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| | * Application/tool announcements | | * Application/tool announcements |
| | * Regional communities | | * Regional communities |
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| − | ''Everything below belongs to previous versions of draft''
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| − | =Letter: Draft #3=
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| − | Please take a look at a '''draft''' paragraph (in wiki paper) describing SEQanswers
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| − | [http://dl.dropbox.com/u/4125508/SEQanswers/SEQanswers.intro.pdf SEQ_introduction]
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| − | *'''To avoid self-plagiarism'''
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| − | * To guide writing of this letter?
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| − | This is the current version. Remember to annotate your edits in the 'Summary:' field when editing.
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| − | During writing, ask yourself what do you want to know if you are even not in the HTS field. Is it just a scientific forum? Or an '''indication of info-sharing paradigm shift.'''
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| − | I think it will be important to add several more things to stress that point of why we need SEQanswers:
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| − | (1) increasing demands for statistical methods and bioinformatics tools and
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| − | (2) there are no data analysis standards and therefore it is important to share the experience of users (both wet-lab and computational)
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| − | (3) Stress the key developers in the field are active SEQanswers members (e.g. Nils Homer, Heng Li, etc.)
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| − | Other things that could be used in the text:
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| − | The increasing affordability of ambitious projects has created a pressing need for rapid dissemination of technical knowledge and software for the analysis of HTS data.
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| − | There has been a proliferation of different wet-lab technologies and many hundreds of different software tools now exist.
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| − | Open science:
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| − | [http://www.openscience.org/blog/?p=269 What is open science]
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| − | [http://michaelnielsen.org/blog/the-future-of-science-2/ The future of science]
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| − | One example of open sourcing science:
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| − | Please take a look at TED talk, search Jay Bradner : [http://blog.ted.com/2011/10/27/open-source-cancer-research-jay-bradner-on-ted-com/ Open-source cancer research]. --[[User:Marcowanger|Marcowanger]] 06:41, 11 November 2011 (PST)
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| − |
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| − | == Text ==
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| − | ''Currently 400 words, aim is ~300''
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| − | ==Why there is SEQanswers==
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| − | Ongoing technological advancements in high-throughput sequencing (HTS) are vastly outstripping Moore's law, fueling research with far-reaching social and economic impacts. The rapidly decreasing cost of sequencing is reflected in a growing number of research groups that incorporate sequencing in their projects. Technological innovation has enabled the exploration of biological questions that were previously out of reach. Now, even experienced scientists have to seek expertise in knowledge on sequencing platforms, novel experimental protocols and data analysis methods. However, <the argument here is to argue the publication system is insufficient to support those who do the actual work, example: Heng Li says in "BWA vs Bowtie2 thread that the methods he used in publication which might seems right at at moment of publication is obviously wrong NOW, so looking at literatures along will guide the readers to a wrong direction. Fix? Search in SEQanswers!>, thus increasing the need for a community-based platform to share knowledge about sample collection, experimental design and bioinformatic analyses. The SEQanswers community (http://SEQanswers.com/), an open scientific forum focused on HTS, was founded in late 2007 to close the information gap and facilitate rapid dissemination of both wet-lab techniques and bioinformatic analyses. SEQwiki, a user-maintained semantic wiki hosted by SEQanswers, facilitates selection from the hundreds of available HTS tools [1].
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| − | '''<x words>'''
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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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| − | ==Brief the readers about SEQanswers==
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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 (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 status, as assessed by quality of contribution, is recognized. More than 10,000 discussions (as of November 11, 2011) provide insights on sequencing technologies, service providers, scientific applications and related issues - information and technical know-how that will otherwise only be found scattered throughout the Internet. Besides, many bioinformatic developers use SEQanswers for pre-publication announcements of new tools and provide extensive post-publication feedback. SEQanswers has been acknowledged in over 30 peer-reviewed publications** '''<some else is needed here>'''.
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| − | '''<x words>'''
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| − |
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| − | ==Implication of SEQanswers to the scientific community and closing remarks==
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| − |
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| − | As technology continues to develop at a staggering pace in many disciplines, the rate of peer-reviewed publication and other traditional forms of information sharing is no able to track all movements in the field. Scientific forums (or similar) will allow instantaneous sharing of results, techniques, and trouble shooting. Most likely, these scientific forums will play an important role in developing the necessary data analysis standards for the HTS field <referring to sci. forum in general, not specific to HTS field; this is one of the main problems of HTS and I think it is a good example here>. Further, 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. <A perfect example for open science?>
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| − | '''<x words>'''
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| − |
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| − | <!-- I think the 3 paragraph layout will be better for a 300 word letter. -->
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| − | Footnote:
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| − | * Registered users visiting SEQanswers within the last 4 weeks.
