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| | [https://docs.google.com/document/d/1PSuq6IIYXwDOCJYn7CWjH4EG-1QT5PWFCf6BQWsyZqE/edit Link here] | | [https://docs.google.com/document/d/1PSuq6IIYXwDOCJYn7CWjH4EG-1QT5PWFCf6BQWsyZqE/edit Link here] |
| − | == Meta-discussion ==
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| − | We need abstract.
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| − | Suggest putting the current letter as abstract.
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| − | 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).
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| − | Perhaps describe more about
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| − | *Open Science <-> SEQanswers, how SEQ open possibility for collaboration, Q&A, etc
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| − | *Success cases study (examples of writing from BioStar paper in PLoS Comp Bio)
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| − | **Suggestions topics: 1. (How open discussion potentially improve algorithms design: Heng Li and Salberg on Bowtie 2 vs BWA)
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| − |
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| − | ===Examples of usage===
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| − | A list of examples provided by marco. Could be used to expand the text.
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| − | *Interactions among peer bioinformatics analysts
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| − | **[http://seqanswers.com/forums/showthread.php?t=1610&highlight=strand+specific How to do denovo assemble of a transcriptome]
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| − | **Discussion by users on a newly released tool. [http://seqanswers.com/forums/showthread.php?t=2952&highlight=DEseq DEGseq developer answer specific questions]
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| − | * Enable dynamic interactions among users and developers. Software developers thus receive a wider pool of potential users
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| − | ** Call for beta-testers
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| − | *** [http://seqanswers.com/forums/showthread.php?t=13695&highlight=announce Cost calculator for NGS experiment]
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| − | **Promotion of published tools
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| − | *** [http://seqanswers.com/forums/showthread.php?t=5502&highlight=announce Bismark : A tool to map and analyze bisulfite sequencing data]
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| − | ** Update of well established tools
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| − | *** [http://seqanswers.com/forums/showthread.php?t=11164&highlight=announce Cufflinks v1.00]
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| − | ** Promotion of unpublished tools
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| − | *** [http://seqanswers.com/forums/showthread.php?t=4805&highlight=HTSeq HTSeq: A python framework to work with high throught sequencing data]
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| − | *** [http://seqanswers.com/forums/showthread.php?t=6936&highlight=announce Cutadapt: adapter removal from NGS dataset]
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| − | *** [http://seqanswers.com/forums/showthread.php?t=4351&highlight=announce Biopieces: A collection of bioinformatics tools]
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| − | ** Feedback to the developers in traditional channel is usually private to the one provides feedback and the developers. In contrast users are encouraged to and are in majority of cases, provide feedback (no matter on practicalities and theoretical sides) in a public environment setting. Preliminary ideas get spun rapidly. Debates on theoretical issue are in depth. All these lead to more solid future software development
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| − |
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| − | ==Titles suggestions (Not in order!)==
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| − | * (1) Embracing open science : community collaboration
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| − | genericforms deleted his earlier suggestions 2 & 3 in favor of #10
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| − | * (6) SEQanswers: An Open Science forum serving the next-generation sequencing community
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| − | * (8) SEQanswers, Reading Biological Sequences as a Community since 2007.
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| − | marcowanger deleted his earlier suggestions 4,5,7 &9 in favor of #10
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| − | * (10) SEQanswers: Leveraging Collective Intelligence to Decode Biological Sequences [title used when presub inquiry was sent to GM]
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| − |
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| − | ==Authors' list (still not in order yet!)==
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| − | * Eric C. Olivares; SEQanswers.com, Union City, CA 94587, USA
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| − | * Jing-Woei Li; School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR
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| − | * David Mittelman; (1)Virginia Bioinformatics Institute (2)Department of Biological Sciences; Virginia Tech, Blacksburg, VA 24061, USA
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| − | * Robert Schmieder; Computational Science Research Center and Department of Computer Science, San Diego State University, San Diego, CA 92182, USA
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| − | * ......
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| − |
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| − | [Need to define an order?]
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| − | *would like to lead --[[User:Marcowanger|Marcowanger]] 11:41, 2 December 2011 (PST)
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| − | *would like to be last author/corresponding --[[User:Genericforms|Genericforms]] 4:45, 5 December 2011 (EST)
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| − |
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| − | ==Abstract==
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| − | 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.
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| − |
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| − | 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.
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| − | ==The Need for an Open Science Platform==
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| − | DATAPOINT on the need for open access as exemplified by SEQanswers: In a global survey conducted in part by Elsevier Publishing in October 2010, in a sample of 51,000 researchers, 62% of respondents say access to data sets/data models/algorithms and programs are very important to their ongoing research but report that among all forms of scholarly information communication listed in the survey, these resources are most difficult to access.
