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Internet Resources for Bioinformatics
Starting Points | General Bioinformatics Sites | Molecular Databases | Biotechnology Products and Services | Associations and Organizations | Other Internet Resources Guides
Starting Points
- Bioinformatics: UC Santa Cruz Science and Engineering Library
This exhaustive page, from a bioinformatics librarian, is the best single place to explore the subject and to examine the full range of appropriate available resources. Some information is proprietary to the University of California, but most databases mentioned are available from the University of Delaware Library Databases page. Includes an introduction to the subject field, several glossaries and dictionaries, tutorials and guides, conferences, and a substantial list of sequence and structure databases. - National Center for Biotechnology Information (NCBI)
Extensive site of resources and information from the National Library of Medicine, including a newsletter, bioinformatics databases, and a link to PubMed MEDLINE, the major medical bibliographic database. - Yahoo! Directory: Medicine: Bioinformatics
Yahoo provides links to pages covering a wide variety of bioinformatics categories, including: Bioinformatic Servers, Conferences, Human Genetics, Institutes, Professional Organizations, Schools, Departments and Programs, and Telemedicine. - 123 Genomics: a Genomics, Proteomics and Bioinformatics Knowledge Base
From a private firm, “the objective of this site is to be a one stop location where one can find most of the freely available internet resources ... grouped into 18 major categories,” which are listed as a table of contents at the top of the page. Includes news, careers, and college degree programs, as well as a list of organizations. - AgBiotechNet
From CABI Publishing (CAB Abstracts), a combination of fee-based and free services, including news, reviews, book chapters, reports, abstracts, calendar, jobs and conference material on agricultural biotech. - 2can Bioinformatics Support Portal: Bioinformatics Resources
“A guide to bioinformatics resources on the internet,” from the European Bioinformatics Institute. - Selected Internet Resources: Molecular Biology and Bioinformatics
Compiled for the Library of Congress by Tomoko Y. Steen, March 2004. Includes Web tutorials and tools, genetic databases, and genome projects. - BioABACUS
“BioABACUS is a searchable database of abbreviations and acronyms in Biotechnology ... [which] include the name of the term, its meaning, the category in which it is mostly used and, when available, a link in which additional information for the term can be found.“ Also includes journal name abbreviations. - Galaxy: Bioengineering
Simple guide to academic institutions, database collections, and organizations.
In the same series, see also: Biomedical Engineering and Biotechnology. - Computational Molecular Biology at NIH
Links to many tools and programs available from the National Institutes of Health for sequence analysis and molecular biology, including databases, protocols and tutorials.
Jump to top of page.General Bioinformatics Sites
- Bioinformatics Org
“A non-profit, academe-based organization committed to opening access to bioinformatics research projects, providing Open Source software for bioinformatics by hosting its development, and keeping biological information freely available. Bioinformatics.Org is a community focused on the freedom of information as it pertains to the biosciences.” - Bioinformatics Online
Tables of Contents and abstracts for Bioinformatics issues published since 1996. - CGB Bioinformatics Resources
From the Center for Genomics and Bioinformatics at Indiana University. Includes links to major Internet resources in bioinformatics and also includes links to granting agencies, meetings, various genome projects and a large list of sequence analysis tools and databases. - EMBL-European Bioinformatics Institute
“The European Bioinformatics Institute (EBI) is a center for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.” The Information section provides information about staff, jobs, conferences and seminars. Access to the following databases is also provided: SRS and the EMBL, TrEMBL, SWISS-PROT, RHdb, MSD databases. - UCSC Genome Bioinformatics
From the University of California, Santa Cruz: “This site contains working drafts for the human genome and the mouse genome. The human genome is over 90% complete. Approximately 85% of the sequence is in a highly accurate ‘finished’ state. The other 15% is merely 'draft' quality. Some care must be taken when interpreting draft regions, but these are still very useful to the working scientist.” - Biological Informatics Blogspot
“A Subject Tracer™ Information Blog developed and created by Marcus P. Zillman, M.S., A.M.H.A. for monitoring biological informatics (health informatics, neuroinformatics, biodiversity informatics and biomolecular informatics resources and sites on the Internet.” Updated daily, an extensive list of Web resources in bioinformatics, including general sites with definitions and sites specific to particular subdisciplines, substances, or structures. Major headings are: Biological Informatics, Health Informatics, Neuroinformatics, Biodiversity Informatics, Biomolecular Informatics, and Online Tools and Applications. There is also a section of Directories. - MyBio
Wiki designed especially for bioinformatics and other life sciences researchers, with open content of over 790 entries arranged into databases; education, training and jobs; sequences and sequence analysis; and companies. Also includes news, protocols and tools. “MyBio is a community-built directory of tools, databases, protocols and other web resources for life sciences researchers in a wiki format which everyone can edit.” - Biohealthmatics.com
“Serving the biomedical informatics community.” Although the primary focus is on the traditional medical informatics field (i.e. record keeping), there are useful listings of news, papers and events that are relevant to bioinformatics, including computer-assisted medicine and surgery and open source software.
