suzuki, Tomohiro; Kobayashi, Masaaki; Dohra, Hideo; Sasaki, Yohei; Hirai, Hirofumi; Yokoyama, Koji; Kawagishi, Hirokazu; Yano, Kentaro

2014-12-03

The angel's wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclose the genes underlying the accident and provide mechanistic insight, we seek to develop an information infrastructure containing omics data. In our previous work, we sequenced the genome and transcriptome using next-generation sequencing techniques. The next step in achieving our goal is to develop a web database to facilitate the efficient mining of large-scale omics data and identification of genes specifically expressed in the mushroom. This paper introduces a web database A-WINGS (http://bioinf.mind.meiji.ac.jp/a-wings/) that provides integrated genomic and transcriptomic information for the angel's wing oyster mushroom. The database contains structure and functional annotations of transcripts and gene expressions. Functional annotations contain information on homologous sequences from NCBI nr and UniProt, Gene Ontology, and KEGG Orthology. Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia. The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches. The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis.

PubMed

Bagger, Frederik Otzen; Sasivarevic, Damir; Sohi, Sina Hadi; Laursen, Linea Gøricke; Pundhir, Sachin; Sønderby, Casper Kaae; Winther, Ole; Rapin, Nicolas; Porse, Bo T

2016-01-04

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan-Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Interactive design of generic chemical patterns.

PubMed

Schomburg, Karen T; Wetzer, Lars; Rarey, Matthias

2013-07-01

Every medicinal chemist has to create chemical patterns occasionally for querying databases, applying filters or describing functional groups. However, the representations of chemical patterns have been so far limited to languages with highly complex syntax, handicapping the application of patterns. Graphic pattern editors similar to chemical editors can facilitate the work with patterns. In this article, we review the interfaces of frequently used web search engines for chemical patterns. We take a look at pattern editing concepts of standalone chemical editors and finally present a completely new, unpublished graphical approach to pattern design, the SMARTSeditor. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simultaneous real-time data collection methods

NASA Technical Reports Server (NTRS)

Klincsek, Thomas

1992-01-01

This paper describes the development of electronic test equipment which executes, supervises, and reports on various tests. This validation process uses computers to analyze test results and report conclusions. The test equipment consists of an electronics component and the data collection and reporting unit. The PC software, display screens, and real-time data-base are described. Pass-fail procedures and data replay are discussed. The OS2 operating system and Presentation Manager user interface system were used to create a highly interactive automated system. The system outputs are hardcopy printouts and MS DOS format files which may be used as input for other PC programs.

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference.

PubMed

Garcia-Garcia, Javier; Schleker, Sylvia; Klein-Seetharaman, Judith; Oliva, Baldo

2012-07-01

Protein-protein interactions (PPIs) play a crucial role in biology, and high-throughput experiments have greatly increased the coverage of known interactions. Still, identification of complete inter- and intraspecies interactomes is far from being complete. Experimental data can be complemented by the prediction of PPIs within an organism or between two organisms based on the known interactions of the orthologous genes of other organisms (interologs). Here, we present the BIANA (Biologic Interactions and Network Analysis) Interolog Prediction Server (BIPS), which offers a web-based interface to facilitate PPI predictions based on interolog information. BIPS benefits from the capabilities of the framework BIANA to integrate the several PPI-related databases. Additional metadata can be used to improve the reliability of the predicted interactions. Sensitivity and specificity of the server have been calculated using known PPIs from different interactomes using a leave-one-out approach. The specificity is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate similarities between sequences. BIPS is freely accessible at http://sbi.imim.es/BIPS.php.

An active visual search interface for Medline.

PubMed

Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Wilson, Justin; Athey, Brian; Watson, Stanley J; Meng, Fan

2007-01-01

Searching the Medline database is almost a daily necessity for many biomedical researchers. However, available Medline search solutions are mainly designed for the quick retrieval of a small set of most relevant documents. Because of this search model, they are not suitable for the large-scale exploration of literature and the underlying biomedical conceptual relationships, which are common tasks in the age of high throughput experimental data analysis and cross-discipline research. We try to develop a new Medline exploration approach by incorporating interactive visualization together with powerful grouping, summary, sorting and active external content retrieval functions. Our solution, PubViz, is based on the FLEX platform designed for interactive web applications and its prototype is publicly available at: http://brainarray.mbni.med.umich.edu/Brainarray/DataMining/PubViz.

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.

A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1997-01-01

This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

A topological multilayer model of the human body.

PubMed

Barbeito, Antonio; Painho, Marco; Cabral, Pedro; O'Neill, João

2015-11-04

Geographical information systems deal with spatial databases in which topological models are described with alphanumeric information. Its graphical interfaces implement the multilayer concept and provide powerful interaction tools. In this study, we apply these concepts to the human body creating a representation that would allow an interactive, precise, and detailed anatomical study. A vector surface component of the human body is built using a three-dimensional (3-D) reconstruction methodology. This multilayer concept is implemented by associating raster components with the corresponding vector surfaces, which include neighbourhood topology enabling spatial analysis. A root mean square error of 0.18 mm validated the three-dimensional reconstruction technique of internal anatomical structures. The expansion of the identification and the development of a neighbourhood analysis function are the new tools provided in this model.

Application Program Interface for the Orion Aerodynamics Database

NASA Technical Reports Server (NTRS)

Robinson, Philip E.; Thompson, James

2013-01-01

The Application Programming Interface (API) for the Crew Exploration Vehicle (CEV) Aerodynamic Database has been developed to provide the developers of software an easily implemented, fully self-contained method of accessing the CEV Aerodynamic Database for use in their analysis and simulation tools. The API is programmed in C and provides a series of functions to interact with the database, such as initialization, selecting various options, and calculating the aerodynamic data. No special functions (file read/write, table lookup) are required on the host system other than those included with a standard ANSI C installation. It reads one or more files of aero data tables. Previous releases of aerodynamic databases for space vehicles have only included data tables and a document of the algorithm and equations to combine them for the total aerodynamic forces and moments. This process required each software tool to have a unique implementation of the database code. Errors or omissions in the documentation, or errors in the implementation, led to a lengthy and burdensome process of having to debug each instance of the code. Additionally, input file formats differ for each space vehicle simulation tool, requiring the aero database tables to be reformatted to meet the tool s input file structure requirements. Finally, the capabilities for built-in table lookup routines vary for each simulation tool. Implementation of a new database may require an update to and verification of the table lookup routines. This may be required if the number of dimensions of a data table exceeds the capability of the simulation tools built-in lookup routines. A single software solution was created to provide an aerodynamics software model that could be integrated into other simulation and analysis tools. The highly complex Orion aerodynamics model can then be quickly included in a wide variety of tools. The API code is written in ANSI C for ease of portability to a wide variety of systems. The input data files are in standard formatted ASCII, also for improved portability. The API contains its own implementation of multidimensional table reading and lookup routines. The same aerodynamics input file can be used without modification on all implementations. The turnaround time from aerodynamics model release to a working implementation is significantly reduced

Systems engineering interfaces: A model based approach

NASA Astrophysics Data System (ADS)

Fosse, E.; Delp, C. L.

The engineering of interfaces is a critical function of the discipline of Systems Engineering. Included in interface engineering are instances of interaction. Interfaces provide the specifications of the relevant properties of a system or component that can be connected to other systems or components while instances of interaction are identified in order to specify the actual integration to other systems or components. Current Systems Engineering practices rely on a variety of documents and diagrams to describe interface specifications and instances of interaction. The SysML[1] specification provides a precise model based representation for interfaces and interface instance integration. This paper will describe interface engineering as implemented by the Operations Revitalization Task using SysML, starting with a generic case and culminating with a focus on a Flight System to Ground Interaction. The reusability of the interface engineering approach presented as well as its extensibility to more complex interfaces and interactions will be shown. Model-derived tables will support the case studies shown and are examples of model-based documentation products.

Challenges of Malaysian Developers in Creating Good Interfaces for Interactive Courseware

ERIC Educational Resources Information Center

Kamaruddin, Norfadilah

2010-01-01

There are many reasons why interface design for interactive courseware fails to support quality of learning experiences. The causes such as the level of interactivity, the availability of the interfaces to interact with the end users and a lack of deep knowledge about the role of interface design by the designers in the development process are…

Is More Always Better?

ERIC Educational Resources Information Center

Bell, Steven J.

2003-01-01

Discusses full-text databases and whether existing aggregator databases are meeting user needs. Topics include the need for better search interfaces; concepts of quality research and information retrieval; information overload; full text in electronic journal collections versus aggregator databases; underrepresentation of certain disciplines; and…

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

PubMed

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Brown, C Titus; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas; Lemaire, Patrick

2018-01-04

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Legacy2Drupal - Conversion of an existing oceanographic relational database to a semantically enabled Drupal content management system

NASA Astrophysics Data System (ADS)

Maffei, A. R.; Chandler, C. L.; Work, T.; Allen, J.; Groman, R. C.; Fox, P. A.

2009-12-01

Content Management Systems (CMSs) provide powerful features that can be of use to oceanographic (and other geo-science) data managers. However, in many instances, geo-science data management offices have previously designed customized schemas for their metadata. The WHOI Ocean Informatics initiative and the NSF funded Biological Chemical and Biological Data Management Office (BCO-DMO) have jointly sponsored a project to port an existing, relational database containing oceanographic metadata, along with an existing interface coded in Cold Fusion middleware, to a Drupal6 Content Management System. The goal was to translate all the existing database tables, input forms, website reports, and other features present in the existing system to employ Drupal CMS features. The replacement features include Drupal content types, CCK node-reference fields, themes, RDB, SPARQL, workflow, and a number of other supporting modules. Strategic use of some Drupal6 CMS features enables three separate but complementary interfaces that provide access to oceanographic research metadata via the MySQL database: 1) a Drupal6-powered front-end; 2) a standard SQL port (used to provide a Mapserver interface to the metadata and data; and 3) a SPARQL port (feeding a new faceted search capability being developed). Future plans include the creation of science ontologies, by scientist/technologist teams, that will drive semantically-enabled faceted search capabilities planned for the site. Incorporation of semantic technologies included in the future Drupal 7 core release is also anticipated. Using a public domain CMS as opposed to proprietary middleware, and taking advantage of the many features of Drupal 6 that are designed to support semantically-enabled interfaces will help prepare the BCO-DMO database for interoperability with other ecosystem databases.

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

PubMed

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

2016-02-01

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

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

PubMed Central

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

2016-01-01

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

OVERSEER: An Expert System Monitor for the Psychiatric Hospital

PubMed Central

Bronzino, Joseph D.; Morelli, Ralph A.; Goethe, John W.

1988-01-01

In order to improve patient care, comply with regulatory guidelines and decrease potential liability, psychiatric hospitals and clinics have been searching for computer systems to monitor the management and treatment of patients. This paper describes OVERSEER: a knowledge based system that monitors the treatment of psychiatric patients in real time. Based on procedures and protocols developed in the psychiatric setting, OVERSEER monitors the clinical database and issues alerts when standard clinical practices are not followed or when laboratory results or other clinical indicators are abnormal. Written in PROLOG, OVERSEER is designed to interface directly with the hospital's database, and, thereby utilizes all available pharmacy and laboratory data. Moreover, unlike the interactive expert systems developed for the psychiatric clinic, OVERSEER does not require extensive data entry by the clinician. Consequently, the chief benefit of OVERSEER's monitoring approach is the unobtrusive manner in which it evaluates treatment and patient responses and provides information regarding patient management.

