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Bio Info Evo
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Table 1. Historical summary (2006–2009) of the number of web servers Table 1. Continued
listed in each subcategory of the Bioinformatics Links Directory
Name 2006 2007 2008 2009a
a
Name 2006 2007 2008 2009
Protein
Computer-related 2-D Structure Prediction 51 58 60 63
Bio- Programming Tools 20 20 20 20 3-D Structural Features 53 70 75 85
C/C++ 3 3 3 3 3-D Structure Comparison 35 45 50 59
Databases 2 2 2 3 3-D Structure Prediction 48 59 60 70
Java 4 4 4 4 3-D Structure Retrieval, Viewing 45 51 52 56
Linux/Unix 12 11 11 11 Biochemical Features 37 40 41 46
PERL 5 5 5 5 Do-it-all Tools for Protein 8 8 13 14
PHP 3 1 1 1 Domains and Motifs 86 112 115 121
Statistics 9 9 9 9 Function and Annotation 35 44 47 53
Web Development 6 2 2 2 Interactions, Pathways, Enzymes 66 88 94 107
Web Services 6 7 7 10 Localization and Targeting 30 38 38 39
DNA Molecular Dynamics and Docking 19 21 27 34
Annotations 38 56 57 62 Phylogeny Reconstruction 36 44 45 53
Gene Prediction 32 33 34 37 Presentation and Format 13 14 14 14
Mapping and Assembly 14 15 15 17 Protein Expression 8 8 8 10
Phylogeny Reconstruction 37 43 46 49 Proteomics 25 27 33 37
Structure and Sequence Feature 118 142 145 150 Sequence Data 7 8 9 10
those from the European Bioinformatics Institute (http:// built on this commitment to the spirit of open access.
www.ebi.ac.uk/Tools/webservices/) and the DNA Data In particular, the authors would like to acknowledge
Bank of Japan (http://www.xml.nig.ac.jp/index.html) all of the contributors to the Bioinformatics Links
which provide remote computational power, as well Directory for their valuable input and suggestions
as several data integration packages such as BioBIKE for improvements to the directory; these individuals
(http://biobike.csbc.vcu.edu/), which ‘enable biologists are listed on the Acknowledgements page at http://
with little programming expertise to combine tools, data bioinformatics.ca/links_directory/acknowledgements/.
and knowledge’. Also introduced in this issue, were a host
of online informatic resources for advanced text/data
mining such as SENT (http://sent.dacya.ucm.es/) for FUNDING
detection of semantic features in text and LitInspector This work was conducted with the support of the Ontario
(http://www.litinspector.org/) for literature and signal Institute for Cancer Research through funding provided
transduction pathway mining in PubMed. by the Government of Ontario. The Open Access publica-
New to the Bioinformatics Links Directory in 2009 is tion charge for this paper has been waived by the Oxford
the addition of ‘Gene Set Analysis’, a new subcategory University Press, in recognition of the work on behalf of
under tools for ‘Expression’ analysis (Table 1), addressing the journal.
the need and introduction of new resources that facilitate
data integration and functional evaluation of gene sets Conflict of interest statement. None declared.