Abstract

The Bioinformatics Links Directory, http://bioinformatics.ca/links_directory, is an actively maintained compilation of servers published in this and previous issues of Nucleic Acids Research issues together with many other useful tools, databases and resources for life sciences research. The 2007 update includes the 130 websites highlighted in the July 2007 Web Server issue of Nucleic Acids Research and brings the total number of servers listed in the Bioinformatics Links Directory to just under 1200 links. In addition to the updated content, the 2007 update of the Bioinformatics Links Directory includes new features for improved navigation, accessibility and open data exchange. A complete listing of all links listed in this Nucleic Acids Research 2007 Web Server issue can be accessed online at, http://bioinformatics.ca/links_directory/narweb2007. The 2007 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries is also available online, at the Nucleic Acids Research web site, http://nar.oupjournals.org.

COMMENTARY

With the publication of the 2007 Nucleic Acids Research Web Server issue, we have a chance to reflect on how the web has transformed the way we conduct scientific research. The internet helps us to communicate, to rapidly access and exchange data, to connect ideas, and to bridge expertise across disciplines. As with any endeavor, it is important that scientists keep pace. In computational biology, we have the development of new tools and algorithms for scientific research that harness the power of the web for accessibility, data sharing and exchange of ideas. With collaborative technologies such as blogs, application programming interfaces (APIs), wikis and Really Simple Syndication (RSS), the pace of progress is accelerating and scientists increasingly need to rely on trusted directories, portals and useful search engines to keep up with the latest science. The Bioinformatics Links Directory is one such directory that includes a compilation of molecular biology servers, bioinformatics tools and online resources for life sciences research.

The Bioinformatics Links Directory, http://bioinformatics.ca/links_directory, is a listing of specialized servers and general purpose resources that aims to help scientists navigate the rapidly changing landscape of online research tools. Researchers can find relevant servers using the straight forward keyword search or by navigating to the biological categories, where tools that do similar tasks are grouped together. Each entry in the Bioinformatics Links Directory is highlighted by providing a short description for each link, listing relevant PubMed citations, and identifying links as servers from the Nucleic Acids Research Web Server Issue. This directory is designed to make it easy to connect information together. Any researcher can assemble a comprehensive listing of resources by downloading and importing the RSS feeds, a format used to publish frequently updated content (http://en.wikipedia.org/wiki/RSS). For example, a researcher can import the RSS feed for a search of the Bioinformatics Links Directory for ‘transcription factor binding site’ and publish it on her wiki alongside the feeds from the ‘RNA, Structure Prediction, Visualization, and Design’ and the ‘Protein, Interactions, Pathways and Enzymes’ subcategories as a resource for the whole research laboratory interested in transcriptional regulatory mechanisms.

The 2007 update of the Bioinformatics Links Directory includes the 130 servers published in this Web Server issue of Nucleic Acids Research. Over the past 5 years, the Web Server issues have published a rich collection of over 680 different internet resources (1,2). The 2007 update brings the total number of servers listed in the Bioinformatics Links Directory close to 1200 links (Table 1). A complete listing of servers from the 2007 Web Server issue can be accessed online at http://bioinformatics.ca/links_directory/narweb2007. The complete 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.oupjournals.org. Together with the long standing Database issue (3), these special issues at Nucleic Acids Research represent a valuable directory of resources for the global life sciences research community.

Table 1.

Summary of the number of web servers listed in each subcategory of the Bioinformatics Links Directory