Diamond Eye: a distributed architecture for image data mining

NASA Astrophysics Data System (ADS)

Burl, Michael C.; Fowlkes, Charless; Roden, Joe; Stechert, Andre; Mukhtar, Saleem

1999-02-01

Diamond Eye is a distributed software architecture, which enables users (scientists) to analyze large image collections by interacting with one or more custom data mining servers via a Java applet interface. Each server is coupled with an object-oriented database and a computational engine, such as a network of high-performance workstations. The database provides persistent storage and supports querying of the 'mined' information. The computational engine provides parallel execution of expensive image processing, object recognition, and query-by-content operations. Key benefits of the Diamond Eye architecture are: (1) the design promotes trial evaluation of advanced data mining and machine learning techniques by potential new users (all that is required is to point a web browser to the appropriate URL), (2) software infrastructure that is common across a range of science mining applications is factored out and reused, and (3) the system facilitates closer collaborations between algorithm developers and domain experts.

Detection of functionally important regions in "hypothetical proteins" of known structure.

PubMed

Nimrod, Guy; Schushan, Maya; Steinberg, David M; Ben-Tal, Nir

2008-12-10

Structural genomics initiatives provide ample structures of "hypothetical proteins" (i.e., proteins of unknown function) at an ever increasing rate. However, without function annotation, this structural goldmine is of little use to biologists who are interested in particular molecular systems. To this end, we used (an improved version of) the PatchFinder algorithm for the detection of functional regions on the protein surface, which could mediate its interactions with, e.g., substrates, ligands, and other proteins. Examination, using a data set of annotated proteins, showed that PatchFinder outperforms similar methods. We collected 757 structures of hypothetical proteins and their predicted functional regions in the N-Func database. Inspection of several of these regions demonstrated that they are useful for function prediction. For example, we suggested an interprotein interface and a putative nucleotide-binding site. A web-server implementation of PatchFinder and the N-Func database are available at http://patchfinder.tau.ac.il/.

Design document for the Surface Currents Data Base (SCDB) Management System (SCDBMS), version 1.0

NASA Technical Reports Server (NTRS)

Krisnnamagaru, Ramesh; Cesario, Cheryl; Foster, M. S.; Das, Vishnumohan

1994-01-01

The Surface Currents Database Management System (SCDBMS) provides access to the Surface Currents Data Base (SCDB) which is maintained by the Naval Oceanographic Office (NAVOCEANO). The SCDBMS incorporates database technology in providing seamless access to surface current data. The SCDBMS is an interactive software application with a graphical user interface (GUI) that supports user control of SCDBMS functional capabilities. The purpose of this document is to define and describe the structural framework and logistical design of the software components/units which are integrated into the major computer software configuration item (CSCI) identified as the SCDBMS, Version 1.0. The preliminary design is based on functional specifications and requirements identified in the governing Statement of Work prepared by the Naval Oceanographic Office (NAVOCEANO) and distributed as a request for proposal by the National Aeronautics and Space Administration (NASA).

A Framework for Mapping User-Designed Forms to Relational Databases

ERIC Educational Resources Information Center

Khare, Ritu

2011-01-01

In the quest for database usability, several applications enable users to design custom forms using a graphical interface, and forward engineer the forms into new databases. The path-breaking aspect of such applications is that users are completely shielded from the technicalities of database creation. Despite this innovation, the process of…

The Web-Database Connection Tools for Sharing Information on the Campus Intranet.

ERIC Educational Resources Information Center

Thibeault, Nancy E.

This paper evaluates four tools for creating World Wide Web pages that interface with Microsoft Access databases: DB Gateway, Internet Database Assistant (IDBA), Microsoft Internet Database Connector (IDC), and Cold Fusion. The system requirements and features of each tool are discussed. A sample application, "The Virtual Help Desk"…

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

How I do it: a practical database management system to assist clinical research teams with data collection, organization, and reporting.

PubMed

Lee, Howard; Chapiro, Julius; Schernthaner, Rüdiger; Duran, Rafael; Wang, Zhijun; Gorodetski, Boris; Geschwind, Jean-François; Lin, MingDe

2015-04-01

The objective of this study was to demonstrate that an intra-arterial liver therapy clinical research database system is a more workflow efficient and robust tool for clinical research than a spreadsheet storage system. The database system could be used to generate clinical research study populations easily with custom search and retrieval criteria. A questionnaire was designed and distributed to 21 board-certified radiologists to assess current data storage problems and clinician reception to a database management system. Based on the questionnaire findings, a customized database and user interface system were created to perform automatic calculations of clinical scores including staging systems such as the Child-Pugh and Barcelona Clinic Liver Cancer, and facilitates data input and output. Questionnaire participants were favorable to a database system. The interface retrieved study-relevant data accurately and effectively. The database effectively produced easy-to-read study-specific patient populations with custom-defined inclusion/exclusion criteria. The database management system is workflow efficient and robust in retrieving, storing, and analyzing data. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

PubMed

Baumbach, Jan; Wittkop, Tobias; Rademacher, Katrin; Rahmann, Sven; Brinkrolf, Karina; Tauch, Andreas

2007-04-30

CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.

The IMUTUS interactive music tuition system

NASA Astrophysics Data System (ADS)

Tambouratzis, George; Bakamidis, Stelios; Dologlou, Ioannis; Carayannis, George; Dendrinos, Markos

2002-05-01

This presentation focuses on the IMUTUS project, which concerns the creation of an innovative method for training users on traditional musical instruments with no MIDI (Musical Instrument Digital Interface) output. The entities collaborating in IMUTUS are ILSP (coordinator), EXODUS, SYSTEMA, DSI, SMF, GRAME, and KTH. The IMUTUS effectiveness is enhanced via an advanced user interface incorporating multimedia techniques. Internet plays a pivotal role during training, the student receiving guidance over the net from a specially created teacher group. Interactiveness is emphasized via automatic-scoring tools, which provide fast yet accurate feedback to the user, while virtual reality methods assist the student in perfecting his technique. IMUTUS incorporates specialized recognition technology for the transformation of acoustic signals and music scores to MIDI format and incorporation in the training process. This process is enhanced by periodically enriching the score database, while customization to each user's requirements is supported. This work is partially supported by European Community under the Information Society Technology (IST) RTD programme. The authors are solely responsible for the content of this communication. It does not represent the opinion of the European Community, and the European Community is not responsible for any use that might be made of data appearing therein.

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

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

The crustal dynamics intelligent user interface anthology

NASA Technical Reports Server (NTRS)

Short, Nicholas M., Jr.; Campbell, William J.; Roelofs, Larry H.; Wattawa, Scott L.

1987-01-01

The National Space Science Data Center (NSSDC) has initiated an Intelligent Data Management (IDM) research effort which has, as one of its components, the development of an Intelligent User Interface (IUI). The intent of the IUI is to develop a friendly and intelligent user interface service based on expert systems and natural language processing technologies. The purpose of such a service is to support the large number of potential scientific and engineering users that have need of space and land-related research and technical data, but have little or no experience in query languages or understanding of the information content or architecture of the databases of interest. This document presents the design concepts, development approach and evaluation of the performance of a prototype IUI system for the Crustal Dynamics Project Database, which was developed using a microcomputer-based expert system tool (M. 1), the natural language query processor THEMIS, and the graphics software system GSS. The IUI design is based on a multiple view representation of a database from both the user and database perspective, with intelligent processes to translate between the views.

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

PubMed Central

Berthold, Michael R.; Hedrick, Michael P.; Gilson, Michael K.

2015-01-01

Today’s large, public databases of protein–small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses. Thus, we describe a collection of KNIME workflows that access BindingDB data via RESTful webservices and, for more intensive queries, via a local distillation of the full BindingDB dataset. We focus in particular on the KNIME implementation of knowledge-based tools to generate informed hypotheses regarding protein targets of bioactive compounds, based on notions of chemical similarity. A number of variants of this basic approach are tested for seven existing drugs with relatively ill-defined therapeutic targets, leading to replication of some previously confirmed results and discovery of new, high-quality hits. Implications for future development are discussed. Database URL: www.bindingdb.org PMID:26384374

Yucca Mountain licensing support network archive assistant.

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

Dunlavy, Daniel M.; Bauer, Travis L.; Verzi, Stephen J.

2008-03-01

This report describes the Licensing Support Network (LSN) Assistant--a set of tools for categorizing e-mail messages and documents, and investigating and correcting existing archives of categorized e-mail messages and documents. The two main tools in the LSN Assistant are the LSN Archive Assistant (LSNAA) tool for recategorizing manually labeled e-mail messages and documents and the LSN Realtime Assistant (LSNRA) tool for categorizing new e-mail messages and documents. This report focuses on the LSNAA tool. There are two main components of the LSNAA tool. The first is the Sandia Categorization Framework, which is responsible for providing categorizations for documents in anmore » archive and storing them in an appropriate Categorization Database. The second is the actual user interface, which primarily interacts with the Categorization Database, providing a way for finding and correcting categorizations errors in the database. A procedure for applying the LSNAA tool and an example use case of the LSNAA tool applied to a set of e-mail messages are provided. Performance results of the categorization model designed for this example use case are presented.« less

Interfaces and Expert Systems for Online Retrieval.

ERIC Educational Resources Information Center

Kehoe, Cynthia A.

1985-01-01

This paper reviews the history of separate online system interfaces which led to efforts to develop expert systems for searching databases, particularly for end users, and introduces the research on such expert systems. Appended is a bibliography of sources on interfaces and expert systems for online retrieval. (Author/EJS)

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

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.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.

PubMed

Attimonelli, Marcella; Catalano, Domenico; Gissi, Carmela; Grillo, Giorgio; Licciulli, Flavio; Liuni, Sabino; Santamaria, Monica; Pesole, Graziano; Saccone, Cecilia

2002-01-01

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organelle genomes. Mitochondrial genomes have been extensively sequenced and analysed and data have been collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc, a database containing detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa. The MitoNuc database can be retrieved through SRS and is available via the web site http://bighost.area.ba.cnr.it/mitochondriome where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, links to other mitochondrial sites and related information, are available. The MitoAln database, related to MitoNuc in the previous release, reporting the multiple alignments of the relevant homologous protein coding regions, is no longer supported in the present release. In order to keep the links among entries in MitoNuc from homologous proteins, a new field in the database has been defined: the cluster identifier, an alpha numeric code used to identify each cluster of homologous proteins. A comment field derived from the corresponding SWISS-PROT entry has been introduced; this reports clinical data related to dysfunction of the protein. The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented.

Section-constrained local geological interface dynamic updating method based on the HRBF surface

NASA Astrophysics Data System (ADS)

Guo, Jiateng; Wu, Lixin; Zhou, Wenhui; Li, Chaoling; Li, Fengdan

2018-02-01

Boundaries, attitudes and sections are the most common data acquired from regional field geological surveys, and they are used for three-dimensional (3D) geological modelling. However, constructing topologically consistent 3D geological models from rapid and automatic regional modelling with convenient local modifications remains unresolved. In previous works, the Hermite radial basis function (HRBF) surface was introduced for the simulation of geological interfaces from geological boundaries and attitudes, which allows 3D geological models to be automatically extracted from the modelling area by the interfaces. However, the reasonability and accuracy of non-supervised subsurface modelling is limited without further modifications generated through explanations and analyses performed by geology experts. In this paper, we provide flexible and convenient manual interactive manipulation tools for geologists to sketch constraint lines, and these tools may help geologists transform and apply their expert knowledge to the models. In the modified modelling workflow, the geological sections were treated as auxiliary constraints to construct more reasonable 3D geological models. The geometric characteristics of section lines were abstracted to coordinates and normal vectors, and along with the transformed coordinates and vectors from boundaries and attitudes, these characteristics were adopted to co-calculate the implicit geological surface function parameters of the HRBF equations and form constrained geological interfaces from topographic (boundaries and attitudes) and subsurface data (sketched sections). Based on this new modelling method, a prototype system was developed, in which the section lines could be imported from databases or interactively sketched, and the models could be immediately updated after the new constraints were added. Experimental comparisons showed that all boundary, attitude and section data are well represented in the constrained models, which are consistent with expert explanations and help improve the quality of the models.

