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At least 433 records · Page 24Linked to original sources

PubMed2006

Expanded protein information at SGD: new pages and proteome browser.

The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance the depth and accessibility of protein annotations. In particular, we have expanded ongoing efforts to improve the integration of experimental information and sequence-based predictions and have redesigned the protein information web pages. A key feature of this redesign is the development of a GBrowse-derived interactive Proteome Browser customized to improve the visualization of sequence-based protein information. This Proteome Browser has enabled SGD to unify the display of hidden Markov model (HMM) domains, protein family HMMs, motifs, transmembrane regions, signal peptides, hydropathy plots and profile hits using several popular prediction algorithms. In addition, a physico-chemical properties page has been introduced to provide easy access to basic protein information. Improvements to the layout of the Protein Information page and integration of the Proteome Browser will facilitate the ongoing expansion of sequence-specific experimental information captured in SGD, including post-translational modifications and other user-defined annotations. Finally, SGD continues to improve upon the availability of genetic and physical interaction data in an ongoing collaboration with BioGRID by providing direct access to more than 82,000 manually-curated interactions.

Computer Graphics↗

PubMed1998

BioViews: Java-based tools for genomic data visualization.

Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a language designed for distributed programming over the Web, the technology now exists to build a genomic data visualization tool that meets these requirements. Using Java we have developed a prototype genome browser applet (BioViews) that incorporates a three-level graphical view of genomic data: a physical map, an annotated sequence map, and a DNA sequence display. Annotated biological features are displayed on the physical and sequence-based maps, and the different views are interconnected. The applet is linked to several databases and can retrieve features and display hyperlinked textual data on selected features. In addition to browsing genomic data, different types of analyses can be performed interactively and the results of these analyses visualized alongside prior annotations. Our genome browser is built on top of extensible, reusable graphic components specifically designed for bioinformatics. Other groups can (and do) reuse this work in various ways. Genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology laboratories can reuse components to publish results as dynamic Web documents.

Animals↗

PubMedDate not supplied

An Internet atlas of mouse development.

A prototype two- and three-dimensional color atlas of mouse development is described. The prototype has been developed using two embryos, a 13.5 d normal mouse embryo and a PATCH mutant embryo of the same age. Serial sections of the embryos, with an external registration marker system, introduced into the paraffin embedding process, were prepared by standard histological methods. For the 2D atlas, color images were digitized from 100 consecutive sections of the normal embryo. For the 3D atlas, 300 gray scale images digitized from the mutant embryo were conformally warped and reconstructed into a 3D volume dataset. The external fiducial system facilitated the three-dimensional reconstruction by providing accurate registration of consecutive images and also allowed for precise spatial calibration and the correction for warping artifacts. The atlases, with their associated anatomical knowledge base, will be integrated into a multimedia on-line information resource via the Internet's World Wide Web (WWW) using an enhanced (patent pending, Eòlas Technologies) version of the Mosaic WWW browser program from the National Center for Supercomputer Applications. These programs will provide research biologists with a set of advanced tools to analyze normal and abnormal development.

Anatomy, Artistic↗

PubMed2003

MUTAGEN: multi-user tool for annotating genomes.

SUMMARY: MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus acidocaldarius genome, and several plasmids and viruses have so far been analysed and annotated using MUTAGEN. AVAILABILITY: MUTAGEN is released as open-source software under GPL. The code is available for download and/or contribution at http://dac.molbio.ku.dk/bioinformatics/MUTAGEN/

Database Management Systems↗

PubMed1996

Creating a virtual materials and resources index for health education using the World Wide Web.

The Internet represents the principal system for distributing information worldwide, offering health educators a powerful communications medium. This article describes an assignment that teaches students how to use the World Wide Web (WWW). The first part provides an overview of the Internet, its principal services. browser software, and Netscape Navigator. The second part describes the assignment, complete with instructional objectives, computer facilities used to implement the strategy, and a summary of classroom and laboratory activities. The third part describes procedures for teaching students how to use the WWW. Students learn how to explore the WWW and to develop a customized virtual directory of health materials and resources using Netscape Navigator Bookmark tools. Recommendations on how the approach can be modified are offered.

Abstracting and Indexing↗

PubMed2006

OryGenesDB: a database for rice reverse genetics.

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (http://orygenesdb.cirad.fr/), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an 'anchoring' option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.

Chromosome Mapping↗

PubMed2006

Web-accessible scientific workflow system for performance monitoring.

We describe the design and implementation of a web-accessible scientific workflow system for environmental performance monitoring. This workflow environment integrates distributed automated data acquisition with server side data management and information visualization through flexible browser-based data access tools. Component technologies include a rich browser-based client, a back-end server for methodical data processing, user management, and result delivery, and third party applications which are invoked by the back-end using web services. This environment allows for reproducible, transparent result generation by a diverse user base, and provides a seamless integration between data selection, analysis applications, and result delivery. This workflow system has been implemented for several sites and monitoring systems with different degrees of complexity.

