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Old 11-12-2010, 08:24 AM   #21
ECO
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Awesome work everyone.

I just updated as Draft 03...feedback welcome. I hope to submit this ASAP. My current thinking is not listing any individual authors on the abstract, as with the short notice many folk have not responded to the call for affiliations, etc. As the poster develops we can create the author list either based on contributions to the final poster, or in a more defined way that Dan (# edits/posts) or James (tag cloud) have suggested.

Quote:
SEQanswers.com: A web community for high-throughput sequencing users

<AUTHOR LIST>

In recent years, dramatic advancements in sequencing technology have created a rapidly advancing and complex field of research. These new technologies give us the capacity to answer biological questions that were previously out of reach. However, the speed with which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing.

SEQanswers (http://SEQanswers.com) was founded to address this gap; the site format facilitates the rapid dissemination of both wet-lab techniques and bioinformatic analyses. Over 12,000 registered users composed of a diverse blend of bioinformaticists, geneticists, and molecular biologists meet and share their experiences and tools. Instead of traditional peer-review through publication, the SEQanswers community offers instantaneous sharing of ideas and review of findings between peers at the cutting edge of the high-throughput sequencing field.

SEQwiki, a wiki site that is edited and updated by the members of the SEQanswers community, provides a categorized archive of high-throughput sequencing data analysis tools. SEQwiki includes links to publications, methods, data formats and types, and links to individual sites about these tools. After only 15 months, the SEQanswers community has created wiki pages for over 300 software tools with 250 scientific references and 400 web links. The use of Semantic MediaWiki extensions provides a simple means for swiftly finding information about the particular tool or experimental technique.

SEQanswers provides resources for scientists on the bleeding edge of high throughput genetics research where experiences, tools and findings can be shared without the filter of a long publication process or the need to directly contact one-another privately. These web-based communities are an invaluable resource for high-throughput sequencing now and in the future.
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Old 11-12-2010, 08:34 AM   #22
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Quote:
Originally Posted by james hadfield View Post

I have used tag clouds to visualise stuff before and it might be a way to look at content of even authors. See http://www.wordle.net/show/wrdl/2715503/SEQAnswers_page for a random SEQanswers page in a cloud format. If we collected a list of authors on every post and used this kind of format it should give credit to eveyone on the basis of their input. Those who post a lot would appear as larger text?
This is a great tool...I'd love to expand it to all the post text in the database, AND the post author list.

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Old 11-12-2010, 09:44 AM   #23
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More changes. AGBT requires a corresponding author, so I have to include at least one person who is registered for the conference. DNS hasn't propagated for members.seqanswers.com but it will work soon...

Quote:
SEQanswers.com: A web community for high-throughput sequencing users

Eric C. Olivares (1), Dan Bolser (2), The SEQanswers Community (3)

1. Founder, SEQanswers.com (Union City, CA, USA)
2. University of Dundee (Scotland, UK)
3. Complete member list at http://members.seqanswers.com

In recent years, dramatic advancements in sequencing technology have created a rapidly advancing and complex field of research. These new technologies give us the capacity to answer biological questions that were previously out of reach. However, the speed with which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing.

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 12,000 registered users composed of a diverse blend of bioinformaticists, geneticists, and molecular biologists meet and share their experiences and tools. SEQwiki, a user-maintained semantic wiki provides links to hundreds of publications, methods, data formats, and bioinformatics tools.

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 is an invaluable resource for worldwide collaboration and education in the modern genomics era.
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Old 11-12-2010, 09:56 AM   #24
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I think it's a very strong abstract, ECO. I like how you broke things up for easy reading.

Don't worry, though, I will nitpick for a second.

I hate semicolons. I feel like when I see a semicolon either a period could have been used or the two sentences could have been joined with a conjunction and/or a comma. In this case I feel like those two sentences could be joined with the word "by" like this:

"SEQanswers (http://SEQanswers.com) was founded to address this gap by providing a community-focused format that facilitates the rapid dissemination of both wet-lab techniques and bioinformatic analyses."

Nit-picking, though, so if you love semicolons, leave it.
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Old 11-12-2010, 10:12 AM   #25
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Thanks for the feedback; I will incorporate it accordingly.
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Old 11-12-2010, 10:59 AM   #26
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Ok, last call for comments/suggestions/edits/mocking. I plan to submit the abstract in post #23 by 2pm PST.
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Old 11-12-2010, 12:07 PM   #27
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I took the top 100 posters on the forum (by post count) and threw them in the Wordle app. Looks like it can't handle that many, so I had to cut it down to the top 50. Here's what came out:



Not really sure the point of it, but it's a cool graphic.

Also: Go Newsbot!
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Old 11-12-2010, 01:15 PM   #28
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Nice work with the abstract, and thanks for the link to Wordle. I tried Tagxedo which has too many options, so mjc beat me to it, but here are some "clouds" based on all members (except newsbot...) with >= 20 posts.

seq.jpg
seq3.jpg

Last edited by Chipper; 11-12-2010 at 01:37 PM. Reason: Tried to resize images...
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Old 11-12-2010, 02:13 PM   #29
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Chipper/MJC, I will definitely be hitting you guys up for some visualizations as we get closer to poster time! Those are excellent!