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.

Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier.

PubMed

Sriwastava, Brijesh K; Basu, Subhadip; Maulik, Ujjwal

2015-01-01

Predicting residues that participate in protein-protein interactions (PPI) helps to identify, which amino acids are located at the interface. In this paper, we show that the performance of the classical support vector machine (SVM) algorithm can further be improved with the use of a custom-designed fuzzy membership function, for the partner-specific PPI interface prediction problem. We evaluated the performances of both classical SVM and fuzzy SVM (F-SVM) on the PPI databases of three different model proteomes of Homo sapiens, Escherichia coli and Saccharomyces Cerevisiae and calculated the statistical significance of the developed F-SVM over classical SVM algorithm. We also compared our performance with the available state-of-the-art fuzzy methods in this domain and observed significant performance improvements. To predict interaction sites in protein complexes, local composition of amino acids together with their physico-chemical characteristics are used, where the F-SVM based prediction method exploits the membership function for each pair of sequence fragments. The average F-SVM performance (area under ROC curve) on the test samples in 10-fold cross validation experiment are measured as 77.07, 78.39, and 74.91 percent for the aforementioned organisms respectively. Performances on independent test sets are obtained as 72.09, 73.24 and 82.74 percent respectively. The software is available for free download from http://code.google.com/p/cmater-bioinfo.

VIEWCACHE: An incremental pointer-base access method for distributed databases. Part 1: The universal index system design document. Part 2: The universal index system low-level design document. Part 3: User's guide. Part 4: Reference manual. Part 5: UIMS test suite

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos

1992-01-01

The goal of the Universal Index System (UIS), is to provide an easy-to-use and reliable interface to many different kinds of database systems. The impetus for this system was to simplify database index management for users, thus encouraging the use of indexes. As the idea grew into an actual system design, the concept of increasing database performance by facilitating the use of time-saving techniques at the user level became a theme for the project. This Final Report describes the Design, the Implementation of UIS, and its Language Interfaces. It also includes the User's Guide and the Reference Manual.

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

PubMed Central

Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet. PMID:28695067

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis.

PubMed

Costa, Raquel L; Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet.

Designing Interactions for Learning: Physicality, Interactivity, and Interface Effects in Digital Environments

ERIC Educational Resources Information Center

Hoffman, Daniel L.

2013-01-01

The purpose of the study is to better understand the role of physicality, interactivity, and interface effects in learning with digital content. Drawing on work in cognitive science, human-computer interaction, and multimedia learning, the study argues that interfaces that promote physical interaction can provide "conceptual leverage"…

Comparative study on the customization of natural language interfaces to databases.

PubMed

Pazos R, Rodolfo A; Aguirre L, Marco A; González B, Juan J; Martínez F, José A; Pérez O, Joaquín; Verástegui O, Andrés A

2016-01-01

In the last decades the popularity of natural language interfaces to databases (NLIDBs) has increased, because in many cases information obtained from them is used for making important business decisions. Unfortunately, the complexity of their customization by database administrators make them difficult to use. In order for a NLIDB to obtain a high percentage of correctly translated queries, it is necessary that it is correctly customized for the database to be queried. In most cases the performance reported in NLIDB literature is the highest possible; i.e., the performance obtained when the interfaces were customized by the implementers. However, for end users it is more important the performance that the interface can yield when the NLIDB is customized by someone different from the implementers. Unfortunately, there exist very few articles that report NLIDB performance when the NLIDBs are not customized by the implementers. This article presents a semantically-enriched data dictionary (which permits solving many of the problems that occur when translating from natural language to SQL) and an experiment in which two groups of undergraduate students customized our NLIDB and English language frontend (ELF), considered one of the best available commercial NLIDBs. The experimental results show that, when customized by the first group, our NLIDB obtained a 44.69 % of correctly answered queries and ELF 11.83 % for the ATIS database, and when customized by the second group, our NLIDB attained 77.05 % and ELF 13.48 %. The performance attained by our NLIDB, when customized by ourselves was 90 %.

Kaizen newspaper

NASA Technical Reports Server (NTRS)

Shearer, Scott C. (Inventor); Proferes, John Nicholas (Inventor); Baker, Sr., Mitchell D. (Inventor); Reilly, Kenneth B. (Inventor); Tiwari, Vijai K. (Inventor)

2013-01-01

Systems, computer program products, and methods are disclosed for tracking an improvement event. An embodiment includes an event interface configured to receive a plurality of entries related to each of a plurality of improvement events. The plurality of entries includes a project identifier for the improvement event, a creation date, an objective, an action related to reaching the objective, and a first deadline related to the improvement event. A database interface is configured to store the plurality of entries in an event database.

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.

A Natural Language Interface to Databases

NASA Technical Reports Server (NTRS)

Ford, D. R.

1990-01-01

The development of a Natural Language Interface (NLI) is presented which is semantic-based and uses Conceptual Dependency representation. The system was developed using Lisp and currently runs on a Symbolics Lisp machine.

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

PubMed Central

Kinjo, Akira R.; Yamashita, Reiko; Nakamura, Haruki

2010-01-01

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/ PMID:20798081

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

PubMed

Kinjo, Akira R; Yamashita, Reiko; Nakamura, Haruki

2010-08-25

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/

Database Software for the 1990s.

ERIC Educational Resources Information Center

Beiser, Karl

1990-01-01

Examines trends in the design of database management systems for microcomputers and predicts developments that may occur in the next decade. Possible developments are discussed in the areas of user interfaces, database programing, library systems, the use of MARC data, CD-ROM applications, artificial intelligence features, HyperCard, and…

THE ECOTOX DATABASE AND ECOLOGICAL SOIL SCREENING LEVEL (ECO-SSL) WEB SITES

EPA Science Inventory

The EPA's ECOTOX database (http://www.epa.gov/ecotox/) provides a web browser search interface for locating aquatic and terrestrial toxic effects information. Data on more than 8100 chemicals and 5700 terrestrial and aquatic species are included in the database. Information is ...

Six Online Periodical Databases: A Librarian's View.

ERIC Educational Resources Information Center

Willems, Harry

1999-01-01

Compares the following World Wide Web-based periodical databases, focusing on their usefulness in K-12 school libraries: EBSCO, Electric Library, Facts on File, SIRS, Wilson, and UMI. Search interfaces, display options, help screens, printing, home access, copyright restrictions, database administration, and making a decision are discussed. A…

Usability Evaluation Methods for Gesture-Based Games: A Systematic Review.

PubMed

Simor, Fernando Winckler; Brum, Manoela Rogofski; Schmidt, Jaison Dairon Ebertz; Rieder, Rafael; De Marchi, Ana Carolina Bertoletti

2016-10-04

Gestural interaction systems are increasingly being used, mainly in games, expanding the idea of entertainment and providing experiences with the purpose of promoting better physical and/or mental health. Therefore, it is necessary to establish mechanisms for evaluating the usability of these interfaces, which make gestures the basis of interaction, to achieve a balance between functionality and ease of use. This study aims to present the results of a systematic review focused on usability evaluation methods for gesture-based games, considering devices with motion-sensing capability. We considered the usability methods used, the common interface issues, and the strategies adopted to build good gesture-based games. The research was centered on four electronic databases: IEEE, Association for Computing Machinery (ACM), Springer, and Science Direct from September 4 to 21, 2015. Within 1427 studies evaluated, 10 matched the eligibility criteria. As a requirement, we considered studies about gesture-based games, Kinect and/or Wii as devices, and the use of a usability method to evaluate the user interface. In the 10 studies found, there was no standardization in the methods because they considered diverse analysis variables. Heterogeneously, authors used different instruments to evaluate gesture-based interfaces and no default approach was proposed. Questionnaires were the most used instruments (70%, 7/10), followed by interviews (30%, 3/10), and observation and video recording (20%, 2/10). Moreover, 60% (6/10) of the studies used gesture-based serious games to evaluate the performance of elderly participants in rehabilitation tasks. This highlights the need for creating an evaluation protocol for older adults to provide a user-friendly interface according to the user's age and limitations. Through this study, we conclude this field is in need of a usability evaluation method for serious games, especially games for older adults, and that the definition of a methodology and a test protocol may offer the user more comfort, welfare, and confidence.

Usability Evaluation Methods for Gesture-Based Games: A Systematic Review

PubMed Central

Simor, Fernando Winckler; Brum, Manoela Rogofski; Schmidt, Jaison Dairon Ebertz; De Marchi, Ana Carolina Bertoletti

2016-01-01

Background Gestural interaction systems are increasingly being used, mainly in games, expanding the idea of entertainment and providing experiences with the purpose of promoting better physical and/or mental health. Therefore, it is necessary to establish mechanisms for evaluating the usability of these interfaces, which make gestures the basis of interaction, to achieve a balance between functionality and ease of use. Objective This study aims to present the results of a systematic review focused on usability evaluation methods for gesture-based games, considering devices with motion-sensing capability. We considered the usability methods used, the common interface issues, and the strategies adopted to build good gesture-based games. Methods The research was centered on four electronic databases: IEEE, Association for Computing Machinery (ACM), Springer, and Science Direct from September 4 to 21, 2015. Within 1427 studies evaluated, 10 matched the eligibility criteria. As a requirement, we considered studies about gesture-based games, Kinect and/or Wii as devices, and the use of a usability method to evaluate the user interface. Results In the 10 studies found, there was no standardization in the methods because they considered diverse analysis variables. Heterogeneously, authors used different instruments to evaluate gesture-based interfaces and no default approach was proposed. Questionnaires were the most used instruments (70%, 7/10), followed by interviews (30%, 3/10), and observation and video recording (20%, 2/10). Moreover, 60% (6/10) of the studies used gesture-based serious games to evaluate the performance of elderly participants in rehabilitation tasks. This highlights the need for creating an evaluation protocol for older adults to provide a user-friendly interface according to the user’s age and limitations. Conclusions Through this study, we conclude this field is in need of a usability evaluation method for serious games, especially games for older adults, and that the definition of a methodology and a test protocol may offer the user more comfort, welfare, and confidence. PMID:27702737

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

Integration of Evidence Base into a Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

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

2011-01-01

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

A Brief Review of RNA–Protein Interaction Database Resources

PubMed Central

Yi, Ying; Zhao, Yue; Huang, Yan; Wang, Dong

2017-01-01

RNA–Protein interactions play critical roles in various biological processes. By collecting and analyzing the RNA–Protein interactions and binding sites from experiments and predictions, RNA–Protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. Here, we briefly review several widely used RNA–Protein interaction database resources developed in recent years to provide a guide of these databases. The content and major functions in databases are presented. The brief description of database helps users to quickly choose the database containing information they interested. In short, these RNA–Protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA–Protein interactions. PMID:29657278

VitisExpDB: a database resource for grape functional genomics.

PubMed

Doddapaneni, Harshavardhan; Lin, Hong; Walker, M Andrew; Yao, Jiqiang; Civerolo, Edwin L

2008-02-28

The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic information on different Vitis species and cultivars, including the European grape vine, Vitis vinifera. Our goal is to develop a comprehensive web data source for Vitaceae. VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for V. vinifera and non-vinifera grape species and varieties. Currently, the database stores approximately 320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of approximately 20,000 non-redundant set of ESTs. Finally, the database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online bioinformatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database. The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website http://cropdisease.ars.usda.gov/vitis_at/main-page.htm.