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| − | http://www.publishingresearch.net/documents/PRCAccessvsImportanceGlobalstudyPhase1Oct2010.pdf
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| − |
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| − | 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.
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| − | '''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'''
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| − | <!-- [COMMENT: I like this but I think it understates the true value of SeqAnswers. It is not simply that there are so many new users that don't know enough. It is that existing experienced users don't know enough. The field is changing so fast that traditional journal publication simply cannot facilitate the dissemination of new information in reasonable timescales. SeqAnswers is not just an information resource. It represents a fundamentally new way of interacting with and sharing scientific advancement. Just my two cents here...]'''<Could you try to work your thoughts into the second paragraph? I added some more things to the first one to strengthen it.>''' -->
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| − | '''<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>'''
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| − | ==SEQanswers - An open scientific forum==
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| − | 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 ([https://docs.google.com/document/d/11yTCdVayUffjz2Y2MpyLR2naGAgdLQUZoM9LLFrpGLg/edit?authkey=COrb4cgH 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 ([https://docs.google.com/document/d/11yTCdVayUffjz2Y2MpyLR2naGAgdLQUZoM9LLFrpGLg/edit?authkey=COrb4cgH Figure 2]).
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| − | 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.
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| − | '''Box 1: Main topics of/in SEQanswers'''
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| − | * General discussion
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| − | * Core facilities
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| − | * Literature
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| − | * Conferences
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| − | * Bioinformatics help discussions (installation, troubleshooting)
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| − | * Jobs forum (Industry/academic/non-profit)
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| − | * Sequencing technologies
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| − | * Scientific applications (Sample prep, resequencing, de novo, metagenomics, epigenetics, RNA sequencing)
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| − | * Application/tool announcements
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| − | * Regional communities
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| − |
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| − | For above topics, we might put them in a TABLE
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| − |
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| − | ==Use Cases and Success Stories==
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| − |
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| − | '''<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>'''
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| − | 3 ways.
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| − |
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| − | * specific discussion on CATEGORIES of success cases MENTIONED in introduction? <yes, maybe similar to the biostar paper>
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| − | * Support from literatures (those method papers e.g. Briefing in Bioinformatics, Nature, etc) <I would use this in the next paragraph>
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| − | * Indirect evidence from figure 3, the access log from around the world. <I would use this in the next paragraph>
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| − |
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| − | Suggested topic: How open discussion potentially improve algorithms design: Heng Li and Salberg on Bowtie 2 vs BWA
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| − |
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| − | ==Implications of SEQanswers for the Scientific Community and the medical field==
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| − |
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| − | 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.
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| − |
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| − | '''<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) >'''
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| − | ==Outlook and Perspective==
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| − | 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.
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| − |
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| − | Figures & References: [https://docs.google.com/document/d/11yTCdVayUffjz2Y2MpyLR2naGAgdLQUZoM9LLFrpGLg/edit?authkey=COrb4cgH Figures & References]
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Signers
- 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
- Felix Krueger, The Babraham Institute.
- Surya Saha, Cornell University
- Colin F. Davenport, Hannover Medical School
- Joann C. Delenick, Woodbridge, CT
- Michael James Clark, Stanford University
- Robert Schmieder, San Diego State University
- Rachel Glover, Food and Environment Research Agency
- Lorena Pantano, Institut de Medicina Predictiva i Personalitzada del Càncer
- David Mittelman, Virginia Tech
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,
- PLoS Com Bio - inquiry by marcowanger, reply on 10 Dec 2011
Thanks for your presubmission inquiry regarding your manuscript 'SEQanswers: Leveraging Collective Intelligence to Decode Biological Sequences [Perspective Article]'. Although we think that your study is interesting, we do not think it suitable for PLoS Computational Biology. I am sympathetic to what you have done and appreciate it might be important. However, we do not currently support an article type where it would be suitable. It might qualify as a Perspective, but this might open a floodgate to similar resources and we have no resources to evaluate them. ONE would seem a good place for this paper.
However, we very much appreciate your wish to present your work in an open-access publication and therefore want to alert you to an alternative that you may find attractive. PLoS ONE is a unique swift, high-volume system for the publication of peer-reviewed research from any scientific discipline. PLoS ONE aims to exploit the full potential of the web to make the most of every piece of research; if you would like to submit your work to PLoS ONE, please visit www.plosone.org and submit your work online.
Thanks for considering PLoS Computational Biology, and good luck with your work.
Yours sincerely,
Philip E. Bourne, Ph.D.
Editor-in-Chief
Previous drafts
Page of previous draft versions
Letter: Draft #Final
The final draft is moved to google document
Link here
