Time to publish SEQanswers?

dan · 10-05-2011, 01:55 PM

During the review of the SEQwiki paper, an important point was raised by the reviewers: the SEQanswers forum has yet to be published, and deserves a good publication.

Why don't we write a letter to Science or Nature about SEQanswers?

The project has already been 'informally' cited dozens of times in the literature, so why not write a nice summary for everyone to cite?

The proposal is to use the wiki to collaboratively draft a letter to Science or Nature (see: wiki:Publication/Letter_for_SEQanswers), with each contributor adding their name to the paper. The final list of authors will be ranked according to (democratically determined) contribution to the final text.

Please contribute (and sign the letter) here!

Meta paper discussion should stay on this thread (wiki sucks for discussion).

marcowanger · 10-06-2011, 12:01 AM

How long will we aim?

Personally, I think we should keep it short.

ulz_peter · 10-06-2011, 12:43 AM

Publishing SeqAnswers for being able to cite it "formally" is a great idea.
I second the opinion of marcowanger to keep it quite short.

andreas.sjodin · 10-06-2011, 01:53 AM

I also think we should aim to keep it short and that it is a great idea. At least if we are going for a letter. An alternative would to write a more extensive "application note" describing the features but that would require much more work.

maubp · 10-06-2011, 03:10 AM

Do we want to mention that SeqAnswers also acts as a useful forum for helping users with problems using NGS tools (sometimes leading to useful bug reports for the tool developers)? Or would that just encourage more of this - which wouldn't be such a bad thing except it can drown out other more important threads, like file format changes etc.

ulz_peter · 10-06-2011, 03:16 AM

I think thats a good idea, as most of the threads in Seqanswers are indeed related to usage questions

marcowanger · 10-06-2011, 03:19 AM

Quote:

Originally Posted by maubp

Do we want to mention that SeqAnswers also acts as a useful forum for helping users with problems using NGS tools (sometimes leading to useful bug reports for the tool developers)? Or would that just encourage more of this - which wouldn't be such a bad thing except it can drown out other more important threads, like file format changes etc.

Maubp, you raised an important point. Helping users with tools selection and bug report and improvement is an important "function" of this forum(IMO). In fact we. have written a bit in the introduction part, maybe we need to stress it more.

maubp · 10-06-2011, 03:30 AM

OK, I've added a bit of text along those lines.

Peter

maubp · 10-06-2011, 03:32 AM

Also, is it worth thinking about an option for real names in forum profiles at this point?

dan · 10-06-2011, 03:34 AM

Quote:

Originally Posted by andreas.sjodin

I also think we should aim to keep it short and that it is a great idea. At least if we are going for a letter. An alternative would to write a more extensive "application note" describing the features but that would require much more work.

That's what I was thinking too... anyone know the guidelines for 'letters' to Science or Nature? Lets stick to one guideline or the other.

fkrueger · 10-06-2011, 03:42 AM

I also think that SEQanswers is an incredibly useful knowledgebase all around NGS and its bioinformatics applications. I especially love its instantaneous character and the (usually) extremely short reaction times of experts and developers in the fields to all sorts of questions, ranging from biological questions to discussion/usage of various bioinformatic tools to bug reports or feature requests. For many questions I have and had in the past, SEQanswers has become my first port of call to look for solutions or help.

ulz_peter · 10-06-2011, 03:44 AM

Any suggestions for the future directions part?

ulz_peter · 10-06-2011, 03:45 AM

found in Science Homepage:

How to Submit a Letter to the Editor

Letters to the Editor are selected for publication that are pertinent to material published in Science or that discuss problems of general interest. Letters may be reviewed. Those selected for publication are intended to reflect the range of opinions received. The author of a paper in question is usually given an opportunity to reply.

Letters are not routinely acknowledged. Full addresses, signatures, and daytime phone numbers should be included. Letters should be brief (300 words or less) and may be edited for reasons of clarity or space. They may appear in print and/or on the World Wide Web. Letter writers are not consulted before publication.