VitisExpDB: A database resource for grape functional genomics

PubMed Central

Doddapaneni, Harshavardhan; Lin, Hong; Walker, M Andrew; Yao, Jiqiang; Civerolo, Edwin L

2008-01-01

Background The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic information on different Vitis species and cultivars, including the European grape vine, Vitis vinifera. Our goal is to develop a comprehensive web data source for Vitaceae. Description VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for V. vinifera and non-vinifera grape species and varieties. Currently, the database stores ~320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of ~20,000 non-redundant set of ESTs. Finally, the database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online bioinformatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database. Conclusion The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website . PMID:18307813

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo.

PubMed

Uhlirova, Hana; Tian, Peifang; Kılıç, Kıvılcım; Thunemann, Martin; Sridhar, Vishnu B; Chmelik, Radim; Bartsch, Hauke; Dale, Anders M; Devor, Anna; Saisan, Payam A

2018-05-04

The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain and process these data. However, the majority of experimental data, especially from individual studies of regular-sized laboratories never reach wider research community. A graphical user interface (GUI) engine called Neurovascular Network Explorer 2.0 (NNE 2.0) has been created as a tool for simple and low-cost sharing and exploring of vascular imaging data. NNE 2.0 interacts with a database containing optogenetically-evoked dilation/constriction time-courses of individual vessels measured in mice somatosensory cortex in vivo by 2-photon microscopy. NNE 2.0 enables selection and display of the time-courses based on different criteria (subject, branching order, cortical depth, vessel diameter, arteriolar tree) as well as simple mathematical manipulation (e.g. averaging, peak-normalization) and data export. It supports visualization of the vascular network in 3D and enables localization of the individual functional vessel diameter measurements within vascular trees. NNE 2.0, its source code, and the corresponding database are freely downloadable from UCSD Neurovascular Imaging Laboratory website 1 . The source code can be utilized by the users to explore the associated database or as a template for databasing and sharing their own experimental results provided the appropriate format.

CoReCG: a comprehensive database of genes associated with colon-rectal cancer

PubMed Central

Agarwal, Rahul; Kumar, Binayak; Jayadev, Msk; Raghav, Dhwani; Singh, Ashutosh

2016-01-01

Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. Database URL: lms.snu.edu.in/corecg PMID:27114494

Interactive Tools to Access the HELCATS Catalogues

NASA Astrophysics Data System (ADS)

Rouillard, Alexis; Plotnikov, Illya; Pinto, Rui; Génot, Vincent; Bouchemit, Myriam; Davies, Jackie

2017-04-01

The propagation tool is a web-based interface written in java that allows users to propagate Coronal Mass Ejections (CMEs), Corotating Interaction Regions (CIRs) and Solar Energetic Particles (SEPs) in the inner heliosphere. The tool displays unique datasets and catalogues through a 2-D visualisation of the trajectories of these heliospheric structures in relation to the orbital position of probes/planets and the pointing direction and extent of different imaging instruments. Summary plots of in-situ data or images of the solar corona and planetary aurorae stored at the CDPP, MEDOC and APIS databases, respectively, can be used to verify the presence of heliospheric structures at the estimated launch or impact times. A great novelty of the tool is the immediate visualisation of J-maps and the possibility to superpose on these maps the HELCATS CME and CIR catalogues.

Interactive Tools to Access the HELCATS Catalogues

NASA Astrophysics Data System (ADS)

Rouillard, A.; Génot, V.; Bouchemit, M.; Pinto, R.

2017-09-01

The propagation tool is a web-based interface written in java that allows users to propagate Coronal Mass Ejections (CMEs), Corotating Interaction Regions (CIRs) and Solar Energetic Particles (SEPs) in the inner heliosphere. The tool displays unique datasets and catalogues through a 2-D visualisation of the trajectories of these heliospheric structures in relation to the orbital position of probes/planets and the pointing direction and extent of different imaging instruments. Summary plots of in-situ data or images of the solar corona and planetary aurorae stored at the CDPP, MEDOC and APIS databases, respectively, can be used to verify the presence of heliospheric structures at the estimated launch or impact times. A great novelty of the tool is the immediate visualisation of J-maps and the possibility to superpose on these maps the HELCATS CME and CIR catalogues.

Spacecraft Orbit Design and Analysis (SODA). Version 2.0: User's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.; Davis, John S.; Zsoldos, Jeffrey S.

1991-01-01

The Spacecraft Orbit Design and Analysis (SODA) computer program, Version 2.0, is discussed. SODA is a spaceflight mission planning system that consists of six program modules integrated around a common database and user interface. SODA runs on a VAX/VMS computer with an Evans and Sutherland PS300 graphics workstation. In the current version, three program modules produce an interactive three dimensional animation of one or more satellites in planetary orbit. Satellite visibility and sensor coverage capabilities are also provided. Circular and rectangular, off nadir, fixed and scanning sensors are supported. One module produces an interactive three dimensional animation of the solar system. Another module calculates cumulative satellite sensor coverage and revisit time for one or more satellites. Currently, Earth, Moon, and Mars systems are supported for all modules except the solar system module.

Acquisition of ICU data: concepts and demands.

PubMed

Imhoff, M

1992-12-01

As the issue of data overload is a problem in critical care today, it is of utmost importance to improve acquisition, storage, integration, and presentation of medical data, which appears only feasible with the help of bedside computers. The data originates from four major sources: (1) the bedside medical devices, (2) the local area network (LAN) of the ICU, (3) the hospital information system (HIS) and (4) manual input. All sources differ markedly in quality and quantity of data and in the demands of the interfaces between source of data and patient database. The demands for data acquisition from bedside medical devices, ICU-LAN and HIS concentrate on technical problems, such as computational power, storage capacity, real-time processing, interfacing with different devices and networks and the unmistakable assignment of data to the individual patient. The main problem of manual data acquisition is the definition and configuration of the user interface that must allow the inexperienced user to interact with the computer intuitively. Emphasis must be put on the construction of a pleasant, logical and easy-to-handle graphical user interface (GUI). Short response times will require high graphical processing capacity. Moreover, high computational resources are necessary in the future for additional interfacing devices such as speech recognition and 3D-GUI. Therefore, in an ICU environment the demands for computational power are enormous. These problems are complicated by the urgent need for friendly and easy-to-handle user interfaces. Both facts place ICU bedside computing at the vanguard of present and future workstation development leaving no room for solutions based on traditional concepts of personal computers.(ABSTRACT TRUNCATED AT 250 WORDS)

Development of the Global Earthquake Model’s neotectonic fault database

USGS Publications Warehouse

Christophersen, Annemarie; Litchfield, Nicola; Berryman, Kelvin; Thomas, Richard; Basili, Roberto; Wallace, Laura; Ries, William; Hayes, Gavin P.; Haller, Kathleen M.; Yoshioka, Toshikazu; Koehler, Richard D.; Clark, Dan; Wolfson-Schwehr, Monica; Boettcher, Margaret S.; Villamor, Pilar; Horspool, Nick; Ornthammarath, Teraphan; Zuñiga, Ramon; Langridge, Robert M.; Stirling, Mark W.; Goded, Tatiana; Costa, Carlos; Yeats, Robert

2015-01-01

The Global Earthquake Model (GEM) aims to develop uniform, openly available, standards, datasets and tools for worldwide seismic risk assessment through global collaboration, transparent communication and adapting state-of-the-art science. GEM Faulted Earth (GFE) is one of GEM’s global hazard module projects. This paper describes GFE’s development of a modern neotectonic fault database and a unique graphical interface for the compilation of new fault data. A key design principle is that of an electronic field notebook for capturing observations a geologist would make about a fault. The database is designed to accommodate abundant as well as sparse fault observations. It features two layers, one for capturing neotectonic faults and fold observations, and the other to calculate potential earthquake fault sources from the observations. In order to test the flexibility of the database structure and to start a global compilation, five preexisting databases have been uploaded to the first layer and two to the second. In addition, the GFE project has characterised the world’s approximately 55,000 km of subduction interfaces in a globally consistent manner as a basis for generating earthquake event sets for inclusion in earthquake hazard and risk modelling. Following the subduction interface fault schema and including the trace attributes of the GFE database schema, the 2500-km-long frontal thrust fault system of the Himalaya has also been characterised. We propose the database structure to be used widely, so that neotectonic fault data can make a more complete and beneficial contribution to seismic hazard and risk characterisation globally.

System for Performing Single Query Searches of Heterogeneous and Dispersed Databases

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Okimura, Takeshi (Inventor); Gurram, Mohana M. (Inventor); Tran, Vu Hoang (Inventor); Knight, Christopher D. (Inventor); Trinh, Anh Ngoc (Inventor)

2017-01-01

The present invention is a distributed computer system of heterogeneous databases joined in an information grid and configured with an Application Programming Interface hardware which includes a search engine component for performing user-structured queries on multiple heterogeneous databases in real time. This invention reduces overhead associated with the impedance mismatch that commonly occurs in heterogeneous database queries.

The Use of AJAX in Searching a Bibliographic Database: A Case Study of the Italian Biblioteche Oggi Database

ERIC Educational Resources Information Center

Cavaleri, Piero

2008-01-01

Purpose: The purpose of this paper is to describe the use of AJAX for searching the Biblioteche Oggi database of bibliographic records. Design/methodology/approach: The paper is a demonstration of how bibliographic database single page interfaces allow the implementation of more user-friendly features for social and collaborative tasks. Findings:…

CottonDB: A resource for cotton genome research

USDA-ARS?s Scientific Manuscript database

CottonDB (http://cottondb.org/) is a database and web resource for cotton genomic and genetic research. Created in 1995, CottonDB was among the first plant genome databases established by the USDA-ARS. Accessed through a website interface, the database aims to be a convenient, inclusive medium of ...

Electronic Reference Library: Silverplatter's Database Networking Solution.

ERIC Educational Resources Information Center

Millea, Megan

Silverplatter's Electronic Reference Library (ERL) provides wide area network access to its databases using TCP/IP communications and client-server architecture. ERL has two main components: The ERL clients (retrieval interface) and the ERL server (search engines). ERL clients provide patrons with seamless access to multiple databases on multiple…

Constructing Effective Search Strategies for Electronic Searching.

ERIC Educational Resources Information Center

Flanagan, Lynn; Parente, Sharon Campbell

Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

The International Space Station Comparative Maintenance Analysis(CMAM)

DTIC Science & Technology

2004-09-01

External Component • Entire ORU Database 2. Database Connectivity The CMAM ORU database consists of three tables: an ORU master parts list , an ISS...Flight table, and an ISS Subsystem table. The ORU master parts list and the ISS Flight table can be updated or modified from the CMAM user interface

A Data Definition Language for GLAD (Graphic Language for Databases).

DTIC Science & Technology

1986-06-20

basic premises. These principles state that a DBMS interface must be descriptive, powerful, easy-to use and easy to learn . This thesis proposes a data...basic premises. These principles state that a DBMS interface must be descriptive, powerful, easy to use and easy to learn . This thesis proposes a data...criteria will be the most successful. 9 If a system is hard to learn , of those capable of mastering the system few may be willing to expend the time and

Optimizing the NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maa, Ming-Hokng

1996-01-01

The NASA Technical Report Server (NTRS), a World Wide Web report distribution NASA technical publications service, is modified for performance enhancement, greater protocol support, and human interface optimization. Results include: Parallel database queries, significantly decreasing user access times by an average factor of 2.3; access from clients behind firewalls and/ or proxies which truncate excessively long Uniform Resource Locators (URLs); access to non-Wide Area Information Server (WAIS) databases and compatibility with the 239-50.3 protocol; and a streamlined user interface.

Interactive Learning Modules: Enabling Near Real-Time Oceanographic Data Use In Undergraduate Education

NASA Astrophysics Data System (ADS)

Kilb, D. L.; Fundis, A. T.; Risien, C. M.