Name URLa 
Computer Related  
    Bio-* Programming Tools 20 
    C/C++ 
    Databases 
    Java 
    Linux/Unix 11 
    PERL 
    PHP 
    Statistics 
    Web Development 
    Web Services 
DNA  
    Annotations 56 
    Gene Prediction 33 
    Mapping and Assembly 15 
    Phylogeny Reconstruction 43 
    Sequence Feature Detection 142 
    Sequence Polymorphisms 39 
    Sequence Retrieval and Submission 30 
    Tools For the Bench 63 
    Utilities 20 
Education  
    Bioinformatics Related News Sources 
    Community 24 
    Courses, Programs and Workshops 
    Directories and Portals 15 
    General 14 
    Tutorials and Directed Learning Resources 
Expression  
    cDNA, EST, SAGE 36 
    Gene Regulation 119 
    Microarrays 89 
    Protein Expression 
    Splicing 19 
Human Genome  
    Annotations 37 
    Ethics 
    Genomics 
    Health and Disease 19 
    Other Resources 29 
    Sequence Polymorphisms 33 
Literature  
    Goldmines 
    Open Access Resources 
    Search Tools 12 
    Text Mining 15 
Model Organisms  
    Fish 11 
    Fly 17 
    General Resources 27 
    Microbes 38 
    Mouse and Rat 35 
    Other Organisms 21 
    Other Vertebrates 10 
    Plants 19 
    Worm 
    Yeast 18 
Other Molecules  
    Carbohydrates 
    Metabolites 
    Small Molecules 
Protein  
    2-D Structure Prediction 58 
    3-D Structural Features 70 
    3-D Structure Comparison 45 
    3-D Structure Prediction 59 
    3-D Structure Retrieval, Viewing 51 
    Biochemical Features 40 
    Do-it-all Tools for Protein 
    Domains and Motifs 112 
    Function 44 
    Interactions, Pathways, Enzymes 88 
    Localization and Targeting 38 
    Molecular Dynamics and Docking 21 
    Phylogeny Reconstruction 44 
    Presentation and Format 14 
    Protein Expression 
    Proteomics 27 
    Sequence Data 
    Sequence Features 31 
    Sequence Retrieval 29 
RNA  
    Functional RNAs 19 
    General Resources 10 
    Motifs 21 
    Sequence Retrieval 10 
    Structure Prediction, Visualization, and Design 47 
Sequence Comparison  
    Alignment Editing and Visualization 21 
    Analysis of Aligned Sequences 59 
    Comparative Genomics 33 
    Multiple Sequence Alignments 50 
    Other Alignment Tools 11 
    Pairwise Sequence Alignments 23 
    Similarity Searching 47 
Name URLa 
Computer Related  
    Bio-* Programming Tools 20 
    C/C++ 
    Databases 
    Java 
    Linux/Unix 11 
    PERL 
    PHP 
    Statistics 
    Web Development 
    Web Services 
DNA  
    Annotations 56 
    Gene Prediction 33 
    Mapping and Assembly 15 
    Phylogeny Reconstruction 43 
    Sequence Feature Detection 142 
    Sequence Polymorphisms 39 
    Sequence Retrieval and Submission 30 
    Tools For the Bench 63 
    Utilities 20 
Education  
    Bioinformatics Related News Sources 
    Community 24 
    Courses, Programs and Workshops 
    Directories and Portals 15 
    General 14 
    Tutorials and Directed Learning Resources 
Expression  
    cDNA, EST, SAGE 36 
    Gene Regulation 119 
    Microarrays 89 
    Protein Expression 
    Splicing 19 
Human Genome  
    Annotations 37 
    Ethics 
    Genomics 
    Health and Disease 19 
    Other Resources 29 
    Sequence Polymorphisms 33 
Literature  
    Goldmines 
    Open Access Resources 
    Search Tools 12 
    Text Mining 15 
Model Organisms  
    Fish 11 
    Fly 17 
    General Resources 27 
    Microbes 38 
    Mouse and Rat 35 
    Other Organisms 21 
    Other Vertebrates 10 
    Plants 19 
    Worm 
    Yeast 18 
Other Molecules  
    Carbohydrates 
    Metabolites 
    Small Molecules 
Protein  
    2-D Structure Prediction 58 
    3-D Structural Features 70 
    3-D Structure Comparison 45 
    3-D Structure Prediction 59 
    3-D Structure Retrieval, Viewing 51 
    Biochemical Features 40 
    Do-it-all Tools for Protein 
    Domains and Motifs 112 
    Function 44 
    Interactions, Pathways, Enzymes 88 
    Localization and Targeting 38 
    Molecular Dynamics and Docking 21 
    Phylogeny Reconstruction 44 
    Presentation and Format 14 
    Protein Expression 
    Proteomics 27 
    Sequence Data 
    Sequence Features 31 
    Sequence Retrieval 29 
RNA  
    Functional RNAs 19 
    General Resources 10 
    Motifs 21 
    Sequence Retrieval 10 
    Structure Prediction, Visualization, and Design 47 
Sequence Comparison  
    Alignment Editing and Visualization 21 
    Analysis of Aligned Sequences 59 
    Comparative Genomics 33 
    Multiple Sequence Alignments 50 
    Other Alignment Tools 11 
    Pairwise Sequence Alignments 23 
    Similarity Searching 47 