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| − | ** http://seqanswers.com/wiki/Papers_Referencing_SEQanswers
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| − | <!-- replace with numbers later -->
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| − |
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| − | =Trimmed letter: Draft #2=
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| − | The current state of the trimmed letter may be accessed as a [https://docs.google.com/document/d/12lpMJxg-7HlYNXjjNrHMNu8-JwREXkkoNrfI0W3OpJc/edit?hl=en_US Google document]
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| − | <snip> # Moved to GDoc
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| − |
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| − | =Background=
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| − | During the review of the SEQwiki paper [1], an important point was raised, by the reviewers, the SEQanswers forum has yet to be published, and deserves a good publication.
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| − | Lets write a short Science letter (< 300 words) [http://www.submit2science.org/ws/begin.asp] or Nature Correspondence (< 350 words) [http://www.nature.com/nature/authors/gta/others.html#correspondence][http://mts-nature.nature.com/cgi-bin/main.plex?form_type=display_auth_instructions] about SEQanswers!
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| − |
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| − | SEQanswers has already been [[Papers Referencing SEQanswers|'informally' cited dozens of times]] in the literature, so why not write a nice summary for everyone to cite?
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| − | Please contribute (and sign the letter) below! The final list of authors will be ranked according to (democratically determined) contribution to the final text.
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| − | Meta paper discussion should stay on the forum thread [http://seqanswers.com/forums/showthread.php?p=53151 here].
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| − | Ideas to convey
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| − | * SEQanswers as a community for interactions among NGS users and between users and developers (UNIQUE)
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| − | * SEQ* is a firmly established community, as reflected by papers that cite SEQ*
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| − |
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| − |
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| − | = Content (Long version)=
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| − | In recent years, dramatic advancements in sequencing technology have created a rapidly advancing and complex field of research. These new technologies have given us the capability to answer biological questions that were previously out of reach. However, the rate at which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field rapidly becoming known for 'big data'.
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| − |
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| − | SEQanswers (http://SEQanswers.com) was founded to address this gap. The community-focused format facilitates the rapid dissemination of both wet-lab techniques and bioinformatic analyses. Over 20,000 registered users composed of a diverse blend of bioinformaticians, geneticists, and molecular biologists meet and share their experiences and tools. SEQwiki (http://seqanswers.com/wiki/SEQanswers), a user-maintained semantic wiki hosted by SEQAnswers, provides an organizational structure to hundreds of publications, methods, data formats, and bioinformatics tools.
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| − | Previously, user feedback was almost exclusively directed directly to authors of the bioinformatics software. Only a few disparate, well-established, or well-funded groups provided publicly archived mailing lists for community discussion. Software reviews by bloggers were similarly posted independently and relatively rarely. Newcomers to the fast evolving sequencing research field faced a seemingly overwhelming challenge to determine the most effective way to analyze their data.
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| − | SEQanswers has fostered lively review of both pre-publication and post-publication tools. Usually, long before peer reviewed publication, tools have been announced in SEQanswers and tested extensively within the community. Post publication improvement and benchmarking among developers is encouraged by discussions in the SEQanswers forums. Moreover, many avid bloggers and individuals from well-established groups contribute to the forum discussions and provide insights that may otherwise only have been found scatter throughout the Internet in various places, if available publicly at all.
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| − |
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| − | As a supplement to traditional forms of scientific communication, SEQanswers offers instantaneous sharing of ideas and review of findings between peers at the cutting edge of high-throughput genome biology. The site has become an important resource for worldwide collaboration and education in the modern genomics era. The Bioinformatics forum in particular has acted as a venue for discussing problems using bioinformatics tools, which can also help tool developers by highlighting areas where their documentation may be lacking, potential for new functionality, and often useful bug reports. In a relatively short time, SEQanswers has thereby become an extensive and firmly established knowledgebase for next generation sequencing and its bioinformatics applications. The rapid response times of experts and developers in various fields to all sorts of questions, ranging from biological questions to the discussion or usage of bioinformatic tools, makes SEQanswers a first port of call for bench scientists and computational biologists alike. Some overlap exists between the bioinformatics forum at SeqAnswers, and the community-driven Bioinformatics Question and Answer website (http://biostar.stackexchange.com). SeqAnswers, however, aims to foster discussion beyond the question-and-answer style of Biostar, and targets a wider audience than just those researchers with a bioinformatics related question.