2012-12-01

The focus of the Education and Public Engagement (EPE) component of the NSF's Ocean Observatories Initiative (OOI) is to provide a new layer of cyber-interactivity for undergraduate educators to bring near real-time data from the global ocean into learning environments. To accomplish this, we are designing six online services including: 1) visualization tools, 2) a lesson builder, 3) a concept map builder, 4) educational web services (middleware), 5) collaboration tools and 6) an educational resource database. Here, we report on our Fall 2012 release that includes the first four of these services: 1) Interactive visualization tools allow users to interactively select data of interest, display the data in various views (e.g., maps, time-series and scatter plots) and obtain statistical measures such as mean, standard deviation and a regression line fit to select data. Specific visualization tools include a tool to compare different months of data, a time series explorer tool to investigate the temporal evolution of select data parameters (e.g., sea water temperature or salinity), a glider profile tool that displays ocean glider tracks and associated transects, and a data comparison tool that allows users to view the data either in scatter plot view comparing one parameter with another, or in time series view. 2) Our interactive lesson builder tool allows users to develop a library of online lesson units, which are collaboratively editable and sharable and provides starter templates designed from learning theory knowledge. 3) Our interactive concept map tool allows the user to build and use concept maps, a graphical interface to map the connection between concepts and ideas. This tool also provides semantic-based recommendations, and allows for embedding of associated resources such as movies, images and blogs. 4) Education web services (middleware) will provide an educational resource database API.

Data Management Applications for the Service Preparation Subsystem

NASA Technical Reports Server (NTRS)

Luong, Ivy P.; Chang, George W.; Bui, Tung; Allen, Christopher; Malhotra, Shantanu; Chen, Fannie C.; Bui, Bach X.; Gutheinz, Sandy C.; Kim, Rachel Y.; Zendejas, Silvino C.;

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

XOP: a multiplatform graphical user interface for synchrotron radiation spectral and optics calculations

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Dejus, Roger J.

1997-11-01

XOP (X-ray OPtics utilities) is a graphical user interface (GUI) created to execute several computer programs that calculate the basic information needed by a synchrotron beamline scientist (designer or experimentalist). Typical examples of such calculations are: insertion device (undulator or wiggler) spectral and angular distributions, mirror and multilayer reflectivities, and crystal diffraction profiles. All programs are provided to the user under a unified GUI, which greatly simplifies their execution. The XOP optics applications (especially mirror calculations) take their basic input (optical constants, compound and mixture tables) from a flexible file-oriented database, which allows the user to select data from a large number of choices and also to customize their own data sets. XOP includes many mathematical and visualization capabilities. It also permits the combination of reflectivities from several mirrors and filters, and their effect, onto a source spectrum. This feature is very useful when calculating thermal load on a series of optical elements. The XOP interface is written in the IDL (Interactive Data Language). An embedded version of XOP, which freely runs under most Unix platforms (HP, Sun, Dec, Linux, etc) and under Windows95 and NT, is available upon request.

EuPathDB: the eukaryotic pathogen genomics database resource

PubMed Central

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

2017-01-01

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

ISAAC - InterSpecies Analysing Application using Containers.

PubMed

Baier, Herbert; Schultz, Jörg

2014-01-15

Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large scale analysis. Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories. To fill this niche, we have developed ISAAC, the InterSpecies Analysing Application using Containers. The central idea of this web based tool is to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. Furthermore, one can easily switch back to previous states and perform new analyses. Currently, sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. As todays research usually is performed in larger teams and consortia, ISAAC provides group based functionalities. Here, sets as well as results of analyses can be exchanged between members of groups. ISAAC fills the gap between primary databases and tools for the analysis of large gene lists. With its highly modular, JavaEE based design, the implementation of new modules is straight forward. Furthermore, ISAAC comes with an extensive web-based administration interface including tools for the integration of third party data. Thus, a local installation is easily feasible. In summary, ISAAC is tailor made for highly explorative interactive analyses of gene, transcript and protein sets in a collaborative environment.

The Brain Database: A Multimedia Neuroscience Database for Research and Teaching

PubMed Central

Wertheim, Steven L.

1989-01-01

The Brain Database is an information tool designed to aid in the integration of clinical and research results in neuroanatomy and regional biochemistry. It can handle a wide range of data types including natural images, 2 and 3-dimensional graphics, video, numeric data and text. It is organized around three main entities: structures, substances and processes. The database will support a wide variety of graphical interfaces. Two sample interfaces have been made. This tool is intended to serve as one component of a system that would allow neuroscientists and clinicians 1) to represent clinical and experimental data within a common framework 2) to compare results precisely between experiments and among laboratories, 3) to use computing tools as an aid in collaborative work and 4) to contribute to a shared and accessible body of knowledge about the nervous system.

Incorporating client-server database architecture and graphical user interface into outpatient medical records.

PubMed Central

Fiacco, P. A.; Rice, W. H.

1991-01-01

Computerized medical record systems require structured database architectures for information processing. However, the data must be able to be transferred across heterogeneous platform and software systems. Client-Server architecture allows for distributive processing of information among networked computers and provides the flexibility needed to link diverse systems together effectively. We have incorporated this client-server model with a graphical user interface into an outpatient medical record system, known as SuperChart, for the Department of Family Medicine at SUNY Health Science Center at Syracuse. SuperChart was developed using SuperCard and Oracle SuperCard uses modern object-oriented programming to support a hypermedia environment. Oracle is a powerful relational database management system that incorporates a client-server architecture. This provides both a distributed database and distributed processing which improves performance. PMID:1807732

An optimal user-interface for EPIMS database conversions and SSQ 25002 EEE parts screening

NASA Technical Reports Server (NTRS)

Watson, John C.

1996-01-01

The Electrical, Electronic, and Electromechanical (EEE) Parts Information Management System (EPIMS) database was selected by the International Space Station Parts Control Board for providing parts information to NASA managers and contractors. Parts data is transferred to the EPIMS database by converting parts list data to the EP1MS Data Exchange File Format. In general, parts list information received from contractors and suppliers does not convert directly into the EPIMS Data Exchange File Format. Often parts lists use different variable and record field assignments. Many of the EPES variables are not defined in the parts lists received. The objective of this work was to develop an automated system for translating parts lists into the EPIMS Data Exchange File Format for upload into the EPIMS database. Once EEE parts information has been transferred to the EPIMS database it is necessary to screen parts data in accordance with the provisions of the SSQ 25002 Supplemental List of Qualified Electrical, Electronic, and Electromechanical Parts, Manufacturers, and Laboratories (QEPM&L). The SSQ 2S002 standards are used to identify parts which satisfy the requirements for spacecraft applications. An additional objective for this work was to develop an automated system which would screen EEE parts information against the SSQ 2S002 to inform managers of the qualification status of parts used in spacecraft applications. The EPIMS Database Conversion and SSQ 25002 User Interfaces are designed to interface through the World-Wide-Web(WWW)/Internet to provide accessibility by NASA managers and contractors.

Dcs Data Viewer, an Application that Accesses ATLAS DCS Historical Data

NASA Astrophysics Data System (ADS)

Tsarouchas, C.; Schlenker, S.; Dimitrov, G.; Jahn, G.

2014-06-01

The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. The Detector Control System (DCS) of ATLAS is responsible for the supervision of the detector equipment, the reading of operational parameters, the propagation of the alarms and the archiving of important operational data in a relational database (DB). DCS Data Viewer (DDV) is an application that provides access to the ATLAS DCS historical data through a web interface. Its design is structured using a client-server architecture. The pythonic server connects to the DB and fetches the data by using optimized SQL requests. It communicates with the outside world, by accepting HTTP requests and it can be used stand alone. The client is an AJAX (Asynchronous JavaScript and XML) interactive web application developed under the Google Web Toolkit (GWT) framework. Its web interface is user friendly, platform and browser independent. The selection of metadata is done via a column-tree view or with a powerful search engine. The final visualization of the data is done using java applets or java script applications as plugins. The default output is a value-over-time chart, but other types of outputs like tables, ascii or ROOT files are supported too. Excessive access or malicious use of the database is prevented by a dedicated protection mechanism, allowing the exposure of the tool to hundreds of inexperienced users. The current configuration of the client and of the outputs can be saved in an XML file. Protection against web security attacks is foreseen and authentication constrains have been taken into account, allowing the exposure of the tool to hundreds of users world wide. Due to its flexible interface and its generic and modular approach, DDV could be easily used for other experiment control systems.

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

PubMed

Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

2013-02-01

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

'Designing Ambient Interactions - Pervasive Ergonomic Interfaces for Ageing Well' (DAI'10)

NASA Astrophysics Data System (ADS)

Geven, Arjan; Prost, Sebastian; Tscheligi, Manfred; Soldatos, John; Gonzalez, Mari Feli

The workshop will focus on novel computer based interaction mechanisms and interfaces, which boost natural interactivity and obviate the need for conventional tedious interfaces. Such interfaces are increasingly used in ambient intelligence environments and related applications, including application boosting elderly cognitive support, cognitive rehabilitation and Ambient Assisted Living (AAL). The aim of the workshop is to provide insights on the technological underpinnings of such interfaces, along with tools and techniques for their design and evaluation.

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

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

PubMed Central

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

2009-01-01

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

Development of an Integrated Hydrologic Modeling System for Rainfall-Runoff Simulation

NASA Astrophysics Data System (ADS)

Lu, B.; Piasecki, M.

2008-12-01

This paper aims to present the development of an integrated hydrological model which involves functionalities of digital watershed processing, online data retrieval, hydrologic simulation and post-event analysis. The proposed system is intended to work as a back end to the CUAHSI HIS cyberinfrastructure developments. As a first step into developing this system, a physics-based distributed hydrologic model PIHM (Penn State Integrated Hydrologic Model) is wrapped into OpenMI(Open Modeling Interface and Environment ) environment so as to seamlessly interact with OpenMI compliant meteorological models. The graphical user interface is being developed from the openGIS application called MapWindows which permits functionality expansion through the addition of plug-ins. . Modules required to set up through the GUI workboard include those for retrieving meteorological data from existing database or meteorological prediction models, obtaining geospatial data from the output of digital watershed processing, and importing initial condition and boundary condition. They are connected to the OpenMI compliant PIHM to simulate rainfall-runoff processes and includes a module for automatically displaying output after the simulation. Online databases are accessed through the WaterOneFlow web services, and the retrieved data are either stored in an observation database(OD) following the schema of Observation Data Model(ODM) in case for time series support, or a grid based storage facility which may be a format like netCDF or a grid-based-data database schema . Specific development steps include the creation of a bridge to overcome interoperability issue between PIHM and the ODM, as well as the embedding of TauDEM (Terrain Analysis Using Digital Elevation Models) into the model. This module is responsible for developing watershed and stream network using digital elevation models. Visualizing and editing geospatial data is achieved by the usage of MapWinGIS, an ActiveX control developed by MapWindow team. After applying to the practical watershed, the performance of the model can be tested by the post-event analysis module.

Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages.

PubMed

de Moraes, Fábio R; Neshich, Izabella A P; Mazoni, Ivan; Yano, Inácio H; Pereira, José G C; Salim, José A; Jardine, José G; Neshich, Goran

2014-01-01

Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html).

Improving Predictions of Protein-Protein Interfaces by Combining Amino Acid-Specific Classifiers Based on Structural and Physicochemical Descriptors with Their Weighted Neighbor Averages

PubMed Central

de Moraes, Fábio R.; Neshich, Izabella A. P.; Mazoni, Ivan; Yano, Inácio H.; Pereira, José G. C.; Salim, José A.; Jardine, José G.; Neshich, Goran

2014-01-01

Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html). PMID:24489849

Integration of a neuroimaging processing pipeline into a pan-canadian computing grid

NASA Astrophysics Data System (ADS)

Lavoie-Courchesne, S.; Rioux, P.; Chouinard-Decorte, F.; Sherif, T.; Rousseau, M.-E.; Das, S.; Adalat, R.; Doyon, J.; Craddock, C.; Margulies, D.; Chu, C.; Lyttelton, O.; Evans, A. C.; Bellec, P.

