Publication/Letter for SEQanswers

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Revision as of 23:46, 5 December 2011 by Genericforms (talk | contribs) (→‎Authors' list (still not in order yet!))
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Pre-inquiry emails

  • Genome Medicine - inquiry by genericforms on 23th Nov 2011

Everyone,

Here is the response I got:

"In principle, we are interested in the manuscript you describe and we think it might be suitable as a Correspondence article, although we would need to see the full manuscript before making a decision. For this manuscript to be considered by Genome Medicine, it would need to be clear that it contains information that is not included in the recently published Nucleic Acids Research issue and that it is applicable and relevant to medical/clinical researchers as well as basic scientists.

Correspondence articles are open access, peer-reviewed articles that include brief reports of particular interest to the community (http://genomemedicine.com/authors/instructions/correspondence). To submit the article, please go to http://genomemedicine.com/manuscript."

  • Genome Biology -inquiry by marcowanger, reply on 29th Nov 2011

Thank you for your email in which you offer to submit a Correspondence manuscript on the SEQanswers community to Genome Biology. I am very sorry about the delay in getting back to you about it. Having discussed and considered your proposal with my colleagues, I am afraid that we are unable to consider the manuscript you describe for publication.

I'm sorry that we can't be more positive but we are sure you won't have any difficulties in publishing your article elsewhere. Thank you for your interest in Genome Biology.

  • PLoS Biology - inquiry by marcowanger, reply on 1st Dec 2011

Thank you for your enquiry about submitting your article "SEQanswers: Leveraging Collective Intelligence to Decode Biological Sequences" to PLoS Biology. I have discussed your proposal with my colleagues and regret that we cannot encourage submission of the full manuscript.

While we cannot consider your manuscript for publication in PLoS Biology, we very much appreciate your wish to present your work in one of PLoS's open-access publications, and would like to suggest that you consider submitting it to one of the other PLoS journals. Full details of all the other PLoS journals are available at http://www.plos.org/journals/. In particular, we would encourage you to consider submitting to PLoS Computational Biology, as we feel that your article would be better suited to the computational biology community.

If you are interested in pursuing this option, please log in at http://www.editorialmanager.com/pcompbiol/, and choose 'Submit Manuscript' from the list of Author Tasks, selecting the article type 'Presubmission Inquiry'. The editors of the journal will then let you know whether your work is suitable for full submission there.

Thank you again for your interest in PLoS Biology.

Best wishes,

Previous drafts

Page of previous draft versions

Letter: Draft #Final

Meta-discussion

We need abstract.

Suggest putting the current letter as abstract.

Expand the original letter as correspondence. No matter which journal to go. We need more than current 400 words (800-3000 required by most journals as correspondence). Perhaps describe more about

  • Open Science <-> SEQanswers, how SEQ open possibility for collaboration, Q&A, etc
  • Success cases study (examples of writing from BioStar paper in PLoS Comp Bio)
    • Suggestions topics: 1. (How open discussion potentially improve algorithms design: Heng Li and Salberg on Bowtie 2 vs BWA)

Examples of usage

A list of examples provided by marco. Could be used to expand the text.

Titles suggestions (Not in order!)

  • (1) Embracing open science : community collaboration

genericforms deleted his earlier suggestions 2 & 3 in favor of #10

  • (6) SEQanswers: An Open Science forum serving the next-generation sequencing community
  • (8) SEQanswers, Reading Biological Sequences as a Community since 2007.

marcowanger deleted his earlier suggestions 4,5,7 &9 in favor of #10

  • (10) SEQanswers: Leveraging Collective Intelligence to Decode Biological Sequences

Authors' list (still not in order yet!)

  • Eric C. Olivares; SEQanswers.com, Union City, CA 94587, USA
  • Jing-Woei Li; School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR
  • David Mittelman; (1)Virginia Bioinformatics Institute (2)Department of Biological Sciences; Virginia Tech, Blacksburg, VA 24061, USA
  • Robert Schmieder; Computational Science Research Center and Department of Computer Science, San Diego State University, San Diego, CA 92182, USA
  • ......

[Need to identify a lead (first) author, a last author that will submit, and the order of all the authors in between.]

would like to lead --Marcowanger 11:41, 2 December 2011 (PST) would like to be last author/corresponding --Genericforms -- will also cover pub fee to Genome Medicine

Abstract

Ongoing technological advancements in high-throughput sequencing (HTS) are vastly outstripping Moore's law, fueling research with far-reaching economical and social impacts. Such innovation have enabled the exploration of biological questions that were previously out of reach. The rapidly decreasing cost of generating sequence data is reflected in a growing number of research groups that incorporate HTS in their projects. In these days, as the bottle-neck of whole genome scale study shifted from the generation of sequence data to designing good experiment and effective analysis strategies, even experienced scientists have to continuously seek expertise from peers around the world. There is thus an increasing need for an open platform to share HTS related knowledge. The SEQanswers community (http://SEQanswers.com/), an open scientific forum focused on HTS, was founded in late 2007 to bridge the information gap and facilitate rapid dissemination both related wet-lab techniques and bioinformatic analyses.

