Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory

Published online 11 June 2010 Nucleic Acids Research, 2010, Vol. 38, Web Server issue W3–W6 doi:10.1093/nar/gkq553 Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory Michelle D. Brazas, Joseph T. Yamada and B. F. Francis Ouellette* Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, Canada M5G 0A3 Received May 29, 2010; Accepted May 31, 2010 ABSTRACT COMMENTARY The annual Nucleic Acids Research Web Server issue presented here, along with the annual Database issue also published by NAR, continues to be an invaluable resource for the scientific community. The 2010 Web Server issue highlights the latest web servers and open access bioinformatic tools available online to guide and enable research in any number of life science domains. The complete listing of URLs cited in the 2010 Web Server issue can be accessed online at the Nucleic *To whom correspondence should be addressed. Tel: +1 416 673 8511; Fax: +1 416 977 7446; Email: ß The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The Links Directory at Bioinformatics.ca continues its collaboration with Nucleic Acids Research to jointly publish and compile a freely accessible, online collection of tools, databases and resource materials for bioinformatics and molecular biology research. The July 2010 Web Server issue of Nucleic Acids Research adds an additional 115 web server tools and 7 updates to the directory at http:// bioinformatics.ca/links_directory/, bringing the total number of servers listed close to an impressive 1500 links. The Bioinformatics Links Directory represents an excellent community resource for locating bioinformatic tools and databases to aid one’s research, and in this context bioinformatic education needs and initiatives are discussed. A complete list of all links featured in this Nucleic Acids Research 2010 Web Server issue can be accessed online at http://bioinformatics.ca/links_ directory/narweb2010/. The 2010 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries, is also available online at the Nucleic Acids Research website, http://nar.oxfordjournals.org/. Acids Research website, http://nar.oxfordjournals.org/, as well as at http://bioinformatics.ca/links_directory/ narweb2010/. In partnership with Nucleic Acids Research since 2005, the Bioinformatics Links Directory (http://bioinformatics. ca/links_directory/) has collected and organized all of the Web Server issue’s published links in its comprehensive public repository (1–5). The Directory is organized by biological subject with subcategories of common tasks relevant to each subject listed. All entries in the Directory contain a short description of the tool’s function, as well as the accompanying PubMed citation and web server URL. Such information facilitates easy browsing of tools relevant for a particular biological subject, as well keyword searches to locate tools that suit a user’s research needs. This year’s Web Server issue introduces an additional 115 web servers, plus 7 server updates (Table 1). The 2010 Nucleic Acids Research Web Server update brings the total number of servers and tools listed in the Bioinformatics Links Directory close to 1500 unique links. Since community input continually adds new links and non-functional links are removed, the list of web servers in Table 1 and online is in constant flux. The up-to-date complete listings accessible through the Bioinformatics Links Directory, including the Nucleic Acids Research 2010 web servers, can be accessed online at http://bioinformatics.ca/links_ directory/. As this list of bioinformatic tools, web servers and databases expands alongside new research technologies, data types and research ideas, there is a growing need for training and educational tools to enable and empower a wider and more varied audience of users. The Bioinformatics Links Directory is only useful if accompanied by user guidelines and training assistance. The challenge then is to provide this training in a manner that addresses both the diversity of research arenas requiring bioinformatics training, and the increasing complexity of data sets and research questions. W4 Nucleic Acids Research, 2010, Vol. 38, Web Server issue Table 1. Historical summary (2006–10) of the number of web servers listed in each subcategory of the Bioinformatics Links Directory Name 2007 2008 2009 2010a 20 3 2 4 12 5 3 9 6 6 20 3 2 4 11 5 1 9 2 7 20 3 2 4 11 5 1 9 2 7 20 3 3 4 11 5 1 9 2 10 18 2 5 4 10 5 1 9 2 17 3 38 32 14 37 118 32 26 55 19 56 33 15 43 142 39 30 63 20 57 34 15 46 145 41 32 65 23 62 37 17 49 150 42 32 71 24 71 37 20 53 161 44 30 76 25 9 19 5 15 15 9 9 24 5 15 14 9 9 23 5 15 14 9 9 23 5 15 14 9 9 18 4 18 14 10 29 96 75 8 16 36 119 89 9 19 44 120 101 17 19 8 48 128 108 22 21 12 11 49 138 121 23 22 16 24 31 7 4 14 25 25 37 8 3 19 29 33 38 8 3 23 29 36 39 8 10 27 29 38 46 6 19 29 31 46 6 2 10 11 6 2 12 15 6 2 12 22 6 3 13 30 5 4 14 31 11 16 23 31 32 18 10 16 9 15 11 17 27 38 35 21 10 19 9 18 11 17 28 45 35 21 10 21 9 18 11 17 29 53 36 21 10 25 9 18 11 21 32 60 42 22 11 28 10 21 6 3 6 3 6 6 4 6 2 6 7 9 6 7 12 13 12 51 53 35 58 70 45 60 75 50 63 85 59 65 100 71 (continued) Computer Related Bio-* Programming Tools C/C++ Databases Java Linux/Unix PERL PHP Statistics Web development Web Services Workflows DNA Annotations Gene Prediction Mapping and Assembly Phylogeny Reconstruction Structure and Sequence Feature Detection Sequence Polymorphisms Sequence Retrieval and Submission Tools For the Bench Utilities Education Bioinformatics Related News Sources Community Courses, Programs and Workshops Directories and Portals General Tutorials and Directed Learning Resources Expression cDNA, EST, SAGE Gene Regulation Transcript Expression and Microarrays Protein Expression Splicing Networks Gene Set Analysis Human Genome Annotations Ethics Genomics Health and Disease Other Resources Sequence Polymorphisms Literature Goldmines Open Access Resources Search Tools Text Mining Model Organisms Fish Fly General Resources Microbes Mouse and Rat Other Organisms Other Vertebrates Plants Worm Yeast Other Molecules Carbohydrates Metabolites Small Molecules Compounds Protein 2-D Structure Prediction 3-D Structural Features 3-D Structure Comparison 2006 Nucleic Acids Research, 2010, Vol. 38, Web Server issue W5 Table 1. Continued 2006 2007 2008 2009 2010a 3-D Structure Prediction 3-D Structure Retrieval, Viewing Biochemical Features Do-it-all Tools for Protein Domains and Motifs Annotation and Function Interactions, Pathways, Enzymes (...truncated)