2012-02-01

The ethos of the neuroimaging field is quickly moving towards the open sharing of resources, including both imaging databases and processing tools. As a neuroimaging database represents a large volume of datasets and as neuroimaging processing pipelines are composed of heterogeneous, computationally intensive tools, such open sharing raises specific computational challenges. This motivates the design of novel dedicated computing infrastructures. This paper describes an interface between PSOM, a code-oriented pipeline development framework, and CBRAIN, a web-oriented platform for grid computing. This interface was used to integrate a PSOM-compliant pipeline for preprocessing of structural and functional magnetic resonance imaging into CBRAIN. We further tested the capacity of our infrastructure to handle a real large-scale project. A neuroimaging database including close to 1000 subjects was preprocessed using our interface and publicly released to help the participants of the ADHD-200 international competition. This successful experiment demonstrated that our integrated grid-computing platform is a powerful solution for high-throughput pipeline analysis in the field of neuroimaging.

Kinetics of protein unfolding at interfaces

NASA Astrophysics Data System (ADS)

Yano, Yohko F.

2012-12-01

The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces.

Intelligent communication assistant for databases

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

Jakobson, G.; Shaked, V.; Rowley, S.

1983-01-01

An intelligent communication assistant for databases, called FRED (front end for databases) is explored. FRED is designed to facilitate access to database systems by users of varying levels of experience. FRED is a second generation of natural language front-ends for databases and intends to solve two critical interface problems existing between end-users and databases: connectivity and communication problems. The authors report their experiences in developing software for natural language query processing, dialog control, and knowledge representation, as well as the direction of future work. 10 references.

Interoperable Solar Data and Metadata via LISIRD 3

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D. M.; Pankratz, C. K.; Snow, M. A.; Woods, T. N.

2015-12-01

LISIRD 3 is a major upgrade of the LASP Interactive Solar Irradiance Data Center (LISIRD), which serves several dozen space based solar irradiance and related data products to the public. Through interactive plots, LISIRD 3 provides data browsing supported by data subsetting and aggregation. Incorporating a semantically enabled metadata repository, LISIRD 3 users see current, vetted, consistent information about the datasets offered. Users can now also search for datasets based on metadata fields such as dataset type and/or spectral or temporal range. This semantic database enables metadata browsing, so users can discover the relationships between datasets, instruments, spacecraft, mission and PI. The database also enables creation and publication of metadata records in a variety of formats, such as SPASE or ISO, making these datasets more discoverable. The database also enables the possibility of a public SPARQL endpoint, making the metadata browsable in an automated fashion. LISIRD 3's data access middleware, LaTiS, provides dynamic, on demand reformatting of data and timestamps, subsetting and aggregation, and other server side functionality via a RESTful OPeNDAP compliant API, enabling interoperability between LASP datasets and many common tools. LISIRD 3's templated front end design, coupled with the uniform data interface offered by LaTiS, allows easy integration of new datasets. Consequently the number and variety of datasets offered by LISIRD has grown to encompass several dozen, with many more to come. This poster will discuss design and implementation of LISIRD 3, including tools used, capabilities enabled, and issues encountered.

Evolutionary diversification of protein-protein interactions by interface add-ons.

PubMed

Plach, Maximilian G; Semmelmann, Florian; Busch, Florian; Busch, Markus; Heizinger, Leonhard; Wysocki, Vicki H; Merkl, Rainer; Sterner, Reinhard

2017-10-03

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein-protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein-protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein-protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein-protein interactions.

WEPP FuME Analysis for a North Idaho Site

Treesearch

William Elliot; Ina Sue Miller; David Hall

2007-01-01

A computer interface has been developed to assist with analyzing soil erosion rates associated with fuel management activities. This interface uses the Water Erosion Prediction Project (WEPP) model to predict sediment yields from hillslopes and road segments to the stream network. The simple interface has a large database of climates, vegetation files and forest soil...

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.

NCX-DB: a unified resource for integrative analysis of the sodium calcium exchanger super-family.

PubMed

Bode, Katrin; O'Halloran, Damien M

2018-04-13

Na + /Ca 2+ exchangers are low-affinity high-capacity transporters that mediate Ca 2+ extrusion by coupling Ca 2+ efflux to the influx of Na + ions. The Na + /Ca 2+ exchangers form a super-family comprised of three branches each differing in ion-substrate selectivity: Na + /Ca 2+ exchangers (NCX), Na + /Ca 2+ /K + exchangers, and Ca 2+ /cation exchangers. Their primary function is to maintain Ca 2+ homeostasis and play a particularly important role in excitable cells that experience transient Ca 2+ fluxes. Research into the role and activity of Na + /Ca 2+ exchangers has focused extensively on the cardio-vascular system, however, growing evidence suggests that Na + /Ca 2+ exchangers play a key role in neuronal processes such as memory formation, learning, oligodendrocyte differentiation, neuroprotection during brain ischemia and axon guidance. They have also been implicated in pathologies such as Alzheimer's disease, Parkinson's disease, Multiple Sclerosis and Epilepsy, however, a clear understanding of their mechanism during disease is lacking. To date, there has never been a central resource or database for Na + /Ca 2+ exchangers. With clear disease relevance and ever-increasing research on Na + /Ca 2+ exchangers from both model and non-model species, a database that unifies the data on Na + /Ca 2+ exchangers is needed for future research. NCX-DB is a publicly available database with a web interface that enables users to explore various Na + /Ca 2+ exchangers, perform cross-species sequence comparison, identify new exchangers, and stay-up to date with recent literature. NCX-DB is available on the web via an interactive user interface with an intuitive design, which is applicable for the identification and comparison of Na + /Ca 2+ exchanger proteins across diverse species.

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.

PubMed

Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

2016-01-01

The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. Database URL: https://extract.hcmr.gr/. © The Author(s) 2016. Published by Oxford University Press.

Coordinating complex decision support activities across distributed applications

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1994-01-01

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

TangibleCubes — Implementation of Tangible User Interfaces through the Usage of Microcontroller and Sensor Technology

NASA Astrophysics Data System (ADS)

Setscheny, Stephan

The interaction between human beings and technology builds a central aspect in human life. The most common form of this human-technology interface is the graphical user interface which is controlled through the mouse and the keyboard. In consequence of continuous miniaturization and the increasing performance of microcontrollers and sensors for the detection of human interactions, developers receive new possibilities for realising innovative interfaces. As far as this movement is concerned, the relevance of computers in the common sense and graphical user interfaces is decreasing. Especially in the area of ubiquitous computing and the interaction through tangible user interfaces a highly impact of this technical evolution can be seen. Apart from this, tangible and experience able interaction offers users the possibility of an interactive and intuitive method for controlling technical objects. The implementation of microcontrollers for control functions and sensors enables the realisation of these experience able interfaces. Besides the theories about tangible user interfaces, the consideration about sensors and the Arduino platform builds a main aspect of this work.

Overview of the interactive task in BioCreative V

PubMed Central

Wang, Qinghua; S. Abdul, Shabbir; Almeida, Lara; Ananiadou, Sophia; Balderas-Martínez, Yalbi I.; Batista-Navarro, Riza; Campos, David; Chilton, Lucy; Chou, Hui-Jou; Contreras, Gabriela; Cooper, Laurel; Dai, Hong-Jie; Ferrell, Barbra; Fluck, Juliane; Gama-Castro, Socorro; George, Nancy; Gkoutos, Georgios; Irin, Afroza K.; Jensen, Lars J.; Jimenez, Silvia; Jue, Toni R.; Keseler, Ingrid; Madan, Sumit; Matos, Sérgio; McQuilton, Peter; Milacic, Marija; Mort, Matthew; Natarajan, Jeyakumar; Pafilis, Evangelos; Pereira, Emiliano; Rao, Shruti; Rinaldi, Fabio; Rothfels, Karen; Salgado, David; Silva, Raquel M.; Singh, Onkar; Stefancsik, Raymund; Su, Chu-Hsien; Subramani, Suresh; Tadepally, Hamsa D.; Tsaprouni, Loukia; Vasilevsky, Nicole; Wang, Xiaodong; Chatr-Aryamontri, Andrew; Laulederkind, Stanley J. F.; Matis-Mitchell, Sherri; McEntyre, Johanna; Orchard, Sandra; Pundir, Sangya; Rodriguez-Esteban, Raul; Van Auken, Kimberly; Lu, Zhiyong; Schaeffer, Mary; Wu, Cathy H.; Hirschman, Lynette; Arighi, Cecilia N.

2016-01-01

Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested. Database URL: http://www.biocreative.org PMID:27589961

Charge interaction between particle-laden fluid interfaces.

PubMed

Xu, Hui; Kirkwood, John; Lask, Mauricio; Fuller, Gerald

2010-03-02

Experiments are described where two oil/water interfaces laden with charged particles move at close proximity relative to one another. The particles on one of the interfaces were observed to be attracted toward the point of closest approach, forming a denser particle monolayer, while the particles on the opposite interface were repelled away from this point, forming a particle depletion zone. Such particle attraction/repulsion was observed even if one of the interfaces was free of particles. This phenomenon can be explained by the electrostatic interaction between the two interfaces, which causes surface charges (charged particles and ions) to redistribute in order to satisfy surface electric equipotential at each interface. In a forced particle oscillation experiment, we demonstrated the control of charged particle positions on the interface by manipulating charge interaction between interfaces.

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 Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

A Data Analysis Expert System For Large Established Distributed Databases

NASA Astrophysics Data System (ADS)

Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

1987-05-01

The purpose of this work is to analyze the applicability of artificial intelligence techniques for developing a user-friendly, parallel interface to large isolated, incompatible NASA databases for the purpose of assisting the management decision process. To carry out this work, a survey was conducted to establish the data access requirements of several key NASA user groups. In addition, current NASA database access methods were evaluated. The results of this work are presented in the form of a design for a natural language database interface system, called the Deductively Augmented NASA Management Decision Support System (DANMDS). This design is feasible principally because of recently announced commercial hardware and software product developments which allow cross-vendor compatibility. The goal of the DANMDS system is commensurate with the central dilemma confronting most large companies and institutions in America, the retrieval of information from large, established, incompatible database systems. The DANMDS system implementation would represent a significant first step toward this problem's resolution.

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

PubMed Central

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

Clinician-Oriented Access to Data - C.O.A.D.: A Natural Language Interface to a VA DHCP Database

PubMed Central

Levy, Christine; Rogers, Elizabeth

1995-01-01

Hospitals collect enormous amounts of data related to the on-going care of patients. Unfortunately, a clinicians access to the data is limited by complexities of the database structure and/or programming skills required to access the database. The COAD project attempts to bridge the gap between the clinical user's need for specific information from the database, and the wealth of data residing in the hospital information system. The project design includes a natural language interface to data contained in a VA DHCP database. We have developed a prototype which links natural language software to certain DHCP data elements, including, patient demographics, prescriptions, diagnoses, laboratory data, and provider information. English queries can by typed onto the system, and answers to the questions are returned. Future work includes refinement of natural language/DHCP connections to enable more sophisticated queries, and optimization of the system to reduce response time to user questions.

Viral genome analysis and knowledge management.

