Publication/Letter for SEQanswers
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/in...correspondence). To submit the article, please go to http://genomemedicine.com/manuscript."
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.
- Interactions among peer bioinformatics analysts
- How to do denovo assemble of a transcriptome
- Discussion by users on a newly released tool. DEGseq developer answer specific questions
- Enable dynamic interactions among users and developers. Software developers thus receive a wider pool of potential users
- Call for beta-testers
- Promotion of published tools
- Update of well established tools
- Promotion of unpublished tools
- 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
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
- ......
[If no one objects, I think we should begin to put order, real names, and full affiliations.]
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.
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. 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.
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.
Why there is SEQanswers
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. <150 words>
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>
Brief the readers about SEQanswers
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. < I'm wondering where the quality of each contribution is captured in the forum > 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]. <158 words>
Implication of SEQanswers to the scientific community and closing remarks
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. <126 words>
<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) >
Footnote:
* Registered users visiting SEQanswers within the last 4 weeks. ** http://seqanswers.com/wiki/Papers_Referencing_SEQanswers (and maybe references listed in the gdoc)
Figures & References: Figures & References
Main topics/Content of the SEQanswers community:
- 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
