Publication/Paper (NAR 2012)

Paper for the NAR annual Database Issue

Note: NAR 2012 is proposed to be a 'wiki special', so I thought it would be a good idea to write up the work done and contents of on SEQwiki for that. For details, see the instructions for the NAR annual Database Issue (all the submitted wikis have to meet those criteria). --Dan 01:49, 1 August 2011 (PDT)

Note: See the NAR general guidelines for authors.

Note: For discussion, use the 'discussion' tab. See also the forum thread.

Title

SEQanswers wiki: A wiki database of tools for high throughput sequencing analysis

Authors

Authors, please fill in details on your user page

Marcowanger, Krobison, Mmartin, Andreas.sjodin, Usad, ECO^, and Dan^.

^ corresponding author

Suggested Reviewers?

NOTES: Authors must supply the names, institutes and email addresses of six suggested referees. They should be scientists working independently (i.e. not recent collaborator) in areas similar to your own who have relevant expertise, such as those included in your reference list. Suggested referees should not be from the same institution or city as any of the authors. Failure to provide names of appropriate referees may significantly delay consideration of the submitted manuscript.

Here are some that come to mind and some reasons. Please add more, and then we can rule out the intelligible.

Alex Bateman, Wellcome Trust Sanger Institute [1] 

Alex is an advocate of Wikipedia, and scientific involvement in Wikipedia in general. He is one of the authors on the WikiGenes and the Rfam wiki project. He seems very smart and fair in his judgements.

Paolo Romano, National Cancer Research Institute [2] 

Paolo was the organizer of the BioWiki conference in Naples last year, and therefore has a good overview of the field and an interest in the area.

Jim Hu, Texas A&M University [3] 

Jim Hu set up Ecoli wiki, and is generally (AFAICT) an open and fair person who will judge the wiki on its merits.

Alexander Pico The Gladstone Institutes, UCSF [4] 

Alexander set up Wikipathways, one of the few BioWikis currently making extensive use of Semantic MediaWiki... I think...

Mark Blaxter, Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh [5] 

Mark is an excellent NGS practitioner, heading up the 'GenePool' sequencing centre in Edinburgh. I know him through the local NGS usergroup meeting, and he seems very smart.

... 

your suggestions here...

Usad suggests

That said Nielsen CB might be a candidate (http://www.cydney.org/) However she might be a bit too early in her career for the editors liking (But was corresponding first author on the Nature Methods paper that cite SEQanswers in positive way)

Keith Robinson suggests

nominating Fritz Roth (U Toronto), Greg Tucker-Kellogg (National University of Singapore) and Barb Bryant (Constellation Pharmaceuticals).

Fritz Roth: roth@lunenfeld.ca ?? Is he (http://www.lunenfeld.ca/researchers/roth) ?

Greg Tucker-Kellogg: Adjunt Associate Professor (Lilly) : I cannot find his email --Marcowanger 07:45, 14 August 2011 (PDT)

Barb Bryant

Barbara Bryant, Ph.D. Computational Biology Constellation Pharmaceuticals 116 Henry Street Cambridge, MA 02139 USA Tel: 617-575-9627 E-mail: barb.bryant@gmail.com www.constellationpharma.com board term expired: 2008 Served as Secretary: 2002-2005 Served as Vice President: 2005-2007

Biostar founder Istvan Albert would also be a potential reviewer (http://www.personal.psu.edu/iua1/)

Abstract

Recent advances in sequencing technology have created unprecedented opportunities for biological research. The surge in data throughput from these new technologies has also created many challenges for data management and analysis. As the demand for sophisticated analyses increases, the development time of software and algorithms is beginning to outpace the speed of peer-reviewed journal publications. In many cases, algorithms and methods may change after publication, making the paper irrelevant for users. The SEQanswers wiki (SEQwiki) is a Semantic MediaWiki site that is edited and actively updated by the members of the SEQanswers community (http://SEQanswers.com/). The wiki provides an extensive catalogue of manually categorized analysis tools, technologies and information about service providers. Within two years, the SEQanswers community has created pages for over 400 unique software tools and associated them with around 350 literature references and 500 web links. This collaborative effort has made SEQwiki the most comprehensive database of high-throughput sequencing related tools anywhere on the web. SEQwiki also hosts focused review on commonly used bioinformatics software tools and information on more than 100 high-throughput sequencing service providers. SEQwiki is available at http://SEQanswers.com/wiki/.

The text has now moved here: https://docs.google.com/document/d/1bV49rXgPrz52wJpIAimn7uNzm2ohoH4cF_0N3H6UjnY/edit?hl=en_US

Content in above google doc is now FREEZED.

Images

Overview of the software hub. The respective tag's size increases as more software packages are tagged with it. In this example, software written in C++ dominates, followed by C, Java and Perl. Most of the softwares run in Linux. The number of softwares with maintenance status still to be confirmed out-weighted the ones with an affirmative. Most softwares are compatible with Illumina and 454 technologies.

Overview of High throughput Sequencing Service Providers. Shown are the type of services provided by different service providers. By default, names are sorted alphabetically. User can customize the sorting. Names can be filtered by services, regions, areas or states. A new service provider can be added (top left box). Existing entries can also be edited. A link on the top of the page provides additional visualizations like e.g. geographical distribution or miscellaneous statistics of sequencing centers and machines.

Description in accordance with BioDBcore standards

Database name	SEQanswers wiki
Main resource URL	http://SEQanswers.com/wiki/
Contact information	webmaster@seqanswers.com
Date resource established (year)	2009 (SEQanswers community: 2007)
Conditions of use (Free, or type of license)	Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported
Scope:
Data types captured	Free text descriptions and literature summaries; Software annotations; Citations;
Curation policy	manual curation
Standards: MIs, Data formats, terminologies
Taxonomic coverage	All
Data accessibility/output options	HTML; export to XML and RDF
Data release frequency	Immediately after modification
Versioning period and access to historical files	Every modification is versioned; full version history is available
Documentation available
User support options	Forum, e-mail
Data submission policy	Any registered user may contribute; registration is not restricted
Relevant publications
Resource's Wikipedia URL	http://en.wikipedia.org/wiki/SEQanswers
Tools available