ETHANol · 10-06-2011, 03:48 AM

I think the future directions section is interesting. Just some ideas on what could be mentioned there:
1) The addition of a wet lab protocols wiki
2) As the size of the community increases, what are measures that can be implemented to keep the ratio of good information high to bad information? Perhaps the addition of energetic application specific moderators. This by the way it should be mentioned in the text that the ratio of good information to bad is really high on this forum.
3) Something else that might be cool is if there was some way to 'like/+1' threads and a section with the most popular threads. Might make browsing more efficient for causal readers.

ulz_peter · 10-06-2011, 03:53 AM

Quote:

Originally Posted by ETHANol

I think the future directions section is interesting. Just some ideas on what could be mentioned there:
1) The addition of a wet lab protocols wiki
2) As the size of the community increases, what are measures that can be implemented to keep the ratio of good information high to bad information? Perhaps the addition of energetic application specific moderators. This by the way it should be mentioned in the text that the ratio of good information to bad is really high on this forum.
3) Something else that might be cool is if there was some way to 'like/+1' threads and a section with the most popular threads. Might make browsing more efficient for causal readers.

I like the idea of the wetlab protocol wiki. That should be feasible with bioinformatic analysis guidelines as well (like the RNA Analysis manual).

So not only a list of available softwares (like the SeqWiki)but how to use them...

However, I think we should separate the Forum from the Wiki for the letter, as the Wiki is getting published already, am I right?

andreas.sjodin · 10-06-2011, 04:13 AM

I think wet lab protocols are better hosted at OpenWetWare.

Adding a section of small "example code snippets" to each software in the SEQwiki would be great. Should be added to wanted features in the SEQwiki.

I think it is better to mainly concentrate on the SEQanswer Forum in the letter.

marcowanger · 10-06-2011, 04:20 AM

Quote:

Originally Posted by andreas.sjodin

I think wet lab protocols are better hosted at OpenWetWare.

Adding a section of small "example code snippets" to each software in the SEQwiki would be great. Should be added to wanted features in the SEQwiki.

I think it is better to mainly concentrate on the SEQanswer Forum in the letter.

Agree that openwetware works better for wet lab protocols. And in fact there are some software walkthrough in SEQwiki already. Snippet would be great

dan · 10-06-2011, 04:24 AM

Quote:

Originally Posted by fkrueger

I also think that SEQanswers is an incredibly useful knowledgebase all around NGS and its bioinformatics applications. I especially love its instantaneous character and the (usually) extremely short reaction times of experts and developers in the fields to all sorts of questions, ranging from biological questions to discussion/usage of various bioinformatic tools to bug reports or feature requests. For many questions I have and had in the past, SEQanswers has become my first port of call to look for solutions or help.

I think you speak for a lot of users. Please go ahead and write this in the letter if you agree :-D

dan · 10-06-2011, 04:27 AM

Quote:

Originally Posted by ulz_peter

However, I think we should separate the Forum from the Wiki for the letter, as the Wiki is getting published already, am I right?

Yup, the point of the letter is to focus on the forum, and hopefully publish before the wiki (coming out in January).

flxlex · 10-06-2011, 04:43 AM

There is some (considerable?) overlap between the bioinformatics forum at SeqAnswers, and biostar.stackexchange.com. Perhaps we should acknowledge that, and comment that SeqAnswer is targeting a wider audience than just those analyzing data using bioinformatic tools?

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10-05-2011, 01:55 PM	#1
dan wiki wiki Location: Cambridge, England Join Date: Jul 2008 Posts: 266	Time to publish SEQanswers? During the review of the SEQwiki paper, an important point was raised by the reviewers: the SEQanswers forum has yet to be published, and deserves a good publication. Why don't we write a letter to Science or Nature about SEQanswers? The project has already been 'informally' cited dozens of times in the literature, so why not write a nice summary for everyone to cite? The proposal is to use the wiki to collaboratively draft a letter to Science or Nature (see: wiki:Publication/Letter_for_SEQanswers), with each contributor adding their name to the paper. The final list of authors will be ranked according to (democratically determined) contribution to the final text. Please contribute (and sign the letter) here! Meta paper discussion should stay on this thread (wiki sucks for discussion). __________________ Homepage: Dan Bolser MetaBase the database of biological databases.