Molecular Databases
Please note that the major database sites are listed under the Databases section of this Subject Guide. These are additional database sites for specific purposes.
- Nucleic Acids Research Database Categories
List
From the annual database issue of this important journal, updated each January. A very useful collection of links to a comprehensive list of over 300 resources. Includes summaries of each entry, with description, recent developments, authors responsible and a contact link - Biology Links
This page includes links to a number of model organism databases, banks and tables, and to a number of genetic databases. Maintained by the Dept. of Molecular & Cellular Biology, Harvard University. - Databases for Molecular Biology
Includes nucleotide databases, protein databases, chromosome maps, enzyme databases, etc.
From the Computational Molecular Biology at NIH Web site. - KEGG
The Kyoto Encyclopedia of Genes and Genomes is “a knowledge base for systematic analysis of gene functions in terms of networks of genes and molecules.” Integrates information from pathway databases such as WIT, sequence and structure databases, and sources such as PROSITE. - PUMA2
High throughput comparative and evolutionary analysis of genomes and metabolic networks with Grid computational backend. PUMA2 contains 1,032 Prokaryotic and Eukaryotic genomes, and allows interactive analysis of the sequence data using a variety of bioinformatics tools. - ExPASy Molecular Biology Server
From the Swiss Institute of Bioinformatics, the major proteomics server dedicated to the analysis of protein sequences and stuctures. Allows searching of multiple protein sequence databases and tools sites. - FlyBase
Drosophila genome databse with tools for genetic maps and sequences, as well as sources for stocks and images. - Mouse Genomics Informatics
The Mouse Genome Informatics Database provides integrated access to data on the genetics, genomics and biology of the laboratory mouse. This site also provides, under “Useful Links,” access to the Whole Mouse Catalog and other Database and Search Tools. Maintained by The Jackson Laboratory. - The Arabidopsis Information Resource (TAIR)
“Provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR consists of a searchable relational database, which includes many different datatypes. The data can be viewed using our interactive MapViewer, and analyzed with our tools.” - Human Genome Sequencing Center at Baylor College of
Medicine
Human Genome Sequencing, Dictyostelium sequencing, Drosophila sequencing, Mouse chromosome Y, cDNA sequencing. - The Center for Molecular Modeling (CMM)
Many molecular modelling programs are available through the link “Research Tools on the Web,” including Molecules To Go, a World Wide Web (WWW) Forms interface which facilitates access (browsing, searching and retrieval) to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB). - Protein Data Bank (PDB)
“The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.” The PDB includes 10132 coordinate entries, 9422 proteins, 698 nucleic acids, and12 carbohydrates. - iPROCLASS
From the Protein Information Resource, a database that integrates structure and function databases to make associations between genomes, proteins, and protein functions.
For additional lists of databases, please go to the Databases section of this Subject Guide.
Biotechnology Products and Services
- American Type Culture Collection
- BIO: Biotechnology Industry Organization
- National Biotech Register from Barry, Inc., Professional Directories
- BioBase Biological Databases, including the Proteome BioKnowledge(R) Library
- Protein Data Bank from the Research Collaboratory for Structural Bioinformatics
- SciWeb, the Life Science Home Page: Online Resources For Biotechnology Professionals
- Bioinformatics and Educational Resources from New Mexico Stae University. Originally created by Southwest Biotechnology and Informatics Center (SWBIC).
Associations and Organizations
- American Medical Informatics Association (AMIA)
- American Society for Biochemistry and Molecular Biology (ASBMB)
- American Society of Microbiology (AMS)
- Biomedical Engineering Society (BMES)
- Center for Biological Informatics (U.S. Geological Survey)
- The European Federation of Biotechnology (EFB)
- European Molecular Biology Organization (EMBO)
- The Genetics Society of America (GSA)
- IEEE Engineering in Medicine and Biology Society (EMBS)
- Institute of Biological Engineering (IBE)
- International Society for Computational Biology (ISCB)
Other Internet Resources Guides
Bioinformatics relies heavily on the methods, practices, and principles of the many scientific disciplines to which it relates. The resources above represent a short list of some of the resources in the physical, biomedical, agricultural, computer, and social sciences supporting research in bioinformatics. Please refer to the drop-down menu “Internet Resources for Related Subjects” on the navigation bar to the left for links to additional sites of interest.