Databases, Factual↗

PubMed2000

Studying clinician-computer interaction in Web-based systems.

A growing of health-care organizations are in the process of modifying their clinical information systems (CIS) to support browser-based access. Consequently, care-providers are expected to modify their workflow to take advantage of the new technology. Intuitive interfaces, fast response and new functionality are few of the features used to promote endorsement of the change. In parallel, administrators are required to constantly assess user compliance and intervene where necessary to prevent rejection. Such monitoring translates to frequent surveys, analysis of logs and prudent utilization of user-groups. These methods tend to further burden users, suffer from "post-hoc" temporality and are difficult to maintain. In this paper we suggest an alternative approach to such data acquisition. "CareQuest" is an interactive Web-based service that can be woven into clinical applications without coding. It acquires information from the clinician at the relevant point in her workflow. It allows extensive interaction customization, data-driven response, real-time Web-based data-analysis, and full Web-based administration.

Evaluation Studies as Topic↗

PubMed2026

OmicsQ: a user-friendly platform for interactive quantitative omics data analysis.

MOTIVATION: High-throughput omics technologies generate complex datasets with thousands of features that are quantified across multiple experimental conditions, but often suffer from incomplete measurements, missing values, and individually fluctuating variances. This requires analytical tools for accurate, deep and insightful biological interpretation, capable of dealing with a large variety of data properties and different amounts of completeness. Software capable of handling such data complexity and integrating with external applications for downstream analysis remains rare and mostly relies on programming-based environments, limiting accessibility for researchers without computational expertise. RESULTS: We present OmicsQ, an interactive, web-based platform designed to streamline quantitative omics data analysis. OmicsQ provides an intuitive, browser-based visualization interface that integrates established statistical processing tools. Those include robust batch correction, automated experimental design annotation, and handling of missing data without imputation, which maintains data integrity and avoids artifacts from a priori assumptions. OmicsQ seamlessly interacts with external applications (e.g. PolySTest, VSClust, ComplexBrowser) for statistical testing, clustering, analysis of protein complex behavior, and pathway enrichment, offering a comprehensive and flexible workflow from data import to biological interpretation that is broadly applicable across domains. AVAILABILITY AND IMPLEMENTATION: OmicsQ is implemented in R and Shiny and is available at https://computproteomics.bmb.sdu.dk/app_direct/OmicsQ. Source code and installation instructions: https://github.com/computproteomics/OmicsQ, DOI: 10.5281/zenodo.17778420.

Software↗

PubMed2006

PRIDE: a public repository of protein and peptide identifications for the proteomics community.

PRIDE, the 'PRoteomics IDEntifications database' (http://www.ebi.ac.uk/pride) is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will typically be from specific species, tissues and sub-cellular locations, perhaps under specific disease conditions. Any post-translational modifications that have been identified on individual peptides can be described. These identifications may be annotated with supporting mass spectra. At the time of writing, PRIDE includes the full set of identifications as submitted by individual laboratories participating in the HUPO Plasma Proteome Project and a profile of the human platelet proteome submitted by the University of Ghent in Belgium. By late 2005 PRIDE is expected to contain the identifications and spectra generated by the HUPO Brain Proteome Project. Proteomics laboratories are encouraged to submit their identifications and spectra to PRIDE to support their manuscript submissions to proteomics journals. Data can be submitted in PRIDE XML format if identifications are included or mzData format if the submitter is depositing mass spectra without identifications. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an internet browser. PRIDE can be searched by experiment accession number, protein accession number, literature reference and sample parameters including species, tissue, sub-cellular location and disease state. Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML.

Databases, Protein↗

PubMed2007

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system (http://www.brenda.uni-koeln.de) is the largest publicly available enzyme information system worldwide. The major parts of its contents are manually extracted from primary literature. It is not restricted to specific groups of enzymes, but includes information on all identified enzymes irrespective of the enzyme's source. The range of data encompasses functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data. Each single entry is linked to the enzyme source and to a literature reference. Recently the data repository was complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). A genome browser, membrane protein prediction and full-text search capacities were added. The newly implemented web service provides instant access to the data for programmers via a SOAP (Simple Object Access Protocol) interface. The BRENDA data can be downloaded in the form of a text file from the beginning of 2007.

Animals↗

PubMed2006

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Databases, Genetic↗

PubMed2001

Internet user profile in the field of parasitology.

