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

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 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. Below, we discuss some education ideas and initiatives that take aim at these challenges.

Brief tutorials and case examples to accompany new applications

Most new applications and bioinformatic tools are posted with supporting readme documentation that contains useful tips on how to navigate within and use a given tool. However, such documentation is often unread, and usually does not contain practical information on how the tool may be applied in research. Brief tutorials or case examples offer a mechanism to enhance the uptake of new computational tools by showing potential users how to perform simple to advanced analyses with the tool or how to use a tool for a given research problem. Good examples of applications with tutorials include many of the tools available through the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/guide/training-tutorials/), the UCSC Genome Browser (http://genome.ucsc.edu/training.html) and Ensembl (http://uswest.ensembl.org/info/website/tutorials/index.html) to name a few.

Roadshow training programs at conferences in diverse fields

With the increasing number and diversity of research fields needing specific computational applications to address their research problem, there are an increasing number of researchers realizing the need for some level of bioinformatic skills training. Conferences offer an ideal venue for hosting a discipline-specific bioinformatics training program, since a large number of researchers from a particular scientific field are already gathered. The International Society for Computational Biology (ISCB) Education Outreach Task Force has recognized this opportunity to empower potential users in applications relevant to their research and has initiated traveling road shows to accompany field-specific conferences with the aim to offer three to five workshops per year. Similarly other larger institutions offer traveling road shows for any of their applications [e.g. NCBI, European Bioinformatics Institute (EBI), etc.], although these are typically on a cost recovery basis.

Open access to collections of online training programs

Online lists or repositories of available educational training materials similarly enable users and potential new users to access and acquire computational skills in a particular application or computational work flow at their own pace and to suit their own research needs. Such lists are an invaluable source of information, and are often the starting point for many researchers. The Bioinformatics Links Directory (http://bioinformatics.ca/links_directory/) maintains an Education category and lists numerous education-related resources including ‘Courses, Programs and Workshops’ and ‘Tutorials and Directed Learning’ resources. Several of the links located in this directory redirect the user to open access, full content bioinformatics training workshops (e.g. Canadian Bioinformatics Workshops, http://bioinformatics.ca) and self-directed tutorials (e.g. OpenHelix, (http://www.openhelix.com).

Effort must be made to continually improve education and training in bioinformatics, to keep pace with the rapid development of novel computational applications and the research communities’ needs. The Bioinformatics Links Directory welcomes new entries both to its ‘Education’ section and other informatic resource sections. Suggestions for new links or updates and corrections to existing links may be submitted through email directly to [email protected].

FUNDING

Ontario Institute for Cancer Research through funding provided by the Government of Ontario. Funding for open access charge: The Open Access publication charge for this paper has been waived by the Oxford University Press, in recognition of the work on behalf of the Journal.

Conflict of interest statement. None declared.

ACKNOWLEDGEMENTS

The authors wish to acknowledge the efforts of Nucleic Acids Research and the researchers and developers worldwide who invest considerable effort into 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 acknowledge all of the contributors to the Bioinformatics Links Directory for their valuable input and suggestions for improvements to the directory; these individuals are listed on the Acknowledgements page at http://bioinformatics.ca/links_directory/acknowledgements/.

REFERENCES