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| − |
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| − | Moreover, as many people involved in sequencing facilities are part of the SEQanswers community already, common-sense decisions of standards such as data-formats or best-practice bioinformatic analyses may be taken much more easily. In the modern Internet era, it has been demonstrated that transactive memory is becoming an increasingly important mechanism for learning and answering difficult questions. [[http://www.sciencemag.org/content/early/2011/07/13/science.1207745 Sparrow et al., 2011]] SeqAnswers consistently shows up in searches by Google for terms related to the fields of next-generation sequencing, genomics and bioinformatics, suggesting it fills a major role in the rapid dissemination of information to scientists all over the world. Within the near future, SEQanswers aims to provide summary pages with links and of various important topics, and continues to provide a platform for discourse among isolated groups of experts across different countries.
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| − |
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| − | ===Summary of forum contents===
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| − | Here is a short summary of the contents covered by the forum. (Could act as help in the writing process)
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| − |
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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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| − | ===Future Directions===
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| − | SEQanswers forum is uniquely poised to lead in developing unbiased, relevant community operating standards at a global scope--ably incorporating all of the myriad platforms currently in use to generate massive sequence datasets. It can offer a panel of authoritative insight to national science funding agencies, both formally and informally, maintaining a global perspective on strategic use of scarce public funds in support of the NGS infrastructure and avoiding duplication of efforts.
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| − |
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| − | Other statements:
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| − | 1) While wet lab protocols are hosted at other sites, there are many posts on SEQanswers forums that instantly address emerging wet lab issues, including reagent batch problems, shearing techniques, sample choices, etc. Much time and money is potentially saved in the course of regular wet lab operations in support of NGS due to the available expertise and experience on tap here.
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| − | 2) The wide range of posts encompass larger issues that need to be addressed by the global NGS community, including ethics, regulatory issues, public/private funding sources for research and availability of resulting NGS data.
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| − | 3) This forum provides a useful interface with the general public interested in pursuing popular applications of next gen techniques. It is a source of information to beginners of all types and backgrounds, from high school interns to MBA's.
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| − |
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| − | ==References==
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| − | [1] SEQwiki paper in NAR 2012<br>
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| − | [2] Sparrow B, Liu J, Wegner DM. (2011) Google effects on memory: cognitive consequences of having information at our fingertips. Science. 2011 Aug 5;333(6043):776-8. Epub 2011 Jul 14. PMID: 21764755<br>
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| − |
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| − | == Signers (to be ordered by most significant contribution) ==
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| − | * Eric C. Olivares, SEQanswers.Com.
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| − | * Jing-Woei Li, The Chinese University of Hong Kong.
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| − | * Dan M. Bolser, University of Dundee.
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| − | * Peter Ulz, Medical University of Graz.
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| − | * Andreas Sjödin, Swedish Defence Research Agency.
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| − | * Peter J. A. Cock, James Hutton Institute.
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| − | * Lex Nederbragt, University of Oslo
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| − | * Felix Krueger, The Babraham Institute.
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| − | * Surya Saha, Cornell University
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| − | * Colin F. Davenport, Hannover Medical School
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| − | * Joann C. Delenick, Woodbridge, CT
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| − | * Michael James Clark, Stanford University
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| − | * Robert Schmieder, San Diego State University
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| − | * Rachel Glover, Food and Environment Research Agency
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| − | * Lorena Pantano, Institut de Medicina Predictiva i Personalitzada del Càncer
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| − | * David Mittelman, Virginia Tech
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| − |
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| − | =Trimmed letter: Draft #1=
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| − | Rapid technological advancement has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field rapidly becoming known for 'big data'. The SEQanswers community (http://SEQanswers.com/) was founded to facilitate rapid dissemination of high-throughput sequencing (HTS) related wet-lab techniques and bioinformatic analyses. Here, over 20,000 registered users '''(ECO may be able to provide numbers of queries per day)''' from a diverse blend of bioinformaticians and molecular biologists meet and share their technical knowhow. Meanwhile, the SEQwiki (http://SEQwiki.org/), a user-maintained semantic wiki hosted by SEQanswers, provides an organized structure to hundreds of bioinformatics tools including their publications, methods and data formats [1].
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| − |
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| − | SEQanswers is uniquely positioned in the HTS field and has become a firmly established knowledge platform. Many researchers and experts contribute extensively to the forum discussions and provide insights that may otherwise only have been found scattered throughout the Internet, if publicly available at all. The SEQanswers community targets a wide audience by providing a platform for debates on trending HTS related issues; reviews of both pre-publication and post-publication tools; and a literature watch. Moreover, the insightful Q&A on biological and informatics problems, make the community a first port of call for both wet-lab scientists and computational biologists [2-12]. SEQanswers also plans to seek partnership with the reputable community-driven bioinformatics Q&A website BioStar (http://biostar.stackexchange.com). In parallel, SEQanswers is inviting a network of high profile bloggers to bring even more content to the site, thereby stimulating more vibrant discussion.
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| − |
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| − | In the Internet era, transactive memory is becoming an increasingly important mechanism for learning and answering difficult questions [13]. SEQanswers ranks highly in Google searches related to HTS, genomics and bioinformatics, suggesting that it is an active, strong and sizeable community playing a major role in the rapid dissemination of information to scientists worldwide. '''The most common search terms leading to SEQanswers include [ECO might be able to put together a list/table of the most common search terms that lead from Google to Seqanswers using Google Analytics if he has it set up here] and the site is regularly accessed from X countries all over the world [ECO might be able to provide a short table with typical hit counts from specific countries].''' SEQanswers will continue to provide a platform for open discourse, allowing the rapid dissemination of knowledge and emerging issues to scientists all over the world.
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| − |
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| − | ===References===
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| − | [1] SEQwiki paper in NAR 2012. <br>
| |
| − | [2] Dassanayake, M., Oh, D.H., Haas, J.S., Hernandez, A., Hong, H., Ali, S., Yun, D.J., Bressan, R.A., Zhu, J.K., Bohnert, H.J. et al. (2011) The genome of the extremophile crucifer Thellungiella parvula. Nature genetics, 43, 913-918.<br>
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| − | [3] Oshlack, A., Robinson, M.D. and Young, M.D. (2010) From RNA-seq reads to differential expression results. Genome Biology, 11, 220.<br>
| |
| − | [4] Zheng, Z., Advani, A., Melefors, O., Glavas, S., Nordstrom, H., Ye, W., Engstrand, L. and Andersson, A.F. (2010) Titration-free massively parallel pyrosequencing using trace amounts of starting material. Nucleic Acids Res, 38, e137.<br>
| |
| − | [5] Huttenhower, C. and Hofmann, O. (2010) A quick guide to large-scale genomic data mining. PLoS Comput Biol, 6, e1000779.<br>
| |
| − | [6] Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform, 11, 473-483.<br>
| |
| − | [7] Huss, M. (2010) Introduction into the analysis of high-throughput-sequencing based epigenome data. Brief Bioinform, 11, 512-523.<br>
| |
| − | [8] Nielsen, C.B., Cantor, M., Dubchak, I., Gordon, D. and Wang, T. (2010) Visualizing genomes: techniques and challenges. Nat Methods, 7, S5-S15.<br>
| |
| − | [9] Flicek, P. and Birney, E. (2009) Sense from sequence reads: methods for alignment and assembly. Nat Methods, 6, S6-S12.<br>
| |
| − | [10] McPherson, J.D. (2009) Next-generation gap. Nat Methods, 6, S2-5.<br>
| |
| − | [11] Trapnell, C. and Salzberg, S.L. (2009) How to map billions of short reads onto genomes. Nat Biotech, 27, 455-457.<br>
| |
| − | [12] Horner, D.S., Pavesi, G., Castrignano, T., De Meo, P.D.O., Liuni, S., Sammeth, M., Picardi, E. and Pesole, G. (2010) Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform, 11, 181-197.<br>
| |
| − | [13] Sparrow, B., Liu, J. and Wegner, D.M. (2011) Google Effects on Memory: Cognitive Consequences of Having Information at Our Fingertips. Science. <br>
| |
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
Previous versions of drafts
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)
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
