Time to publish SEQanswers?

[robs]

Originally Posted by Joann

For an additional orientation towards Genome Medicine, perhaps it would be possible to promise a future restructuring of the forum to collect and highlight such topics in a specific section.

This would be a good point for the last part of the article. Feel free to write something about this in the wiki.

Originally Posted by Joann

Finally, I think it is important to measure the fact of a strong global participation in the forum. [...] identification of the locations of posters if this data can be harvested at some point.

I think this will make a nice figure and some points for the discussion. Maybe we can get this data from ECO? Additionally, it would be nice to get the location data from the google analytics of this site.

[robs]

Originally Posted by genericforms

So far it seems that Genome Medicine is supporting our publication and Genome Biology is not (I am not surprised). What remains to be seen is if the PLOS journals express interest. I feel if they do not, or they have not responded by this Friday, we should work from Rob's latest revisions, further define discussion points, and work towards publication in Genome Medicine.

Friday seems to be a good deadline for that. Could you post a link to the journal guidelines ones we have decided on one?

[adaptivegenome]

Originally Posted by robs

Friday seems to be a good deadline for that. Could you post a link to the journal guidelines ones we have decided on one?

Yes. On Friday if no one else gets back to us I will post a link and also just paste in the instructions for Genome Medicine. We can quickly refocus the article and as Joann suggested, give it a slightly medical spin. Then we can assign parts to everyone and get it done real quick.

Since I talked to the editor of GM November 23rd, we really should get something out to them soon if we end up going with their journal.

[marcowanger]

Originally Posted by robs

This would be a good point for the last part of the article. Feel free to write something about this in the wiki.



I think this will make a nice figure and some points for the discussion. Maybe we can get this data from ECO? Additionally, it would be nice to get the location data from the google analytics of this site.

Robs, I have previously obtained such data. I will send it out

[marcowanger]

Originally Posted by genericforms

Yes. On Friday if no one else gets back to us I will post a link and also just paste in the instructions for Genome Medicine. We can quickly refocus the article and as Joann suggested, give it a slightly medical spin. Then we can assign parts to everyone and get it done real quick.

Since I talked to the editor of GM November 23rd, we really should get something out to them soon if we end up going with their journal.

Yes, it takes so long for PLoS to reply. I sent them out last Thursday, now 6 days has passed...I think we should only wait for additional 1 to 2 days....

[adaptivegenome]

Originally Posted by marcowanger

Robs, I have previously obtained such data. I will send it out

This will be interesting to see.

[adaptivegenome]

Originally Posted by marcowanger

Yes, it takes so long for PLoS to reply. I sent them out last Thursday, now 6 days has passed...I think we should only wait for additional 1 to 2 days....

Agreed. Let's decided end of day Friday.

[marcowanger]

Originally Posted by robs

...geographical..global participation

Robs, please check your email.

Anyone want to produce a figure from the stats?

[adaptivegenome]

Originally Posted by marcowanger

Robs, please check your email.

Anyone want to produce a figure from the stats?

Send me the data as well. I will take a look. You have my email...

[Joann]

Originally Posted by robs

This would be a good point for the last part of the article. Feel free to write something about this in the wiki.

As you have seen from journal editor comments already available, it's very important to carefully avoid duplication of material already published in the NAR article. A number of points and observations related to what I had offered in the Wiki drafts with respect to the forum previously did become incorporated into the Wiki article. (I am an expert contributor at the forum site and not the Wiki site). I do not know why the authors decided to provide material about the forum to the degree of creating a section in the Wiki article, thus expanding it into a larger article, since the NAR topic request was for the Wiki material.

Clearly, however, it can be demonstrated that one aspect of the forum's ongoing importance to the Wiki is the community's desire to maintain and support (a repository of) extensive and active discussion concerning tools cataloged at the forum's younger sister site, the SeqWiki.

Now, there are many other aspects to the importance of the forum, SeqAnswers, which is why good editorial feedback suggested an article in it's own right. But any material taken pretty much directly from the published NAR article is not going to fly no matter how hard you spin it.

[robs]

Originally Posted by marcowanger

Robs, please check your email.

Thanks! I got it. Will work on it during the weekend.

[marcowanger]

Originally Posted by robs

Thanks! I got it. Will work on it during the weekend.

Thank you robs

[Joann]

Hi Marco,
For the benefit of all the great contributers and contributions to this thread I am posting an editorial reply you have previously posted on the Wiki.

"Genome Biology -inquiry by marcowanger, reply on 29th Nov 2011
Thank you for your email in which you offer to submit a Correspondence manuscript on the SEQanswers community to Genome Biology. I am very sorry about the delay in getting back to you about it. Having discussed and considered your proposal with my colleagues, I am afraid that we are unable to consider the manuscript you describe for publication.

I'm sorry that we can't be more positive but we are sure you won't have any difficulties in publishing your article elsewhere. Thank you for your interest in Genome Biology."

Also for the benefit of all contributers to this particular thread, I request that you disclose reviewer comments from the NAR Wiki article and post a copy of the initial August 16 2011 draft as well as the revised October 25, 2011 draft submitted by you , Dan, and ECO. Thanks.

[marcowanger]

Originally Posted by Joann

Hi Marco,
For the benefit of all the great contributers and contributions to this thread I am posting an editorial reply you have previously posted on the Wiki.

"Genome Biology -inquiry by marcowanger, reply on 29th Nov 2011
Thank you for your email in which you offer to submit a Correspondence manuscript on the SEQanswers community to Genome Biology. I am very sorry about the delay in getting back to you about it. Having discussed and considered your proposal with my colleagues, I am afraid that we are unable to consider the manuscript you describe for publication.