aA complete listing of all URLs listed in the Nucleic Acids Research 2007 Web Server Issue can be accessed online at: http://bioinformatics.ca/links_directory/narweb2007

In addition to the updated content, the 2007 update of the Bioinformatics Links Directory includes new features that embrace accessibility and open data exchange. For example, the Bioinformatics Links Directory has become a LinkOut provider for the NCBI (4). With this data exchange, it is now easier for researchers to jump directly from searches in PubMed to Web Server listings in the Bioinformatics Links Directory. Since the last update, we have also implemented a new CSS based design to improve the look and feel of the Bioinformatics Links Directory (http://en.wikipedia.org/wiki/Css). This new design makes it easier to browse the categories of the directory and is fully compliant with current web standards (http://webstandards.org/learn/faq/). RSS feeds are now available for any page that you can navigate to in the Bioinformatics Links Directory. The Bioinformatics Links Directory is an example of a community resource driven by researchers who invest considerable efforts ensuring that their research is freely accessible and in the public domain. Suggestions for additions, revisions or corrections to the Bioinformatics Links Directory are strongly encouraged. Please use the suggested URL link found at http://bioinformatics.ca/links_directory/add.php or email your suggestions directly to links@bioinformatics.ca.

Many scientists are now recognizing the value of harnessing the power of the web for conducting world-class research. To this end, many of the new features that we have incorporated into the 2007 update of the Bioinformatics Links Directory were driven by Web 2.0 concepts (O’Reilly, T. 2005. What is Web 2.0: Design Patterns and Business Models for the next generation of software. http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html). Scientists already embrace many of these Web 2.0 concepts, such as the value of very large data sets and open exchange of software, ideas and publications. There are also a number of research servers that provide APIs for programmatic access to their resources (5). However, there are some Web 2.0 concepts that could help to increase the value of the online resources coming from scientific groups. For example, an improved focus on users and usability of servers is needed. In addition, very few of the Web Servers listed here are compliant with current web standards, such as XHTML accessibility and CSS-based design (http://webstandards.org/learn/faq/). Increased use of emerging web technologies such as RSS feeds, APIs and wikis that encourage easy data exchange, aggregation, and participation would also be an advantage. The research groups who design, develop and host servers for the scientific community who also stay at the forefront of web technologies will be at a distinct advantage. These concepts will bring users to your tools, and make your servers accessible to non-experts. Recognizing your community of users as a valuable resource will help aid the development of your server and push the boundaries of your own research. This two way interaction mediated through the web represents a new collaborative atmosphere in which we should all want to conduct science.

ACKNOWLEDGEMENTS

The authors would like to acknowledge the efforts of Nucleic Acids Research and the researchers and developers worldwide who invest considerable efforts ensuring that their research is freely accessible to all. The Bioinformatics Links Directory is a community resource built on this commitment to the spirit of open access. In particular, the authors would like to recognize all contributors listed on the Acknowledgements page of the Bioinformatics Links Directory, http://bioinformatics.ca/links_directory/acknowledgments.php, for their valuable input and suggestions for improvements to the Bioinformatics Links Directory. The Open Access publication charge for this paper has been waived by Oxford University Press in recognition of the work on behalf of the journal.

Conflict of interest statement. None declared.

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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