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Vol. 28 no. 9 2012, pages 1272–1273

BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/bts128

Genome analysis Advance Access publication March 13, 2012

SEQanswers: an open access community for collaboratively

decoding genomes
Jing-Woei Li1 , Robert Schmieder2 , R. Matthew Ward3 , Joann Delenick4 ,
Eric C. Olivares5,∗ and David Mittelman3,6,∗
1 School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, 2 Computational
Science Research Center and Department of Computer Science, San Diego University, San Diego, CA 92182,
3 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, 4 Department of Biology,
Graduate School of Arts & Sciences, Yale University, New Haven, CT 06520, 5 SEQanswers.com, Union City,
CA 94587 and 6 Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
Associate Editor: Alfonso Valencia

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ABSTRACT the optimization of an entire pipeline, from sample preparation to
Summary: The affordability of high-throughput sequencing has computational analysis.
created an unprecedented surge in the use of genomic data in basic, As HTS begins to transform nearly all aspects of biological
translational and clinical research. The rapid evolution of sequencing and medical science, more labs will incorporate the production
technology, coupled with its broad adoption across biology and analysis of genomic data into their studies. However, these
and medicine, necessitates fast, collaborative interdisciplinary experimental and computational methods are evolving at an
discussion. SEQanswers provides a real-time knowledge-sharing incredible pace and it is increasingly challenging for smaller research
resource to address this need, covering experimental and groups outside of major genome centers to stay current. Real-time,
computational aspects of sequencing and sequence analysis. interdisciplinary collaboration helps large genome centers optimize
Developers of popular analysis tools are among the >4000 active analysis pipelines and methods, and allows smaller groups to exploit
members, and ∼40 peer-reviewed publications have referenced them, even if they did not have resources to facilitate the initial
SEQanswers. development.
Availability: The SEQanswers community is freely accessible at
http://SEQanswers.com/
Contact: [email protected]; [email protected] 2 THE SEQANSWERS COMMUNITY
Supplementary information: Supplementary data are available at SEQanswers was launched in 2007 as an open forum to enable
Bioinformatics online. scientists across disciplines to collaboratively advance genomics
and, particularly, HTS technologies. To date, there are >4000
Received on February 24, 2012; revised on February 24, 2012;
active users visiting the online community each month. There
accepted on March 02, 2012
is a rapidly growing number of discussion threads (currently
>10 000) that span topics from sequencing platforms, experimental
1 INTRODUCTION design, data analysis and biological interpretation (Fig. 1A).
The SEQanswers community is truly global (Supplementary
The Human Genome Project represents one of the greatest concerted Fig. S1) and includes members from major genome centers
achievements of the life sciences. This massive global effort and individual groups, as well as key developers of popular
jump-started the genomics era and enabled more ambitious and data analysis tools and methods. The community currently hosts
collaborative projects such as the Cancer Genome Atlas (Cancer >300 new questions, and 1800 new responses per month. This
Genome Atlas Research Network, 2008), 1000 Genome Project incredibly high rate of participation has led to rapid responses
(1000 Genomes Project Consortium, 2010) and Human Microbiome to questions, shortening initial response time from a week in
Project (The NIH HMP Working Group et al., 2009). These large early 2008 to less than a day in 2011 (Fig. 1B). Collaborative
population-scale studies, powered by high-throughput sequencing and transparent discussion on SEQanswers has triggered the
(HTS) technologies, have generated massive amounts of genomic development of new experimental techniques, data analysis methods
data with the potential to revolutionize genetics and medicine. and pipelines, as well as collaborative assessment of analysis
The translation of these data to actionable medicine, however, is standards (Supplementary Table S1). This innovation is captured in
complicated by the challenges of extracting meaningful information part by >30 peer-reviewed publications that cite SEQanswers so far
from HTS data (Mardis, 2010). The challenge is not purely (http://seqanswers.com/wiki/Papers_Referencing_SEQanswers).
computational, as bioinformatics is bound by the experimental SEQanswers is not the only online resource for knowledge sharing
methods employed to produce genomic data (Alkan et al., 2011). and collaboration: major sequencing technology companies have
A successful experiment minimizes false positives and depends on platform-centric user communities, but these are often restricted
to customers and exclude the greater scientific community. In
∗ To whom correspondence should be addressed. contrast, BioStar (Parnell et al., 2011), an open, community-driven

© The Author(s) 2012. 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/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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 Copyedited by: TRJ MANUSCRIPT CATEGORY: APPLICATIONS NOTE

SEQanswers

bioinformatics resource, currently hosts >2300 threads, which far A

exceeds the sum of discussions found on communities operated
by sequencing companies (Supplementary Table S2). BioStar’s
principle feature is to enable researchers to ask questions and obtain
brief answers, ranked by community vote, to bioinformatics-related
problems. BioStar’s success can be attributed to its well-defined
scope and focus on a simple question and answer format for
bioinformatics. However, this format precludes other forms of
collaboration, discussion and debate.
SEQanswers differs from BioStar both in format and scope. In
an almost complementary capacity, SEQanswers eschews the Q&A
format in favor of a more traditional forum format to facilitate
collective discussion of technologies, methods and standards of
practice. The traditional forum format emphasizes the chronology
and evolution of collective thought, rather than focusing on B
identifying a single, best answer. The scope of SEQanswers
differs from BioStar’s exclusive bioinformatics focus, including all

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aspects of genomics, experimental and computational. Finally, in
recognition of the sometimes lengthy and tediously detailed threads
that can emerge from sequential discussion, we have developed
a manually curated database, SEQwiki (Li et al., 2012), that
consists of frequently asked questions, analysis methods, tutorials
and sequencing service providers.

3 CONCLUSION
The massive amounts of data and rapid pace of genome technology
development necessitates innovations in scientific communication. Fig. 1. SEQanswers is an active and fast growing community. (A) Monthly
The current standard for scientific communication between disparate contributions to SEQanswers measured by the number of new posts (blue
research groups focuses on peer-reviewed research published in points/line) and discussions (orange points/line). Discussion counts include
threads with at least two posts and exclude those with no answers.
traditional scientific journals. These journals have evolved for the
Also excluded are automated publication announcements. (B) The average
Internet age, especially with the new emphasis on open access and response time to a new forum thread.
fast publishing from both new, exclusively open access journals
to traditional journals that have created new outlets for open
access publication. While scientific journals will continue to have Conflict of Interest: none declared.
important roles as curators of research and referees for the peer-
review process, there is an opportunity for open, internet-based
platforms to supplement traditional journals by enabling the rapid REFERENCES
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1 In a global survey, 62% of respondents claimed data accessibility is very

important among all information to their research (Elsevier, 2010).

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