PubMed

Kuiken, Carla; Yoon, Hyejin; Abfalterer, Werner; Gaschen, Brian; Lo, Chienchi; Korber, Bette

2013-01-01

One of the challenges of genetic data analysis is to combine information from sources that are distributed around the world and accessible through a wide array of different methods and interfaces. The HIV database and its footsteps, the hepatitis C virus (HCV) and hemorrhagic fever virus (HFV) databases, have made it their mission to make different data types easily available to their users. This involves a large amount of behind-the-scenes processing, including quality control and analysis of the sequences and their annotation. Gene and protein sequences are distilled from the sequences that are stored in GenBank; to this end, both submitter annotation and script-generated sequences are used. Alignments of both nucleotide and amino acid sequences are generated, manually curated, distilled into an alignment model, and regenerated in an iterative cycle that results in ever better new alignments. Annotation of epidemiological and clinical information is parsed, checked, and added to the database. User interfaces are updated, and new interfaces are added based upon user requests. Vital for its success, the database staff are heavy users of the system, which enables them to fix bugs and find opportunities for improvement. In this chapter we describe some of the infrastructure that keeps these heavily used analysis platforms alive and vital after nearly 25 years of use. The database/analysis platforms described in this chapter can be accessed at http://hiv.lanl.gov http://hcv.lanl.gov http://hfv.lanl.gov.

A New Interface for the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Koppers, A. A. P.; Tauxe, L.; Constable, C.; Shaar, R.; Jonestrask, L.

2014-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of uploading data, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Data uploading has been simplified and no longer requires the use of the Excel SmartBook interface. Instead, properly formatted MagIC text files can be dragged-and-dropped onto an HTML 5 web interface. Data can be uploaded one table at a time to facilitate ease of uploading and data error checking is done online on the whole dataset at once instead of incrementally in an Excel Console. Searching the database has improved with the addition of more sophisticated search parameters and with the ability to use them in complex combinations. Searches may also be saved as permanent URLs for easy reference or for use as a citation in a publication. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. Data from the MagIC database may be downloaded from individual contributions or from online searches for offline use and analysis in the tab delimited MagIC text file format. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

Key technology research of HILS based on real-time operating system

NASA Astrophysics Data System (ADS)

Wang, Fankai; Lu, Huiming; Liu, Che

2018-03-01

In order to solve the problems that the long development cycle of traditional simulation and digital simulation doesn't have the characteristics of real time, this paper designed a HILS(Hardware In the Loop Simulation) system based on the real-time operating platform xPC. This system solved the communication problems between HMI and Simulink models through the MATLAB engine interface, and realized the functions of system setting, offline simulation, model compiling and downloading, etc. Using xPC application interface and integrating the TeeChart ActiveX chart component to realize the monitoring function of real-time target application; Each functional block in the system is encapsulated in the form of DLL, and the data interaction between modules was realized by MySQL database technology. When the HILS system runs, search the address of the online xPC target by means of the Ping command, to establish the Tcp/IP communication between the two machines. The technical effectiveness of the developed system is verified through the typical power station control system.

Tele-rehabilitation using in-house wearable ankle rehabilitation robot.

PubMed

Jamwal, Prashant K; Hussain, Shahid; Mir-Nasiri, Nazim; Ghayesh, Mergen H; Xie, Sheng Q

2018-01-01

This article explores wide-ranging potential of the wearable ankle robot for in-house rehabilitation. The presented robot has been conceptualized following a brief analysis of the existing technologies, systems, and solutions for in-house physical ankle rehabilitation. Configuration design analysis and component selection for ankle robot have been discussed as part of the conceptual design. The complexities of human robot interaction are closely encountered while maneuvering a rehabilitation robot. We present a fuzzy logic-based controller to perform the required robot-assisted ankle rehabilitation treatment. Designs of visual haptic interfaces have also been discussed, which will make the treatment interesting, and the subject will be motivated to exert more and regain lost functions rapidly. The complex nature of web-based communication between user and remotely sitting physiotherapy staff has also been discussed. A high-level software architecture appended with robot ensures user-friendly operations. This software is made up of three important components: patient-related database, graphical user interface (GUI), and a library of exercises creating virtual reality-specifically developed for ankle rehabilitation.

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

PubMed

Kuhn, Stefan; Schlörer, Nils E

2015-08-01

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.

Layout Design of Human-Machine Interaction Interface of Cabin Based on Cognitive Ergonomics and GA-ACA.

PubMed

Deng, Li; Wang, Guohua; Yu, Suihuai

2016-01-01

In order to consider the psychological cognitive characteristics affecting operating comfort and realize the automatic layout design, cognitive ergonomics and GA-ACA (genetic algorithm and ant colony algorithm) were introduced into the layout design of human-machine interaction interface. First, from the perspective of cognitive psychology, according to the information processing process, the cognitive model of human-machine interaction interface was established. Then, the human cognitive characteristics were analyzed, and the layout principles of human-machine interaction interface were summarized as the constraints in layout design. Again, the expression form of fitness function, pheromone, and heuristic information for the layout optimization of cabin was studied. The layout design model of human-machine interaction interface was established based on GA-ACA. At last, a layout design system was developed based on this model. For validation, the human-machine interaction interface layout design of drilling rig control room was taken as an example, and the optimization result showed the feasibility and effectiveness of the proposed method.

Layout Design of Human-Machine Interaction Interface of Cabin Based on Cognitive Ergonomics and GA-ACA

PubMed Central

Deng, Li; Wang, Guohua; Yu, Suihuai

2016-01-01

In order to consider the psychological cognitive characteristics affecting operating comfort and realize the automatic layout design, cognitive ergonomics and GA-ACA (genetic algorithm and ant colony algorithm) were introduced into the layout design of human-machine interaction interface. First, from the perspective of cognitive psychology, according to the information processing process, the cognitive model of human-machine interaction interface was established. Then, the human cognitive characteristics were analyzed, and the layout principles of human-machine interaction interface were summarized as the constraints in layout design. Again, the expression form of fitness function, pheromone, and heuristic information for the layout optimization of cabin was studied. The layout design model of human-machine interaction interface was established based on GA-ACA. At last, a layout design system was developed based on this model. For validation, the human-machine interaction interface layout design of drilling rig control room was taken as an example, and the optimization result showed the feasibility and effectiveness of the proposed method. PMID:26884745

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

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

2010-01-01

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

International Shock-Wave Database: Current Status

NASA Astrophysics Data System (ADS)

Levashov, Pavel

2013-06-01

Shock-wave and related dynamic material response data serve for calibrating, validating, and improving material models over very broad regions of the pressure-temperature-density phase space. Since the middle of the 20th century vast amount of shock-wave experimental information has been obtained. To systemize it a number of compendiums of shock-wave data has been issued by LLNL, LANL (USA), CEA (France), IPCP and VNIIEF (Russia). In mid-90th the drawbacks of the paper handbooks became obvious, so the first version of the online shock-wave database appeared in 1997 (http://www.ficp.ac.ru/rusbank). It includes approximately 20000 experimental points on shock compression, adiabatic expansion, measurements of sound velocity behind the shock front and free-surface-velocity for more than 650 substances. This is still a useful tool for the shock-wave community, but it has a number of serious disadvantages which can't be easily eliminated: (i) very simple data format for points and references; (ii) minimalistic user interface for data addition; (iii) absence of history of changes; (iv) bad feedback from users. The new International Shock-Wave database (ISWdb) is intended to solve these and some other problems. The ISWdb project objectives are: (i) to develop a database on thermodynamic and mechanical properties of materials under conditions of shock-wave and other dynamic loadings, selected related quantities of interest, and the meta-data that describes the provenance of the measurements and material models; and (ii) to make this database available internationally through the Internet, in an interactive form. The development and operation of the ISWdb is guided by an advisory committee. The database will be installed on two mirrored web-servers, one in Russia and the other in USA (currently only one server is available). The database provides access to original experimental data on shock compression, non-shock dynamic loadings, isentropic expansion, measurements of sound speed in the Hugoniot state, and time-dependent free-surface or window-interface velocity profiles. Users are able to search the information in the database and obtain the experimental points in tabular or plain text formats directly via the Internet using common browsers. It is also possible to plot the experimental points for comparison with different approximations and results of equation-of-state calculations. The user can present the results of calculations in text or graphical forms and compare them with any experimental data available in the database. A short history of the shock-wave database will be presented and current possibilities of ISWdb will be demonstrated. Web-site of the project: http://iswdb.info. This work is supported by SNL contracts # 1143875, 1196352.

MoleCoolQt – a molecule viewer for charge-density research

PubMed Central

Hübschle, Christian B.; Dittrich, Birger

2011-01-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS. PMID:22477783

PACS-based interface for 3D anatomical structure visualization and surgical planning

NASA Astrophysics Data System (ADS)

Koehl, Christophe; Soler, Luc; Marescaux, Jacques

2002-05-01

The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

SeqWare Query Engine: storing and searching sequence data in the cloud.

PubMed

O'Connor, Brian D; Merriman, Barry; Nelson, Stanley F

2010-12-21

Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets.

SeqWare Query Engine: storing and searching sequence data in the cloud

PubMed Central

2010-01-01

Background Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. Results In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). Conclusions The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets. PMID:21210981

Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation

NASA Astrophysics Data System (ADS)

Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.

2012-02-01

In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.

BioMart: a data federation framework for large collaborative projects.

PubMed

Zhang, Junjun; Haider, Syed; Baran, Joachim; Cros, Anthony; Guberman, Jonathan M; Hsu, Jack; Liang, Yong; Yao, Long; Kasprzyk, Arek

2011-01-01

BioMart is a freely available, open source, federated database system that provides a unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects between different research groups. BioMart contains several levels of query optimization to efficiently manage large data sets and offers a diverse selection of graphical user interfaces and application programming interfaces to ensure that queries can be performed in whatever manner is most convenient for the user. The software has now been adopted by a large number of different biological databases spanning a wide range of data types and providing a rich source of annotation available to bioinformaticians and biologists alike.

CADB: Conformation Angles DataBase of proteins

PubMed Central

Sheik, S. S.; Ananthalakshmi, P.; Bhargavi, G. Ramya; Sekar, K.

2003-01-01

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/. PMID:12520049

MEIMAN: Database exploring Medicinal and Edible insects of Manipur

PubMed Central

Shantibala, Tourangbam; Lokeshwari, Rajkumari; Thingnam, Gourshyam; Somkuwar, Bharat Gopalrao

2012-01-01

We have developed MEIMAN, a unique database on medicinal and edible insects of Manipur which comprises 51 insects species collected through extensive survey and questionnaire for two years. MEIMAN provides integrated access to insect species thorough sophisticated web interface which has following capabilities a) Graphical interface of seasonality, b) Method of preparation, c) Form of use - edible and medicinal, d) habitat, e) medicinal uses, f) commercial importance and g) economic status. This database will be useful for scientific validations and updating of traditional wisdom in bioprospecting aspects. It will be useful in analyzing the insect biodiversity for the development of virgin resources and their industrialization. Further, the features will be suited for detailed investigation on potential medicinal and edible insects that make MEIMAN a powerful tool for sustainable management. Availability The database is available for free at www.ibsd.gov.in/meiman PMID:22715305

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

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

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

Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

2002-01-01

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easymore » access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.« less

A Mobile, Map-Based Tasking Interface for Human-Robot Interaction

DTIC Science & Technology

2010-12-01

A MOBILE, MAP-BASED TASKING INTERFACE FOR HUMAN-ROBOT INTERACTION By Eli R. Hooten Thesis Submitted to the Faculty of the Graduate School of...SUBTITLE A Mobile, Map-Based Tasking Interface for Human-Robot Interaction 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...3 II.1 Interactive Modalities and Multi-Touch . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 II.2

Theoretical investigation of magnetic properties in interfaces of magnetic nanoparticles and amorphous carbons

NASA Astrophysics Data System (ADS)

Sun, Shih-Jye; Hsu, Hua-Shu; Ovchinnikov, Sergei; Chen, Guan-Long

2017-06-01

Based on the experimental finding of the exchange bias in amorphous carbon samples with embedded Co nanoparticles and on the graphited character of the amorphous carbon interface confirmed by molecular dynamics simulations we have proposed the interface of graphited carbon to be antiferromagnetic. A theoretical model, which comprises the Kondo interactions in the interfaces of Co nanoparticles and the induced antiferromagnetic interactions in the graphited carbons, is employed to evaluate the ferromagnetism of the interfaces of Co nanoparticles. We have shown that the ferromagnetism of interfaces of Co nanoparticles will be enhanced by the increase of antiferromagnetic interaction as well as the increase of electron density in the graphited carbons. In particular, we found that the antiferromagnetic interactions in graphited carbons will change the spin-wave excitation in interfaces of Co nanoparticles from the quasiacoustic mode to the quasioptical one.