This study determined a profile of current Internet users in parasitology, their use patterns on the Internet for parasitologic purposes, and the Web sites they would recommend. In a European survey, 689 parasitologically engaged scientists were asked to fill out a questionnaire about Internet access, current problems, current and future use, and which Web sites they would recommend as well as about the use of e-mail. In all, 153 (22.2%) of the interviewees returned the questionnaire. Only one participant had no access to the Internet. Time expenditure was considered the main problem involved in use of the Internet. The Internet was mainly used for e-mail (96.1%); for literature research (93.5%); for reading of electronic journals (51.6%); and for gathering of information, e.g., about institutes and colleagues (58.2%) and about congresses (49.7%). In the future, 71.9% of the respondents would like to read electronic journals more often and 49.7% would like to use the web more intensively for acquisition of information about congresses, universities, and institutions. Requests for the future included an easier application of the browser software (33%) and a shorter response time (47.7%). The survey demonstrates that the Internet has assumed a definite place in the lives of researchers in the field of parasitology. Survey responses indicate a need for electronic journals. In our opinion, universities and parasitology societies should be urged to publish journals electronically on the Web. To diminish current problems involved in the finding of relevant information on the Internet, we strongly recommend careful reading of the instructions regarding the search engines used. Web pages with clear structures, small file sizes, precise HTML (hypertext markup language) key-word editing, and page titles would facilitate more accurate discovery of specific sites. In addition, there seems to be a need for regular publication of reviewed parasitology-link collections.

Computer Literacy↗

PubMed2005

FPC Web tools for rice, maize, and distribution.

Many clone-based physical maps have been built with the FingerPrinted Contig (FPC) software, which is written in C and runs locally for fast and flexible analysis. If the maps were viewable only from FPC, they would not be as useful to the whole community since FPC must be installed on the user machine and the database downloaded. Hence, we have created a set of Web tools so users can easily view the FPC data and perform salient queries with standard browsers. This set includes the following four programs: WebFPC, a view of the contigs; WebChrom, the location of the contigs and genetic markers along the chromosome; WebBSS, locating user-supplied sequence on the map; and WebFCmp, comparing fingerprints. For additional FPC support, we have developed an FPC module for BioPerl and an FPC browser using the Generic Model Organism Project (GMOD) genome browser (GBrowse), where the FPC BioPerl module generates the data files for input into GBrowse. This provides an alternative to the WebChrom/WebFPC view. These tools are available to download along with documentation. The tools have been implemented for both the rice (Oryza sativa) and maize (Zea mays) FPC maps, which both contain the locations of clones, markers, genetic markers, and sequenced clone (along with links to sites that contain additional information).

Chromosomes, Plant↗

PubMed1999

Internet-based physician's workbench as user interface for a central medical case repository.

Two World Health Organization Radiation Medical Emergency Preparedness and Assistance Network centers have constructed a standardized central repository of acute radiation syndrome case histories. The case histories are stored on a database server. Radiation protection centers can remotely access the database by user-friendly client software over the Internet. Physicians can use the medical information system to retrieve similar case histories for decision support, to improve their medical knowledge by inspecting real case histories, and for research on the acute radiation syndrome. The system architecture is presented and it is shown in detail how the information system can be employed to deliver medical decision support. Dialogue-response times over narrow-bandwidth Internet connections are better than when using conventional World-Wide-Web technology. However, the latter does not require the installation of client software other than a browser. A Java applet as client could combine the advantages of the two approaches.

Acute Disease↗

PubMed2002

HealthCyberMap: a semantic visual browser of medical Internet resources based on clinical codes and the human body metaphor.

OBJECTIVES: HealthCyberMap (HCM-http://healthcybermap.semanticweb.org) is a web-based service for healthcare professionals and librarians, patients and the public in general that aims at mapping parts of the health information resources in cyberspace in novel ways to improve their retrieval and navigation. METHODS AND SERVICE DESCRIPTION: HCM adopts a clinical metadata framework built upon a clinical coding ontology for the semantic indexing, classification and browsing of Internet health information resources. A resource metadata base holds information about selected resources. HCM then uses GIS (Geographic Information Systems) spatialization methods to generate interactive navigational cybermaps from the metadata base. These visual cybermaps are based on familiar medical metaphors. CONCLUSIONS: HCM cybermaps can be considered as semantically spatialized, ontology-based browsing views of the underlying resource metadata base. Using a clinical coding scheme as a metric for spatialization ('semantic distance') is unique to HCM and is very much suited for the semantic categorization and navigation of Internet health information resources. Clinical codes ensure reliable and unambiguous topical indexing of these resources. HCM also introduces a useful form of cyberspatial analysis for the detection of topical coverage gaps in the resource metadata base using choropleth (shaded) maps of human body systems.

Abstracting and Indexing↗

PubMed2006

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Animals↗

PubMed2025

SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences.

SUMMARY: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often restricted to experts in programming and mathematics. This is due to the need to implement entire models and solvers from the mathematical notation models are normally presented as. Here, we present SBMLtoOdin, an R package that translates differential equation models in SBML format from the BioModels database into executable R code using the R package odin, allowing researchers to easily reuse models. We also present Menelmacar, a web-based application that provides interactive visualisations of these models by solving their differential equations in the browser. This platform allows non-experts to simulate and investigate models using an easy-to-use interface. AVAILABILITY AND IMPLEMENTATION: SBMLtoOdin is published under the open source Apache 2.0 licence at https://github.com/bacpop/SBMLtoOdin and can be installed as an R package. The code for the Menelmacar website is published under the MIT License at https://github.com/bacpop/odinviewer, and the website can be found at https://biomodels.bacpop.org/.

Software↗