SEQanswers

Go Back   SEQanswers > Site News > Site Feedback/Suggestions



Similar Threads
Thread Thread Starter Forum Replies Last Post
Minimum Criteria to Publish ChIP-seq data ETHANol Epigenetics 7 12-04-2011 04:35 AM
Lets publish the Wiki! dan Wiki Discussion 108 09-07-2011 09:10 AM
SEQanswers mentioned for the second time in a major journal ECO Site Announcements 3 08-01-2011 08:51 AM
Jim Watson in Excruciating Detail: 454/Baylor Publish Complete Genome Sequence ECO Literature Watch 1 04-16-2008 02:43 PM
Welcome to SEQanswers.com! ECO Site Announcements 0 10-28-2007 03:59 PM

Reply
 
Thread Tools
Old 10-05-2011, 12:55 PM   #1
dan
wiki wiki
 
Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
Arrow 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.
dan is offline   Reply With Quote
Old 10-05-2011, 11:01 PM   #2
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

How long will we aim?

Personally, I think we should keep it short.
__________________
Marco
marcowanger is offline   Reply With Quote
Old 10-05-2011, 11:43 PM   #3
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

Publishing SeqAnswers for being able to cite it "formally" is a great idea.
I second the opinion of marcowanger to keep it quite short.
ulz_peter is offline   Reply With Quote
Old 10-06-2011, 12:53 AM   #4
andreas.sjodin
Member
 
Location: Umeň, Sweden

Join Date: Apr 2009
Posts: 27
Default

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.
andreas.sjodin is offline   Reply With Quote
Old 10-06-2011, 02:10 AM   #5
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

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 is offline   Reply With Quote
Old 10-06-2011, 02:16 AM   #6
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

I think thats a good idea, as most of the threads in Seqanswers are indeed related to usage questions
ulz_peter is offline   Reply With Quote
Old 10-06-2011, 02:19 AM   #7
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Quote:
Originally Posted by maubp View Post
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.
__________________
Marco
marcowanger is offline   Reply With Quote
Old 10-06-2011, 02:30 AM   #8
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

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

Peter
maubp is offline   Reply With Quote
Old 10-06-2011, 02:32 AM   #9
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Also, is it worth thinking about an option for real names in forum profiles at this point?
maubp is offline   Reply With Quote
Old 10-06-2011, 02:34 AM   #10
dan
wiki wiki
 
Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
Default

Quote:
Originally Posted by andreas.sjodin View Post
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.
__________________
Homepage: Dan Bolser
MetaBase the database of biological databases.
dan is offline   Reply With Quote
Old 10-06-2011, 02:42 AM   #11
fkrueger
Senior Member
 
Location: Cambridge, UK

Join Date: Sep 2009
Posts: 620
Default

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.
fkrueger is online now   Reply With Quote
Old 10-06-2011, 02:44 AM   #12
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

Any suggestions for the future directions part?
ulz_peter is offline   Reply With Quote
Old 10-06-2011, 02:45 AM   #13
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

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.
ulz_peter is offline   Reply With Quote
Old 10-06-2011, 02:48 AM   #14
ETHANol
Senior Member
 
Location: Western Australia

Join Date: Feb 2010
Posts: 308
Default

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
ETHANol is offline   Reply With Quote
Old 10-06-2011, 02:53 AM   #15
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

Quote:
Originally Posted by ETHANol View Post
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?
ulz_peter is offline   Reply With Quote
Old 10-06-2011, 03:13 AM   #16
andreas.sjodin
Member
 
Location: Umeň, Sweden

Join Date: Apr 2009
Posts: 27
Default

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.
andreas.sjodin is offline   Reply With Quote
Old 10-06-2011, 03:20 AM   #17
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Quote:
Originally Posted by andreas.sjodin View Post
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
__________________
Marco
marcowanger is offline   Reply With Quote
Old 10-06-2011, 03:24 AM   #18
dan
wiki wiki
 
Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
Smile

Quote:
Originally Posted by fkrueger View Post
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
__________________
Homepage: Dan Bolser
MetaBase the database of biological databases.
dan is offline   Reply With Quote
Old 10-06-2011, 03:27 AM   #19
dan
wiki wiki
 
Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
Default

Quote:
Originally Posted by ulz_peter View Post
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).
__________________
Homepage: Dan Bolser
MetaBase the database of biological databases.
dan is offline   Reply With Quote
Old 10-06-2011, 03:43 AM   #20
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

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?
flxlex is offline   Reply With Quote
Reply

Tags
publication

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO