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Old 11-09-2010, 12:14 PM   #1
dan
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Thumbs up SEQanswers/SEQwiki AGBT poster abstract?

ECO came up with the plan of submitting a SEQanswers / SEQwiki poster to AGBT 2011 (The 12th annual Advances in Genome Biology and Technology):

http://www.agbt.org/about.html


The current draft abstract is here, and I'd welcome any input (the deadline is Friday!):

http://seqanswers.com/wiki/Talk:SEQanswers


I thought it would be cool to acknowledge all the wiki contributors in the author list of the poster. As hundreds of authors is a bit of a logistical pain, I've just listed the top 20 contributors.

Let me know what you think!
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Old 11-10-2010, 06:52 AM   #2
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As biologist(s) clamour to exploit these new opportunities...
The pace of progress is accelerating beyond anything which has been (cross out "which has been") seen before...
...developing a variety (of) tools to exploit the new data.
the SEQanswers forum has proved an invaluable stop-gap for NGS software developers and users, allowing new tools and(cross out "and") to be rapidly announced, tested and benchmarked within the community.

Maybe it is me being paranoid on grammar, but think that maybe a few small changes can make it easier to read. Just my 2 cents.
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Old 11-10-2010, 08:03 AM   #3
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All suggestions welcome janejane! Please feel free to edit the text directly on the wiki! It makes it easier to review and/or accept/reject changes.

Cheers,
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Old 11-10-2010, 08:09 AM   #4
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Quote:
Originally Posted by dan View Post
All suggestions welcome janejane! Please feel free to edit the text directly on the wiki! It makes it easier to review and/or accept/reject changes.

Cheers,
Thanks. I made the changes on the wiki.
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Old 11-10-2010, 11:59 AM   #5
Michael.James.Clark
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I think it's a great idea. I am a little confused, though: Is this JUST about the SEQwiki or is it about SEQanswers as a whole including SEQwiki?

My suggestions here are assuming it's the latter.

If it is the latter, I think the abstract is missing the mark a little on describing precisely the incredible usefulness of SEQanswers as a community. It describes accurately that SEQanswers is a good place for rapid dissemination of analysis tools. However, it leaves out that SEQanswers is the go-to source for discussion on optimal ways of performing high-throughput sequencing from the bench all the way through analysis as well as for troubleshooting (and it honestly is the place to go for these things online). I think it's important to mention explicitly the community aspect of this site because it is really a meeting place for geneticists and bioinformaticians unlike anything else out there. It is a resource for those of us on the bleeding edge of this type of research where we can share experiences, tools and findings without having to go through the long process of publication or having to meet in person or over the phone. It is really a "forum" in the traditional sense for genomics research. I think that's a key point that should be made about why this site is such a valuable tool.

Also, I don't want to be "that guy" who quibbles over author lists, but this site is a community-driven resource, but this list picks particular people to include as contributors to the "project" and poster. In my opinion, the author list should probably be ECO, Dan, whoever physically puts together the poster (assuming it's not ECO or Dan) and "the SEQanswers/SEQwiki community". Just my two cents on that, but I think it would be very cool to put it that way as yet another way of emphasizing the whole concept to the people at AGBT.

If it's just about the Wiki, I think expansion on the use of the Wiki and the usefulness of the wiki medium for this kind of sharing is needed. Everyone pretty much knows what a wiki is, sure, but it would be great to describe how the wiki format is conducive to rapid dissemination of bioinformatic tools and optimal analytical techniques for the sequencing community.
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Old 11-10-2010, 07:07 PM   #6
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Quote:
Originally Posted by janejane View Post
Thanks. I made the changes on the wiki.
Thanks for the edit!

Quote:
Originally Posted by Michael.James.Clark View Post
I think it's a great idea. I am a little confused, though: Is this JUST about the SEQwiki or is it about SEQanswers as a whole including SEQwiki?

My suggestions here are assuming it's the latter.

**snip**
Hi MJC,

Thanks for your thoughtful comments, my original intent was your second suggestion, that the poster be about the site in general, including both community aspects and the wiki. I actually think you made some great first steps towards writing the abstract! I feel a bit awkward writing it myself, because it feels like I'm being too self-promotional when it really is the contributors that have made the site so useful. Having a member write it would make it all the more community-driven (*hint* *hint*).

I like your thoughts on authorship, both because some contributors may not want to be listed as an author, and to not risk offending people by drawing an arbitrary cut-off through who is an author and who isn't. I need to give it some more thought, as I'd love to recognize everyone but that could literally be hundreds of authors. Maybe an anonymous IP-geolocation visualization overlaid on the world map?!

I could imagine some really interesting visualizations of the information we have in the wiki (tools vs. applications vs. views, etc) and the forums (keywords, geographical correlations, etc), unfortunately I'm not qualified to generate most of them. I also need to get with Nick Loman and James Hadfield to potentially bring in the NGS machine map as that is also a pretty nice resource.

Lastly, the most ambitious goal/suggestion would be to use the community resources to actually do some community-driven science. I guarantee, if I put out the call we could get some instrument time donated by one of the many service providers that frequent the site, and I know that the community would rise to an informatics challenge. Just need a humanitarian idea and some samples. Maybe for next year's AGBT.

An additional wrinkle is that while I will be at AGBT, I probably can't officially present this poster as I will be wearing my day job attire and presenting a poster in that capacity as well. Should be a fun meeting!

Thanks again for your feedback...we are running out of time but the abstract should be fairly straightforward to generate.
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Old 11-10-2010, 08:52 PM   #7
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Quote:
Originally Posted by ECO View Post
Thanks for the edit!

...
Lastly, the most ambitious goal/suggestion would be to use the community resources to actually do some community-driven science. I guarantee, if I put out the call we could get some instrument time donated by one of the many service providers that frequent the site, and I know that the community would rise to an informatics challenge. Just need a humanitarian idea and some samples. Maybe for next year's AGBT.
...
Isn't data from the 1000 genomes project starting to flow?
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Old 11-10-2010, 08:58 PM   #8
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Quote:
Originally Posted by Jeremy View Post
Isn't data from the 1000 genomes project starting to flow?
I was thinking something more intimate, with defined goals (publication), that is tractable by this community.

That's not to say that anyone with free time/cpu's shouldn't be looking at the 1k-genome data...
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Old 11-11-2010, 04:39 AM   #9
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Quote:
Originally Posted by ECO View Post
Thanks for the edit!
I could imagine some really interesting visualizations of the information we have in the wiki (tools vs. applications vs. views, etc) and the forums (keywords, geographical correlations, etc), unfortunately I'm not qualified to generate most of them. I also need to get with Nick Loman and James Hadfield to potentially bring in the NGS machine map as that is also a pretty nice resource.
That is very interesting. I guess you'd be fine with sending a dump of the sql database so we can do some mining? I can try to plot some data.

P.S I have to admit I have not used the wiki too much. That is going to change.
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Old 11-11-2010, 08:07 AM   #10
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Re: Map, go for it. Let me know what you need if anything. If you can put James and I on the poster authors and acknowledge the community effort that goes into maintaining the map that would be great. If you need stats or something else let me know.
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Old 11-11-2010, 08:12 AM   #11
dan
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Hi Michael,

Thanks for the excellent contribution!

Could you try to add your suggestions to the rough or final abstract? It's here:

http://seqanswers.com/wiki/Talk:SEQanswers



Quote:
Originally Posted by Michael.James.Clark View Post
Also, I don't want to be "that guy" who quibbles over author lists, but this site is a community-driven resource, but this list picks particular people to include as contributors to the "project" and poster. In my opinion, the author list should probably be ECO, Dan, whoever physically puts together the poster (assuming it's not ECO or Dan) and "the SEQanswers/SEQwiki community". Just my two cents on that, but I think it would be very cool to put it that way as yet another way of emphasizing the whole concept to the people at AGBT.
Don't worry, several people have suggested that this way of creating the author list is a bit... weird?


I can only speak for the wiki, because that is where I've been involved (however, I assume something similar *could* be done for the forum? ECO, can you do this?).

By including the wiki's 'top contributors' on the author list of the poster, I'm trying to give more formal recognition to the useful work that has been done by those contributors. The point is that there have been some incredible contributors, without whom the wiki would be almost worthless. These people have gone over and above what could be reasonably expected. I wouldn't feel comfortable 'publishing' something about the wiki without including at least some of the top contributors, and my personal feeling is, the more the better. However, I know that there are certain logistics (I don't think people NOT wanting to be on the author list is a problem), so I cut the list at 10 edits or more. Yup, it's arbitrary, but so are most author lists ;-)


This community is somewhat unique, so why why not use a unique publication model?


For reference, here is the complete and unabridged list of contributors:


rev_user_text edits
Dan 1457
Krobison 913
Andreas.sjodin 216
Mmartin 126
ECO 96
Fhach 40
Annestover 30
Fkrueger 24
Jkbonfield 22
Smice 22
Zee 21
Alperyilmaz 18
Simonandrews 15
Maubp 14
Foolishbrat 13
Nomijill 13
Springbok28 13
Cariaso 11
TheLight 11
Nilshomer 11
Jvhaarst 11
Fabien Campagne 10
Dongliang Ge 10
Joa ds 9
Sjackman 9
Koadman 8
Lmilne 8
Simon Anders 8
Imanh 7
Fhormozd 7
Adalca 7
Flxlex 7
Jinyu Wu 7
Mmclella 7
BaCh 7
Simonvh 7
NicoBxl 7
Mfiume 6
Isuxyang 6
Taoliu 6
Apfejes 6
Tumorim 6
[email protected] 5
CATCH 5
Genelab 5
Timo Lassmann 5
Bioinfosm 4
Ondovb 4
Spyderspyder 4
134.36.64.135 4
BluGene 4
Micha 4
Tim Hague 4
Martinha 4
Uhjish 4
Hepcat72 4
Weese 4
130.223.44.176 3
Mfursov 3
Xuguorong 3
Brentp 3
Quinlana 3
Yxi 3
Btiwari 3
Mgogol 3
Tcga 3
Lh3 3
Michael.James.Clark 3
Rmervis 3
M elena bioinfo 3
TonyJose 3
Guillaum 3
Dfornika 3
HAA 3
Jonathan 3
Wjeck 3
Ohomann 3



OK, I lied. I cut it at >2 to avoid the 'heavy tail' of ~ one time editors.
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Last edited by dan; 11-11-2010 at 08:18 AM. Reason: Asking about the list of forum contributors.
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Old 11-11-2010, 08:15 AM   #12
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Quote:
Originally Posted by nickloman View Post
Re: Map, go for it. Let me know what you need if anything. If you can put James and I on the poster authors and acknowledge the community effort that goes into maintaining the map that would be great. If you need stats or something else let me know.
Thanks Nick. Can you send me your and James' desired affiliations?
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Old 11-11-2010, 10:20 AM   #13
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I'm a bit busy right now, I'll take a look and try to update the abstract this afternoon.
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Old 11-11-2010, 11:59 AM   #14
james hadfield
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Hi All,

An AGBT poster is a great idea and I would say to Eric don't worry about self promotion. You deserve this one!

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?

Listing some authors over others might not be fair but if it is done as a list of the top 5% of posters based on average posts it should be defensible. Scientists can’t argue with normal distributions! I am sure anyone that did make it onto the poster would be happy to be on it.

I would like to see the poster focus on the community aspect and the fact that this is THE place to go for info on next-gen.

Using the map to visualise where members are located might be good. The map was used in a recent Nature editorial and I was really pleased with the use of something which was created as a community resource to display what scientists across the world are doing with the technology.

Happy to help out more on a final poster.

Why not post the ppt file on Dropbox and ask people to save updates separately. I am not sure if there is a good PowerPoint collaboration tool?

James
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Old 11-11-2010, 02:22 PM   #15
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Default My $00.02

There should also be emphasis on the abundant and timely wet lab advice and analysis expertise that have been readily obtained from this forum. Who knows how many research $$'s already saved on costly reagents otherwise wasted plus biological samples due to this valuable resource.

Please illustrate the global distribution of (active) members and how the number of posts received per member sort out.

Invite others actively interested to become members.

Extend a request for suggestions on possible community project(s).
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Old 11-11-2010, 02:51 PM   #16
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^ I think that's a very good suggestion as well. The bioinformatics forum is probably the most busy, but there are valuable and important discussions on the wet lab as well.

Examples of important discussions/findings about the best way to do things could be included on the poster.

If you use Google Analytics to track site stats, you might have a lot of cool info on where users are coming from, pages with the most page views etc.
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Old 11-11-2010, 04:44 PM   #17
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kudos to the idea! That will be a useful poster. Let me know how I could help, though I have mostly been active here on SeqAnswers, not so on the wiki page.

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Old 11-11-2010, 08:41 PM   #18
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Okay, I wrote up something taking ideas from the group. I added it as "Draft 2" on the Wiki. 296 words.

The "XXXX"s need to be replaced with actual numbers from the site.

Here it is pasted on the forum:

"Over the past few years, significant advancements in genome sequencing technology have created a rapidly advancing and complex field of research. These new technologies give us the capacity to answer genetic questions that were previously out of our 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. To facilitate the rapid dissemination of biochemical techniques and bioinformatic analysis tools to deal with high throughput sequencing technologies, we present SEQanswers, an online community with over XXXX users including some of the brightest minds in genomics and bioinformatics. The SEQanswers community is a literal forum for geneticists and bioinformaticians to meet and share their experiences and tools. Instead of traditional peer-review through publication, the SEQanswers community offers instant sharing of ideas and review of findings between individuals at the cutting edge of the high-throughput sequencing field. SEQwiki, a wiki site that is edited and updated by the members of SEQanswers, 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 bioinformatic tools. After only XXX months, the SEQanswers community has created SEQwiki pages for over 300 software tools with around 250 scientific references and 400 web links. A search tool provides a simple means for swiftly finding information about the particular tool or experimental technique one is searching for. SEQanswers and SEQwiki are 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 11-11-2010, 09:14 PM   #19
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This looks good. Made a minor edit on the wiki (addition of "-" between high and throughput).
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Old 11-12-2010, 12:38 AM   #20
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Quote:
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This looks good. Made a minor edit on the wiki (addition of "-" between high and throughput).
Just in case people don't realise, you can track all the changes made to the wiki page here:
http://seqanswers.com/w/index.php?ti...action=history

(Click the 'View history' tab when on the discussion page itself).


From the history page you can bring up diffs of individual pairs of edits. For example, I just 'attacked' Draft 02 and you can find the diff here:

http://seqanswers.com/w/index.php?ti...523&oldid=3522


Please don't worry, attacking is the wiki way ;-) Be bold!

Dan.
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