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

Evaluation of used fuel disposition in clay-bearing rock

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

Jove-Colon, Carlos F.; Hammond, Glenn Edward; Kuhlman, Kristopher L.

The R&D program from the DOE Used Fuel Disposition Campaign (UFDC) has documented key advances in coupled Thermal-Hydrological-Mechanical-Chemical (THMC) modeling of clay to simulate its complex dynamic behavior in response to thermal and hydrochemical feedbacks. These efforts have been harnessed to assess the isolation performance of heat-generating nuclear waste in a deep geological repository in clay/shale/argillaceous rock formations. This report describes the ongoing disposal R&D efforts on the advancement and refinement of coupled THMC process models, hydrothermal experiments on barrier clay interactions, used fuel and canister material degradation, thermodynamic database development, and reactive transport modeling of the near-field under non-isothermalmore » conditions. These play an important role to the evaluation of sacrificial zones as part of the EBS exposure to thermally-driven chemical and transport processes. Thermal inducement of chemical interactions at EBS domains enhances mineral dissolution/precipitation but also generates mineralogical changes that result in mineral H2O uptake/removal (hydration/dehydration reactions). These processes can result in volume changes that can affect the interface / bulk phase porosities and the mechanical (stress) state of the bentonite barrier. Characterization studies on bentonite barrier samples from the FEBEX-DP international activity have provided important insight on clay barrier microstructures (e.g., microcracks) and interactions at EBS interfaces. Enhancements to the used fuel degradation model outlines the need to include the effects of canister corrosion due the strong influence of H2 generation on the source term.« less

Evolutionary diversification of protein–protein interactions by interface add-ons

PubMed Central

Plach, Maximilian G.; Semmelmann, Florian; Busch, Florian; Busch, Markus; Heizinger, Leonhard; Wysocki, Vicki H.; Sterner, Reinhard

2017-01-01

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein–protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein–protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein–protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein–protein interactions. PMID:28923934

Generating Animated Displays of Spacecraft Orbits

NASA Technical Reports Server (NTRS)

Candey, Robert M.; Chimiak, Reine A.; Harris, Bernard T.

2005-01-01

Tool for Interactive Plotting, Sonification, and 3D Orbit Display (TIPSOD) is a computer program for generating interactive, animated, four-dimensional (space and time) displays of spacecraft orbits. TIPSOD utilizes the programming interface of the Satellite Situation Center Web (SSCWeb) services to communicate with the SSC logic and database by use of the open protocols of the Internet. TIPSOD is implemented in Java 3D and effects an extension of the preexisting SSCWeb two-dimensional static graphical displays of orbits. Orbits can be displayed in any or all of the following seven reference systems: true-of-date (an inertial system), J2000 (another inertial system), geographic, geomagnetic, geocentric solar ecliptic, geocentric solar magnetospheric, and solar magnetic. In addition to orbits, TIPSOD computes and displays Sibeck's magnetopause and Fairfield's bow-shock surfaces. TIPSOD can be used by the scientific community as a means of projection or interpretation. It also has potential as an educational tool.

The Wannabee Culture: Why No-One Does What They Used To.

ERIC Educational Resources Information Center

Dixon, Anne

1998-01-01

Electronic publishing has been an agent for change in not just how one publishes but in what one publishes. Describes HyperCite, a joint project with the Institution of Electrical Engineers (IEE) to create INSPEC database. Highlights include the database; the research phase (cross database searching and new interface); and what and how much was…

Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

ERIC Educational Resources Information Center

Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

2016-01-01

Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

MaizeGDB update: New tools, data, and interface for the maize model organism database

USDA-ARS?s Scientific Manuscript database

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, ...

Expedition Memory: Towards Agent-based Web Services for Creating and Using Mars Exploration Data.

NASA Technical Reports Server (NTRS)

Clancey, William J.; Sierhuis, Maarten; Briggs, Geoff; Sims, Mike

2005-01-01

Explorers ranging over kilometers of rugged, sometimes "feature-less" terrain for over a year could be overwhelmed by tracking and sharing what they have done and learned. An automated system based on the existing Mobile Agents design [ I ] and Mars Exploration Rover experience [2], could serve as an "expedition memory" that would be indexed by voice as wel1 as a web interface, linking people, places, activities, records (voice notes, photographs, samples). and a descriptive scientific ontology. This database would be accessible during EVAs by astronauts, annotated by the remote science team, linked to EVA plans, and allow cross indexing between sites and expeditions. We consider the basic problem, our philosophical approach, technical methods, and uses of the expedition memory for facilitating long-term collaboration between Mars crews and Earth support teams. We emphasize that a "memory" does not mean a database per se, but an interactive service that combines different resources, and ultimately could be like a helpful librarian.

A Dashboard for the Italian Computing in ALICE

NASA Astrophysics Data System (ADS)

Elia, D.; Vino, G.; Bagnasco, S.; Crescente, A.; Donvito, G.; Franco, A.; Lusso, S.; Mura, D.; Piano, S.; Platania, G.; ALICE Collaboration

2017-10-01

A dashboard devoted to the computing in the Italian sites for the ALICE experiment at the LHC has been deployed. A combination of different complementary monitoring tools is typically used in most of the Tier-2 sites: this makes somewhat difficult to figure out at a glance the status of the site and to compare information extracted from different sources for debugging purposes. To overcome these limitations a dedicated ALICE dashboard has been designed and implemented in each of the ALICE Tier-2 sites in Italy: in particular, it provides a single, interactive and easily customizable graphical interface where heterogeneous data are presented. The dashboard is based on two main ingredients: an open source time-series database and a dashboard builder tool for visualizing time-series metrics. Various sensors, able to collect data from the multiple data sources, have been also written. A first version of a national computing dashboard has been implemented using a specific instance of the builder to gather data from all the local databases.

[Research and Development of A Kinect Based Virtual System for Upper Limb Rehabilitation].

PubMed

Ding, Weili; Zheng, Yazhuo; Su, Yuping; Li, Xiaoli; Wei, Xiuli

2015-06-01

We developed a rehabilitation system by using the virtual reality technique and the Kinect in this paper. The system combines rehabilitation training with HMI and serious game organically, and provides a game and motion database to meet different patients' demands. Extended interface of game database is provided in two ways: personalized games can be developed by Virtools and Flash games which are suitable for patients' rehabilitation can be download from the Internet directly. In addition, the system provides patients with flexible interaction and easy control mode, and also presents real time data recording. An objective and subjective evaluation method is proposed to review the effectiveness of the rehabilitation training. According to the results of short questionnaires and the evaluation results of patients' rehabilitation training, the system compared with traditional rehabilitation can record and analyze the training data, which is useful to make rehabilitation plans. More entertainment and lower cost will increase patients' motivation, which helps to increase the rehabilitation effectiveness.

Specificity of molecular interactions in transient protein-protein interaction interfaces.

PubMed

Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

2006-11-15

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of antibody-antigen complexes, the sign is somewhat ambiguous. From the evolutionary perspective, while protease-inhibitors and sig-naling proteins have optimized their interfaces to suit their biological functions, antibody-antigen interactions are the happenstance, implying that antibody-antigen complexes do not show distinctive interaction types. Persistent interaction types such as pi...pi, amide-carbonyl, and hydroxyl-carbonyl interaction, are also investigated. Analyzing the structural orientations of the pi...pi stacking interactions, we find that herringbone shape is a major configuration in transient protein-protein interfaces. This result is different from that of protein core, where parallel-displaced configurations are the major configuration. We also analyze overall trend of amide-carbonyl and hydroxyl-carbonyl interactions. It is noticeable that nearly 82% of the interfaces have at least one hydroxyl-carbonyl interactions. (c) 2006 Wiley-Liss, Inc.

A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying Drug Off-Targets

PubMed Central

Engin, H. Billur; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2014-01-01

Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can ‘attack’ nodes or edges of a protein-protein interaction network. In this work, we propose a new network strategy, “The Interface Attack”, based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model which we call “Protein Interface and Interaction Network (P2IN)”, which is the integration of protein-protein interface structures and protein interaction networks. This interface-based network organization clarifies which protein pairs have structurally similar interfaces, and which proteins may compete to bind the same surface region. We built the P2IN of p53 signaling network and performed network robustness analysis. We show that (1) ‘hitting’ frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes); (2) frequent interfaces are not always topologically critical elements in the network; and (3) interface attack may reveal functional changes in the system better than attack of single proteins. In the off-target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D. PMID:22817115

Role of air-water interfaces in colloid transport in porous media: A review

NASA Astrophysics Data System (ADS)

Flury, Markus; Aramrak, Surachet

2017-07-01

Air-water interfaces play an important role in unsaturated porous media, giving rise to phenomena like capillarity. Less recognized and understood are interactions of colloids with the air-water interface in porous media and the implications of these interactions for fate and transport of colloids. In this review, we discuss how colloids, both suspended in the aqueous phase and attached at pore walls, interact with air-water interfaces in porous media. We discuss the theory of colloid/air-water interface interactions, based on the different forces acting between colloids and the air-water interface (DLVO, hydrophobic, capillary forces) and based on thermodynamic considerations (Gibbs free energy). Subsurface colloids are usually electrostatically repelled from the air-water interface because most subsurface colloids and the air-water are negatively charged. However, hydrophobic interactions can lead to attraction to the air-water interface. When colloids are at the air-water interface, capillary forces are usually dominant over other forces. Moving air-water interfaces are effective in mobilizing and transporting colloids from surfaces. Thermodynamic considerations show that, for a colloid, the air-water interface is the favored state as compared with the suspension phase, except for hydrophilic colloids in the nanometer size range. Experimental evidence indicates that colloid mobilization in soils often occurs through macropores, although matrix transport is also prevalent in absence of macropores. Moving air-water interfaces, e.g., occurring during infiltration, imbibition, or drainage, have been shown to scour colloids from surfaces and translocate colloids. Colloids can also be pinned to surfaces by thin water films and capillary menisci at the air-water-solid interface line, causing colloid retention and immobilization. Air-water interfaces thus can both mobilize or immobilize colloids in porous media, depending on hydrodynamics and colloid and surface chemistry.

Conditions Database for the Belle II Experiment

NASA Astrophysics Data System (ADS)

Wood, L.; Elsethagen, T.; Schram, M.; Stephan, E.

2017-10-01

The Belle II experiment at KEK is preparing for first collisions in 2017. Processing the large amounts of data that will be produced will require conditions data to be readily available to systems worldwide in a fast and efficient manner that is straightforward for both the user and maintainer. The Belle II conditions database was designed with a straightforward goal: make it as easily maintainable as possible. To this end, HEP-specific software tools were avoided as much as possible and industry standard tools used instead. HTTP REST services were selected as the application interface, which provide a high-level interface to users through the use of standard libraries such as curl. The application interface itself is written in Java and runs in an embedded Payara-Micro Java EE application server. Scalability at the application interface is provided by use of Hazelcast, an open source In-Memory Data Grid (IMDG) providing distributed in-memory computing and supporting the creation and clustering of new application interface instances as demand increases. The IMDG provides fast and efficient access to conditions data via in-memory caching.

Database Search Engines: Paradigms, Challenges and Solutions.

PubMed

Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.