Time to publish SEQanswers?

[dan]

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]

How long will we aim?

Personally, I think we should keep it short.

[ulz_peter]

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]

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]

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]

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

[marcowanger]

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]

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

Peter

[maubp]

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

[dan]

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]

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]

Any suggestions for the future directions part?

[ulz_peter]

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]

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]

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?