The bioinformatics links directory: A community curated collection of bioinformatics links, tools and databases (original) (raw)
Related papers
Nucleic Acids Research, 2007
To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Ò Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine Ò , which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt. edu/guides/genetics/obrc).
BioSuite: a comprehensive bioinformatics software package (A unique industry-academia collaboration)
2007
CURRENT SCIENCE, VOL. 92, NO. 1, 10 JANUARY 2007 29 The team consists of Tata Consultancy Services: M. Vidyasagar, S. Mande, S. Rajgopal, B. Gopalkrishnan, S. T. P. T. Srinivas, C. Uma Maheswara Rao, T. Kathiravan, K. Mastanarao, S. Narendranath, S. Rohini, A. Irshad, T. Murali, C. Subrahmanyam, T. Mona, S. Sankha, V. Priya, D. Suman, V. V. Raja Rao, P. Nageswara Rao, R. Issaac, H. Yashodeep, B. Arundhoti, G. Nishant, S Jignesh, K. S. Chaitanya, S. P. V. Prasad Reddy; Bose Institute: P. Chakraborty; Centre for DNA Fingerprinting and Diagnosis: S. E. Hasnain, S. Mande, A. Nagarajaram, A. Ranjan, M. S. Acharya, M. Anwaruddin, S. K. Arun, Gyanrajkumar, D. Kumar, S. Priya, S. Ranjan, B. R. Reddi, J. Seshadri, P. Sravan Kumar, S. Swaminathan, P. Umadevi, V. Vindal, S. Vijaykrishnan; Central Drug Research Institute: A. K. Saxena, A. Dixit, P. Prathipati, S. K. Kashaw; Indian Institute of Chemical Biology: C. Mandal, S. Bag; Indian Institute of Science: N. Balakrishnan, M. Bansal, N. R. Ch...
The bio.tools registry of software tools and data resources for the life sciences
Genome Biology
Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.
Public web-based services from the European Bioinformatics Institute
Nucleic Acids Research, 2004
The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all parts of the scientific community in ways that promote scientific progress. To fulfil this mission, the EBI provides a wide variety of free, publicly available bioinformatics services. These can be divided into data submissions processing; access to query, analysis and retrieval systems and tools; ftp downloads of software and databases; training and education and user support. All of these services are available at the EBI website: http:// www.ebi.ac.uk/services. This paper provides a detailed introduction to the interactive analysis systemsthatare available from the EBI and a brief introduction to other, related services.
EnsMart: A generic system for fast and flexible access to biological data
2004
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets. 3 Corresponding author. E-MAIL arek@ebi.ac.uk; FAX 44-1223-494468. Article and publication are at
Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, 2012
eBiomics (www.ebiomics.org) is an e-learning interactive platform in bioinformatics intended as a support to postgraduate students and scientists involved in-omics or systems biology projects. The heterogeneity and the multitude of bioinformatics resources (databases or tools) make their individual use and appreciation difficult though difficulties can be overcome through indexing examples of use in specific contexts. eBiomics is presented as a didactic guide for an extensive range of on-line databases and tools commonly referred to in-omics applications. In its self-training version, it was developed with a free content management system and contains light textual information complemented with numerous screenshots and visual information in a user-friendly environment. A collection of protocols and case studies is indexed for finding representative and practical usages of each of the resources described. Most references to on-line databases and tools are accessible in real time through cross-links. The content covers main-omics related topics. Such a flexible tool allows keeping up with the constant evolution imposed by frequent new releases of databases, upgrades of on-line software and regular changes of query interfaces, which usually precludes from publishing helpful tutorials in books and manuals (otherwise rapidly becoming obsolete). In addition, it offers access to a self-testing section. A complementing sister website focused on biomedical academic studies includes part of the self-training content in a different environment.
Database resources of the national center for biotechnology information
Nucleic acids …, 2006
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.
Database resources of the National Center for Biotechnology Information: 2002 update
Nucleic Acids …, 2002
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 the NCBI 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 (COGs), Retroviral Genotyping Tools, 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 is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
doi: 10.1093/nar/gku301 InterMine: extensive web services for modern biology
2014
InterMine (www.intermine.org) is a biological data warehousing system providing extensive automati-cally generated and configurable RESTful web ser-vices that underpin the web interface and can be re-used in many other applications: to find and fil-ter data; export it in a flexible and structured way; to upload, use, manipulate and analyze lists; to provide services for flexible retrieval of sequence segments, and for other statistical and analysis tools. Here we describe these features and discuss how they can be used separately or in combinations to support inte-grative and comparative analysis.