10-06-2011, 12:01 AM	#2
marcowanger Senior Member Location: Hong Kong Join Date: Dec 2008 Posts: 350	How long will we aim? Personally, I think we should keep it short. __________________ Marco

10-06-2011, 03:48 AM	#14
ETHANol Senior Member Location: Western Australia Join Date: Feb 2010 Posts: 308	I think the future directions section is interesting. Just some ideas on what could be mentioned there: 1) The addition of a wet lab protocols wiki 2) As the size of the community increases, what are measures that can be implemented to keep the ratio of good information high to bad information? Perhaps the addition of energetic application specific moderators. This by the way it should be mentioned in the text that the ratio of good information to bad is really high on this forum. 3) Something else that might be cool is if there was some way to 'like/+1' threads and a section with the most popular threads. Might make browsing more efficient for causal readers. __________________ -------------- Ethan

10-06-2011, 12:43 AM	#3
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	Publishing SeqAnswers for being able to cite it "formally" is a great idea. I second the opinion of marcowanger to keep it quite short.

10-06-2011, 01:53 AM	#4
andreas.sjodin Member Location: Umeå, Sweden Join Date: Apr 2009 Posts: 27	I also think we should aim to keep it short and that it is a great idea. At least if we are going for a letter. An alternative would to write a more extensive "application note" describing the features but that would require much more work.

10-06-2011, 03:10 AM	#5
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Do we want to mention that SeqAnswers also acts as a useful forum for helping users with problems using NGS tools (sometimes leading to useful bug reports for the tool developers)? Or would that just encourage more of this - which wouldn't be such a bad thing except it can drown out other more important threads, like file format changes etc.

10-06-2011, 03:16 AM	#6
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	I think thats a good idea, as most of the threads in Seqanswers are indeed related to usage questions

10-06-2011, 03:30 AM	#8
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	OK, I've added a bit of text along those lines. Peter

10-06-2011, 03:32 AM	#9
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Also, is it worth thinking about an option for real names in forum profiles at this point?

10-06-2011, 03:42 AM	#11
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 625	I also think that SEQanswers is an incredibly useful knowledgebase all around NGS and its bioinformatics applications. I especially love its instantaneous character and the (usually) extremely short reaction times of experts and developers in the fields to all sorts of questions, ranging from biological questions to discussion/usage of various bioinformatic tools to bug reports or feature requests. For many questions I have and had in the past, SEQanswers has become my first port of call to look for solutions or help.

10-06-2011, 03:44 AM	#12
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	Any suggestions for the future directions part?

10-06-2011, 03:45 AM	#13
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	found in Science Homepage: How to Submit a Letter to the Editor Letters to the Editor are selected for publication that are pertinent to material published in Science or that discuss problems of general interest. Letters may be reviewed. Those selected for publication are intended to reflect the range of opinions received. The author of a paper in question is usually given an opportunity to reply. Letters are not routinely acknowledged. Full addresses, signatures, and daytime phone numbers should be included. Letters should be brief (300 words or less) and may be edited for reasons of clarity or space. They may appear in print and/or on the World Wide Web. Letter writers are not consulted before publication.

10-06-2011, 04:13 AM	#16
andreas.sjodin Member Location: Umeå, Sweden Join Date: Apr 2009 Posts: 27	I think wet lab protocols are better hosted at OpenWetWare. Adding a section of small "example code snippets" to each software in the SEQwiki would be great. Should be added to wanted features in the SEQwiki. I think it is better to mainly concentrate on the SEQanswer Forum in the letter.

10-06-2011, 04:43 AM	#20
flxlex Moderator Location: Oslo, Norway Join Date: Nov 2008 Posts: 415	There is some (considerable?) overlap between the bioinformatics forum at SeqAnswers, and biostar.stackexchange.com. Perhaps we should acknowledge that, and comment that SeqAnswer is targeting a wider audience than just those analyzing data using bioinformatic tools?