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| | + | == Signers, (ordered by time of sign) == |
| | + | * 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 |
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| | + | |
| | =Pre-inquiry emails= | | =Pre-inquiry emails= |
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| | Correspondence articles are open access, peer-reviewed articles that | | Correspondence articles are open access, peer-reviewed articles that |
| | include brief reports of particular interest to the community | | include brief reports of particular interest to the community |
| − | (http://genomemedicine.com/authors/in...correspondence). To | + | (http://genomemedicine.com/authors/instructions/correspondence). To |
| | submit the article, please go to http://genomemedicine.com/manuscript." | | submit the article, please go to http://genomemedicine.com/manuscript." |
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| − | * '''Genome Biology''' -inquiry by marcowanger, reply on 29th Nov 2011
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| − | Thank you for your email in which you offer to submit a Correspondence
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| − | manuscript on the SEQanswers community to Genome Biology. I am very
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| − | sorry about the delay in getting back to you about it. Having discussed
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| − | and considered your proposal with my colleagues, I am afraid that we are
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| − | ''unable to consider the manuscript you describe for publication''.
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| − | I'm sorry that we can't be more positive but we are sure you won't have
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| − | any difficulties in publishing your article elsewhere. Thank you for
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| − | your interest in Genome Biology.
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| | | | |
| | =Previous drafts= | | =Previous drafts= |
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| | =Letter: Draft #Final = | | =Letter: Draft #Final = |
| − | == 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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| − | ==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
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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 identify a lead (first) author, a last author that will submit, and the order of all the authors in between.]
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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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| − | Over the last four years, SEQanswers has become a firmly established HTS knowledge-sharing platform currently used by over 4,000 active members that participate in an increasing number of discussions. Part of its success can be attributed to the way it mirrors the broader scientific community, where communication of knowledge between peers is paramount. More than 10,000 discussions (as of November 11, 2011) provide insights on sequencing technologies, data analysis methods, service providers and other HTS related issues - 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 the publication. Post-publication vibrant discussion involving the interactions between users and developers and debates on theoretical issues among tools developers all lead to ideas to develop better tools. HTS related bioinformatic tools are extensively categorized in the user-maintained SEQanswers wiki.
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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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| − | 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 - A Platform/Community for ...==
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| − | 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. Over the last four years, SEQanswers has become a firmly established HTS knowledge-sharing platform currently used by over 4,000 active* members that participate in an increasing number of discussions (Figure 1). Part of its success 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 quality of contribution, is recognized.
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| − | '''< I'm wondering where the quality of each contribution is captured in the forum >'''
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| − | More than 10,000 discussions (as of November 11, 2011) provide insights on sequencing technologies, data analysis methods, service providers and other HTS related issues - 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 the publication. Post-publication vibrant discussion involving the interactions between users and developers and debates on theoretical issues among tools developers all lead to ideas to develop better tools. HTS related bioinformatic tools are extensively categorized in the user-maintained SEQanswers wiki [1].<!-- SEQanswers has been acknowledged in over 30 peer-reviewed publications**. (use the footnote for the last paragraph to save words) -->
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| − | ==Use Cases and Success Stories==
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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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| − | ==Implications of SEQanswers for the Scientific Community==
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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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| − | '''<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 will continue to provide an open platform to scientists all over the world.
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| − | Footnotes:
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| − | * Registered users visiting SEQanswers within the last 4 weeks.
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| − | ** http://seqanswers.com/wiki/Papers_Referencing_SEQanswers (and maybe references listed in the gdoc)
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| − | <!-- replace with numbers later in the gdoc -->
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| − | Figures & References: [https://docs.google.com/document/d/11yTCdVayUffjz2Y2MpyLR2naGAgdLQUZoM9LLFrpGLg/edit?authkey=COrb4cgH Figures & References]
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| − | '''<I would add this maybe as a box or in the text if we have enough space>'''
| + | The final draft is moved to google document |
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| − | '''Box 1: Main topics of the SEQanswers community.'''
| + | [https://docs.google.com/document/d/1PSuq6IIYXwDOCJYn7CWjH4EG-1QT5PWFCf6BQWsyZqE/edit Link here] |
| − | * 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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