Publication/Letter for SEQanswers

During the review of the SEQwiki paper [1], an important point was raised, by the reviewers, the SEQanswers forum has yet to be published, and deserves a good publication.

Lets write a short (300 words or less for Science) letter to Science [1] or Nature [2] about SEQanswers!

SEQanswers has already been 'informally' cited dozens of times in the literature, so why not write a nice summary for everyone to cite?

Please contribute (and sign the letter) below! The final list of authors will be ranked according to (democratically determined) contribution to the final text.

Meta paper discussion should stay on the forum thread here.

Letter text

In recent years, dramatic advancements in sequencing technology have created a rapidly advancing and complex field of research. These new technologies give us the capacity to answer biological questions that were previously out of reach. However, the rate at which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a research field not used to handle 'big data'.

Previously, user feedback was almost exclusively directed directly to authors of the respective software. Only a few disparate, well established, or well funded groups provided publicly archived mailing lists for community discussion. Software reviews by bloggers were similarly posted independently and relatively rarely. Newcomers to the fast evolving sequencing research field faced a seemingly overwhelming challenge to collect and analyze needed information.

SEQanswers (http://SEQanswers.com) was founded to address this gap; the community-focused format facilitates the rapid dissemination of both wet-lab techniques and bioinformatic analyses. Over 20,000 registered users composed of a diverse blend of bioinformaticists, geneticists, and molecular biologists meet and share their experiences and tools. SEQwiki (http://seqanswers.com/wiki/SEQanswers), a user-maintained semantic wiki hosted by SeqAnswers, provides an organizational structure to hundreds of publications, methods, data formats, and bioinformatics tools.

SEQanswers has fostered lively review of both pre-publication and post-publication tools. Usually, long before peer review publication, tools have been announced in SEQanswers and tested extensively within the community. Post publication improvement and benchmarking among developers is encouraged by discussions in SEQanswers forums.

As a supplement to traditional forms of scientific communication, SEQanswers offers instantaneous sharing of ideas and review of findings between peers at the cutting edge of high-throughput genome biology. The site has become an important resource for worldwide collaboration and education in the modern genomics era. The Bioinformatics forum in particular has acted as a venue for discussing problems using bioinformatics tools, which can also help tool developers by highlighting areas where their documentation may be lacking, potential for new functionality, and often useful bug reports. Some overlap exists between the bioinformatics forum at SeqAnswers, and the well-functioning, community-driven Bioinformatics Question and Answer website (http://biostar.stackexchange.com). SeqAnswers, however, aims to foster discussion beyond the question-and-answer style of Biostar, and targets a wider audience than just those researchers with a bioinformatics related question.

Moreover, as many people involved in sequencing facilities already are part of the SEQanswers community, common-sense decisions of standards such as data-formats or best-practice bioinformatic analyses may be taken much more easily.

Summary of forum contents

Here is a short summary of the contents covered by the forum. (Could act as help in the writing process)

• General discussion
• Core facilities
• Literature
• Conferences
• Bioinformatics help discussions
• Jobs forum (Industry/academic/non-profit)
• Sequencing technologies
• Scientific applications (Sample prep, resequencing, de novo, metagenomics, epigenetics, RNA sequencing)
• Regional communities

References

[1] SEQwiki paper in NAR 2012

Signers (to be ordered by most significant contribution)

• Eric C. Olivares, SEQanswers.Com.
• Jing-Woei Li, The Chinese University of Hong Kong.
• Dan M. Bolser, University of Dundee.
• Peter Ulz, Medical University of Graz.
• Andreas Sjödin, Swedish Defence Research Agency.
• Peter J. A. Cock, James Hutton Institute.
• Lex Nederbragt, University of Oslo
• Signer A, Affiliation(s)
• Signer B, Affiliation(s)