As technology continues to be developed at a staggering pace in many disciplines, the rate of peer-reviewed publication and other traditional information sharing means are unlikely to be able to track all movements in the field in a timely manner. Scientific forums (or similar) allow instantaneous sharing of results, techniques, and trouble shooting. Most likely, these scientific forums will play an important role in developing community-wide data analysis gold standard for the fields. Exemplified in the HTS field, scientific discussion in an open forum inspires development of better computational algorithms and experimental approaches as knowledge is shared among biologists, bioinformaticians and bioinformatic tool developers. Already an important resource for global collaboration and education in the modern genomics era, SEQanswers will continue to provide an open platform to scientists all over the world.

The Need for an Open Science Platform

Ongoing technological advancements in high-throughput sequencing (HTS) are vastly outstripping Moore's law, fueling research with far-reaching economical and social impacts. Such innovation have enabled the exploration of biological questions that were previously out of reach. The rapidly decreasing cost of generating sequence data is reflected in a growing number of research groups that incorporate HTS in their projects. In these days, as the bottle-neck of whole genome scale study shifted from the generation of sequence data to designing good experiment and effective analysis strategies, even experienced scientists have to continuously seek expertise from peers around the world. There is thus an increasing need for an open platform to share HTS related knowledge.

Should start by talking about the need for Open Science, then the call for SEQanswers (as a model of Open Science). SEQanswers will not be the only one, but one of the most important pioneers


<the argument here is to argue the publication system is insufficient to support those who do the actual work, example: Heng Li said in BWA vs Bowtie2 thread that the methods he used in publication which might have seemed right at the moment of publication is obviously wrong NOW, so looking at literatures along will guide the readers to a wrong direction. Fix? Search in SEQanswers! many journals allow commenting on articles and this alraedy goes into the direction; the argument here is not that content of publications can change, but that the publication system is too slow (at least that is what we start off with); The third paragraph tells the readers that journals are unlikely to keep track of all the changes in the field already, I think it's fine just to say there is a need for a forum; Honestly, I never see a comment in the Journal's comment section that can lead to a constructive debate. Mostly likely, who want to start such a debate would go for a PLoS One paper / Write to Nature response to paper section....But, I saw that kind of constructive debate in SEQanswers, which is amazing>


SEQanswers - An open scientific forum

The SEQanswers community, which can be accessed at http://SEQanswers.com/, is an open scientific forum focusing on HTS. The forum was founded in late 2007 to bridge the information gap and facilitate rapid dissemination of both wet-lab techniques and bioinformatic analyses. Over the last four years, SEQanswers has become a firmly established HTS knowledge-sharing platform currently used by over 4,000 active members (registered users visiting within the last four weeks) that participate in an increasing number of discussions (Figure 1). In October 2011, more than 300 new questions and more than 1,800 new answers were posted by members of the SEQanswers community. This high rate of participation is the main factor for the average time of less than one day between asking a question and receiving an answer (Figure 2).

Part of the success of SEQanswers can be attributed to the way it mirrors the broader scientific community, where communication of knowledge between peers is paramount, and member's status, as assessed by the number of contributions, is recognized. More than 10,000 discussions (as of November 11, 2011) provide answers and insights on sequencing technologies, data analysis methods, service providers and other HTS related issues (Box 1) - information and technical know-how that will otherwise only be found scattered throughout the Internet. In addition, many bioinformatic developers announce their tools in SEQanswers long before their publication. Post-publication vibrant discussion involving the interactions between users and developers, and debates on theoretical issues among tool developers all lead to ideas to develop better tools. As part of SEQanswers, the SEQwiki [Ref] manages categorized and user-maintained information of HTS related bioinformatic tools that provide additional help for researchers.

Box 1: Main topics of/in SEQanswers

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

Use Cases and Success Stories

<Incorporate here that SEQanswers was cited more than 30 times (http://seqanswers.com/wiki/Papers_Referencing_SEQanswers, and maybe references listed in the gdoc) and maybe figure 3 with the visitors from different countries>

Suggested topic: How open discussion potentially improve algorithms design: Heng Li and Salberg on Bowtie 2 vs BWA

Implications of SEQanswers for the Scientific Community and the medical field

As technology continues to be developed at a staggering pace in many disciplines, the rate of peer-reviewed publication and other traditional information sharing means are unlikely to be able to track all movements in the field in a timely manner. Scientific forums (or similar) allow instantaneous sharing of results, techniques, and trouble shooting. Most likely, these scientific forums will play an important role in developing community-wide data analysis gold standard for the fields. Exemplified in the HTS field, scientific discussion in an open forum inspires development of better computational algorithms and experimental approaches as knowledge is shared among biologists, bioinformaticians and bioinformatic tool developers.

<referring to sci. forum in general, not specific to HTS field; this is one of the main problems of HTS and I {who? (RobS)} think it is a good example here; But we are talking about the implication, so we should be broad (marco) >

Outlook and Perspective

Already an important resource for global collaboration and education in the modern genomics era (SEQanswers was cited more than 30 times (http://seqanswers.com/wiki/Papers_Referencing_SEQanswers)), SEQanswers will continue to provide an open platform to scientists all over the world.


Figures & References: Figures & References

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