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Nucleic Acids Research 2005 33(Web Server Issue):W3-W24; doi:10.1093/nar/gki594
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers

Joanne A. Fox, Stefanie L. Butland, Scott McMillan, Graeme Campbell and B. F. Francis Ouellette*

UBC Bioinformatics Centre, University of British Columbia 2185 East Mall, Vancouver, BC, Canada V6T 1Z4

*To whom correspondence should be addressed. Tel: +1 604 822 3648; Fax: +1 604 608 4795; Email: francis{at}bioinformatics.ubc.ca

Received May 17, 2005. Accepted May 24, 2005.


   ABSTRACT
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 ABSTRACT
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The Bioinformatics Links Directory is an online community resource that contains a directory of freely available tools, databases, and resources for bioinformatics and molecular biology research. The listing of the servers published in this and previous issues of Nucleic Acids Research together with other useful tools and websites represents a rich repository of resources that are openly provided to the research community using internet technologies. The 166 servers highlighted in the 2005 Web Server Issue are included in the more than 700 links to useful online resources that are currently contained within the descriptive biological categories of the Bioinformatics Links Directory. This curated listing of bioinformatics resources is available online at the Bioinformatics Links Directory web site, http://bioinformatics.ubc.ca/resources/links_directory/. A complete listing of the 2005 Nucleic Acids Research Web Server Issue servers is available online at the Nucleic Acids web site, http://nar.oupjournals.org/, and on the Bioinformatics Links Directory web site, http://bioinformatics.ubc.ca/resources/links_directory/narweb2005/.


   COMMENTARY
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 ABSTRACT
 COMMENTARY
REFERENCES
 
For the last two years, Nucleic Acids Research has published a special issue devoted to web servers. This Web Server Issue highlights bioinformatics servers that are provided to the research community using internet technologies. This issue represents a rich repository of resources that are freely accessible, ready to use, and have been subjected to rigorous peer review. In the 2005 Web Server issue, there are 160 articles that describe the utility and functionality of 166 servers. The scope of the server applications described in this issue covers diverse ground and is hosted on servers in many different locations around the world. Among the tools included are those for text mining (1,2), sequence feature detection (3,4), predicting aspects of protein 3D structure (5,6) and performing expression analyses (7,8). Combined with the annual Database Issue (9), these special issues at Nucleic Acids Research represent a valuable directory of resources for the global life sciences research community.

Starting in 2005, Nucleic Acids Research has teamed with the UBC Bioinformatics Centre at the University of British Columbia (UBC) to ensure that all of the URLs and a short description from the Web Server Issue are listed in the Bioinformatics Links Directory, a curated listing of bioinformatics resources. The Bioinformatics Links Directory (http://bioinformatics.ubc.ca/resources/links_directory/) is a community resource that contains a directory of freely available tools, databases and resources for bioinformatics research organized within categories familiar to a biologist. All servers from the Web Server Issue, as well as other selected resources, are categorized within the directory. Table 1 displays a summary of web servers from this issue organized within the Bioinformatics Links Directory classification scheme. This scheme organizes links under 11 top level categories (DNA, Protein, RNA, Other Molecules, Expression, Sequence Comparison, Model Organisms, Human Genome, Education, Literature and Computer Related) to enable quick and easy access to listings of relevant servers. For an online version of this listing of the 2005 Nucleic Acids Research Web Server Issue servers, please see http://bioinformatics.ubc.ca/resources/links_directory/narweb2005/.


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  		Table 1 Summary of servers from the Nucleic Acids Research 2005 Web Server Issue in the Bioinformatics Links Directory listed by category

 
The Bioinformatics Links Directory highlights web resources by providing a short synopsis for each link, placing links within descriptive biological categories, providing relevant PubMed citations, and identifying links as servers from the Nucleic Acids Research Web Server Issue. The Bioinformatics Links Directory is fully searchable and can be browsed through the biological categories. RSS feeds are available for recently added links and from within any biological category. All links are automatically checked to ensure that no broken links are presented.

The Bioinformatics Links Directory is a community-driven resource and aims to offer a useful resource that is more than just a search engine. Therefore, the sites listed in the directory are suggested by the research community, are carefully selected and are curated by experts. Individuals who know of a resource that should be listed in the Bioinformatics Links Directory should suggest the URL here: http://bioinformatics.ubc.ca/resources/links_directory/add.php


   ACKNOWLEDGEMENTS
 
The Bioinformatics Links Directory would not be possible without the considerable efforts from scientists and developers, such as those highlighted in the current Web Server Issue, who demonstrate a true commitment to the spirit of open access by making their research tools accessible to everyone. Funding to pay the Open Access publication charges for this article was provided by the University of British Columbia.

Conflict of interest statement. None declared.


   REFERENCES
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  1. Maier, H., Dohr, S., Grote, K., O'Keeffe, S., Werner, T., Hrabe de Angelis, M., Schneider, R. (2005) LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts Nucleic Acids Res., 33, W779–W782[Abstract/Free Full Text] .

  2. Goetz, T. and von der Lieth, C.W. (2005) PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts Nucleic Acids Res., 33, W774–W778[Abstract/Free Full Text] .

  3. Jegga, A.G., Gupta, A., Gowrisankar, S., Connolly, S., Finley, K., Aronow, B.J. (2005) CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes Nucleic Acids Res., 33, W512–W515[Abstract/Free Full Text] .

  4. Yan, T., Yoo, D., Berardini, T.Z., Mueller, L.A., Weems, D.C., Weng, S., Cherry, J.M., Rhee, S.Y. (2005) PatMatch: a program for finding patterns in peptide and nucleotide sequences Nucleic Acids Res., 33, W262–W266[Abstract/Free Full Text] .

  5. Bryson, K., McGuffin, L.J., Marsden, R.L., Ward, J.J., Sodhi, J.S., Jones, D.T. (2005) Protein structure prediction servers at University College London Nucleic Acids Res., 33, W36–W38[Abstract/Free Full Text] .

  6. Sobolev, V., Eyal, E., Gerzon, S., Potapov, V., Babor, M., Prilusky, J., Edelman, M. (2005) SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment Nucleic Acids Res., 33, W39–W43[Abstract/Free Full Text] .

  7. Hsaio, A., Ideker, T., Olefsky, J.M., Subramaniam, S. (2005) VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Nucleic Acids Res., 33, W627–W632[Abstract/Free Full Text] .

  8. Aburatani, S., Goto, K., Saito, S., Toh, H., Horimoto, K. (2005) ASIAN: a web server for inferring a regulatory network framework from gene expression profiles Nucleic Acids Res., 33, W659–W664[Abstract/Free Full Text] .

  9. Galperin, M.Y. (2005) The Molecular Biology Database Collection: 2005 Update Nucleic Acids Res., 33, D5–D24[Abstract/Free Full Text] .


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This Article
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