Abstract has been submitted as of 3:12pm PST, thanks to all that have contributed, I will definitely acknowledge everyone in some way on the poster!

Quote:
Hi AGBT!

Please find below the abstract describing the resources available as part of
my sequencing community website.

Thanks very much, I look forward to your feedback.

Sincerely,

Eric C. Olivares, Ph.D.
eric@seqanswers.com
http://www.linkedin.com/in/ericolivares


*******************************************

TITLE: SEQanswers.com: A Web Community for High-throughput Sequencing Users

Eric C. Olivares (1), Dan Bolser (2), The SEQanswers Community (3)

1. Founder, SEQanswers.com (Union City, CA, USA)
2. University of Dundee (Scotland, UK)
3. Complete member list at http://members.seqanswers.com

In recent years, dramatic advancements in sequencing technology have created
a rapidly advancing and complex field of research. These new technologies
give us the capacity to answer biological questions that were previously out
of reach. However, the speed with which these technological advancements
have come about has outpaced the speed of peer-reviewed publication and
other traditional forms of information sharing.

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 12,000 registered users
composed of a diverse blend of bioinformaticists, geneticists, and molecular
biologists meet and share their experiences and tools. SEQwiki, a
user-maintained semantic wiki provides links to hundreds of publications,
methods, data formats, and bioinformatics tools.

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 is an
invaluable resource for worldwide collaboration and education in the modern
genomics era.
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Old 11-13-2010, 08:44 PM   #30
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And now...we wait...just got the confirmation:

Quote:

fromRita Dunton <ritad@gcorp.org>
to"Eric @ SEQanswers"<admin@seqanswers.com>
dateSat, Nov 13, 2010 at 9:39 PM
subjectRe: Abstract Submission: SEQanswers.com: A Web Community for High-throughput Sequencing Users

Dear Dr. Olivares,

Your abstract for the 2011 AGBT Meeting has been received.

Thank you,

Rita

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Old 11-15-2010, 11:23 AM   #31
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Quote:
Originally Posted by Chipper View Post
Nice work with the abstract, and thanks for the link to Wordle. I tried Tagxedo which has too many options, so mjc beat me to it, but here are some "clouds" based on all members (except newsbot...) with >= 20 posts.

Attachment 543
Attachment 544
Those 2 seem to be really useful tools! thanks for sharing
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Old 11-18-2010, 01:48 AM   #32
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In Draft01 SEQWiki has presented as a categorised archive of tools.
The word CATEGORISED is also repeated at the end of the paragraph. So, probably it's better change this last part:

"This collection of categorised tools allows searches to be performed and overviews to be obtained. "
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Old 11-18-2010, 02:04 AM   #33
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Quote:
Originally Posted by m_elena_bioinfo View Post
In Draft01 SEQWiki has presented as a categorised archive of tools.
The word CATEGORISED is also repeated at the end of the paragraph. So, probably it's better change this last part:

"This collection of categorised tools allows searches to be performed and overviews to be obtained. "
Hi Elena, thanks for making those change on the wiki!
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Old 11-30-2010, 10:58 AM   #34
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interesting leads once we come to paper writing, etc!!

http://www.wikigenes.org/e/pub/e/85....F6B283A08.jvm1
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Old 11-30-2010, 02:02 PM   #35
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Quote:
Originally Posted by bioinfosm View Post
interesting leads once we come to paper writing, etc!!

http://www.wikigenes.org/e/pub/e/85....F6B283A08.jvm1
I'd really encourage any GWAS experts to contribute there! I just met Robert Hoffmann at the BioWiki conference, and he seems to have a good vision for collaborative scientific authorship on the internet. Seems like a good opportunity for a nature genetics article, and a nice experiment in community authorship.
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Old 01-27-2011, 10:41 AM   #36
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Hi all,

I'm a little bit annoyed to report that due to an unfortunate misunderstanding regarding my attendance, AGBT did not hold a spot for our poster.

I will definitely be in attendance and am looking forward to meeting as many of you as possible...
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Old 01-27-2011, 01:04 PM   #37
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Should we make a poster anyway? I'm sure you could find a spot for it somewhere... Or perhaps we can start a new trend in scientific t-shirts? Each member of the forum could print a t-shirt with the logo and a few key facts, and then mill around the conference....
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Old 01-27-2011, 01:38 PM   #38
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I'm happy to take it and try to put it up, but I fear I won't be able to spend much time working on it, nor next to it at the conference... :/
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Old 02-04-2011, 12:29 PM   #39
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So what happened to the poster? Did Eco make it and took it to the conference?
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Old 02-04-2011, 03:38 PM   #40
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I made it physically, but not with a poster.
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