Free Database Software
In recognition of a fresh new year and a fresh new direction for Bitesize Bio, I thought I’d start my tenure as the fresh new Bioinformatics “guru” by introducing you to a handful of websites that will help you locate established as well as fresh new and (mostly) free online molecular biology and bioinformatics databases and tools.
And I promise not to use the phrase “fresh new” again.
There are already thousands of online bioinformatics resources available, with undoubtedly many more to come. One of the limiting factors of the field is the difficulty in navigating the vast array of resources to identify the most appropriate tool(s) for what you need to do, whether that’s finding information on SNPs, locating pathway analysis software, or designing PCR primers. Here are four websites that will help you with your search.
Online Bioinformatics Resource Collection (OBRC)
The OBRC contains links and annotations for over 2,000 bioinformatics databases and software tools. It was created in 2006 by the Molecular Biology Information Service for the Health Sciences Library System at the University of Pittsburgh and can be accessed from their webpage via search.HSLS.MolBio. The purpose of the manually curated OBRC is to bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources. This freely available, searchable database arranges resources by categories and sub-categories such as Structure Databases and Analysis Tools, Proteomics Resources, and Enzymes and Pathways. The OBRC is the largest online collection of its kind and the only one with advanced search results clustering. It is a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. Full disclosure: although I didn’t create the OBRC, I am currently its curator. Feel free to contact me if you have any questions or suggestions.
BioMed Central Databases
The BioMed Central Databases maintains a catalog of Web-based databases as well as a Biology Image Library. The collection can be browsed by subject area or searched by name, description, contents, and/or subject area. The scientific community is welcome to create a database or simply house it on the BioMed Central Databases site.
OReFiL
OReFiL is the Online Resource Finder for Lifesciences. Developed by computational biologists, it provides searches for online resources introduced in peer-reviewed papers in the life sciences. A crawler automatically extracts all URLs listed in MEDLINE abstracts and full-text papers from BioMed Central open-access journals and maintains them in a freely available, searchable database.
Nucleic Acids Research Bioinformatics Links Directory
The Bioinformatics Links Directory features curated links to molecular resources, tools, and databases culled from the annual Database issue and Web Server issue of the journal Nucleic Acids Research (NAR). NAR is a highly ranked open access journal that publishes articles on the biological, biochemical, physical, and chemical aspects of proteins and nucleic acids involved in nucleic acid interactions and/or metabolism. The freely available Bioinformatics Link Directory provides links to the resources themselves, as well as to the NAR published articles about those resources.
Happy hunting! And please leave comments, especially if you know of other meta-resources for bioinformatics tools and databases.
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In recognition of a fresh new year and a fresh new direction for Bitesize Bio, I thought I’d start my tenure as the fresh new Bioinformatics “guru” by introducing you to a handful of websites that will help you locate established as well as fresh new and (mostly) free online molecular biology and bioinformatics databases and tools.
And I promise not to use the phrase “fresh new” again.
There are already thousands of online bioinformatics resources available, with undoubtedly many more to come. One of the limiting factors of the field is the difficulty in navigating the vast array of resources to identify the most appropriate tool(s) for what you need to do, whether that’s finding information on SNPs, locating pathway analysis software, or designing PCR primers. Here are four websites that will help you with your search.
Online Bioinformatics Resource Collection (OBRC)
The OBRC contains links and annotations for over 2,000 bioinformatics databases and software tools. It was created in 2006 by the Molecular Biology Information Service for the Health Sciences Library System at the University of Pittsburgh and can be accessed from their webpage via search.HSLS.MolBio. The purpose of the manually curated OBRC is to bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources. This freely available, searchable database arranges resources by categories and sub-categories such as Structure Databases and Analysis Tools, Proteomics Resources, and Enzymes and Pathways. The OBRC is the largest online collection of its kind and the only one with advanced search results clustering. It is a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. Full disclosure: although I didn’t create the OBRC, I am currently its curator. Feel free to contact me if you have any questions or suggestions.
BioMed Central Databases
The BioMed Central Databases maintains a catalog of Web-based databases as well as a Biology Image Library. The collection can be browsed by subject area or searched by name, description, contents, and/or subject area. The scientific community is welcome to create a database or simply house it on the BioMed Central Databases site.
OReFiL
OReFiL is the Online Resource Finder for Lifesciences. Developed by computational biologists, it provides searches for online resources introduced in peer-reviewed papers in the life sciences. A crawler automatically extracts all URLs listed in MEDLINE abstracts and full-text papers from BioMed Central open-access journals and maintains them in a freely available, searchable database.
Nucleic Acids Research Bioinformatics Links Directory
The Bioinformatics Links Directory features curated links to molecular resources, tools, and databases culled from the annual Database issue and Web Server issue of the journal Nucleic Acids Research (NAR). NAR is a highly ranked open access journal that publishes articles on the biological, biochemical, physical, and chemical aspects of proteins and nucleic acids involved in nucleic acid interactions and/or metabolism. The freely available Bioinformatics Link Directory provides links to the resources themselves, as well as to the NAR published articles about those resources.
Happy hunting! And please leave comments, especially if you know of other meta-resources for bioinformatics tools and databases.
ARTICLES IN YOUR INBOX
Enter your email to be informed when we publish more articles like this on BsB, and also get access to all of these goodies:
Free ebooks and audiobooks on the topics that matter to you
Access to Member’s-only articles and Videos
Advance notice of new webinars and eBooks
Access to make comments and ask questions on BsB
Images
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