I'm sorry that we can't be more positive but we are sure you won't have any difficulties in publishing your article elsewhere. Thank you for your interest in Genome Biology."

Also for the benefit of all contributers to this particular thread, I request that you disclose reviewer comments from the NAR Wiki article and post a copy of the initial August 16 2011 draft as well as the revised October 25, 2011 draft submitted by you , Dan, and ECO. Thanks.

Thanks. Joann,

The reviewers' comment and our replies are disclosed in the wiki page
(http://seqanswers.com/wiki/Publicati...AR_2012)/Reply)
We discussed and replied with the writing exactly as described in the wiki.

The initial draft is at here (http://seqanswers.com/wiki/Publication/Paper_(NAR_2012))

The revised MS (except the correction made on spelling and typos) is exactly as you can get in NAR website now. The corrections made on the 25th Oct 2011 version are deposited in (http://seqanswers.com/wiki/Publicati...2)/Corrections).

Thanks for asking this. We have started disclosing everything from the initial idea, to drafting, to submission, answering reviewers' comment, and correction to production proof copy, everything on the SEQwiki page.

[marcowanger]

Originally Posted by Joann

Hi Marco,
For the benefit of all the great contributers and contributions to this thread I am posting an editorial reply you have previously posted on the Wiki.

"Genome Biology -inquiry by marcowanger, reply on 29th Nov 2011
Thank you for your email in which you offer to submit a Correspondence manuscript on the SEQanswers community to Genome Biology. I am very sorry about the delay in getting back to you about it. Having discussed and considered your proposal with my colleagues, I am afraid that we are unable to consider the manuscript you describe for publication.

I'm sorry that we can't be more positive but we are sure you won't have any difficulties in publishing your article elsewhere. Thank you for your interest in Genome Biology."

Also for the benefit of all contributers to this particular thread, I request that you disclose reviewer comments from the NAR Wiki article and post a copy of the initial August 16 2011 draft as well as the revised October 25, 2011 draft submitted by you , Dan, and ECO. Thanks.

To let more people know (in case you don't browse the SEQwiki).

PLoS Biology - inquiry by marcowanger, reply on 1st Dec 2011
Thank you for your enquiry about submitting your article "SEQanswers: Leveraging Collective Intelligence to Decode Biological Sequences" to PLoS Biology. I have discussed your proposal with my colleagues and regret that we cannot encourage submission of the full manuscript.
While we cannot consider your manuscript for publication in PLoS Biology, we very much appreciate your wish to present your work in one of PLoS's open-access publications, and would like to suggest that you consider submitting it to one of the other PLoS journals. Full details of all the other PLoS journals are available at http://www.plos.org/journals/. In particular, we would encourage you to consider submitting to PLoS Computational Biology, as we feel that your article would be better suited to the computational biology community.
If you are interested in pursuing this option, please log in at http://www.editorialmanager.com/pcompbiol/, and choose 'Submit Manuscript' from the list of Author Tasks, selecting the article type 'Presubmission Inquiry'. The editors of the journal will then let you know whether your work is suitable for full submission there.
Thank you again for your interest in PLoS Biology.
Best wishes,

[adaptivegenome]

I think we should move forward with Genome Medicine as our target journal. We should prepare a COMMENTARY article as the editor suggested. I will post the requirements again, shortly.

[marcowanger]

Originally Posted by genericforms

I think we should move forward with Genome Medicine as our target journal. We should prepare a COMMENTARY article as the editor suggested. I will post the requirements again, shortly.

Agree, should not let the interested editor wait too long.

[adaptivegenome]

Originally Posted by marcowanger

Agree, should not let the interested editor wait too long.

Points to focus on:
"Genome Medicine publishes open access research articles of outstanding quality and broad interest in all areas of medicine studied from a genomic or post-genomic perspective. The journal has a special focus on the latest technologies, including genomic methods, proteomics, bioinformatics and computational biology, and findings that have an impact on the understanding and management of human health and disease. Correspondence items discuss material published in Genome Medicine or issues of exceptional interest to the broad readership of the journal."

1. How does SEQanswers advance genomics and how does the board specifically enable the use or improvement of the latest genomic methods, bioinformatics methods, etc.?

2. Why would SEQanswers be of broad interest to the readership of Genome Medicine? In other words, how is this useful to bioinformatics, genome biologists, and clinical researchers. The BWA vs BOWTIE2 thread is a good example for bioinformatics. There are some good examples also for wet lab sequencing methods as well. To be relevant to human medicine, it does not mean we must discuss disease. There are lots of model systems that would be interesting. Also methods/discussions that concern population genetics are of CRITICAL value to clinicians understanding human patient groups. In addition for personal genomics, reducing FPs is a big issue. The larger the list of mutations, the less likely they will actionable. So really even the BWA vs. BOWTIE2 thread is relevant in medicine, as is discussions of dbSNP, etc.

"Correspondence should be between 800-3000 words."
I think we if take what we have, along with Rob's excellent figures; and then add a discussion of the above two points, we will have a nice correspondence that will probably be close to 1000-1500 words or so. No need to write anymore than is necessary especially if we are including those figures.

We will also need an up to 200 word abstract. Obviously for a correspondence of 1500 words I do not think our abstract really has to be 200 words, but that is the reported maximum.

[adaptivegenome]

We received our feedback almost two weeks ago, so I would recommend we finalize the text and figures next week. I would be happy to work on the two points I suggested in the previous post. I think that we should quickly decide if we want a table/figure with the demographic data. Sounds like Rob will do this over the weekend.

We should also determine the final author list (sorted however everyone wants). I think Marco and Rob have taken a real lead on this manuscript but there are have been other contributors as well so we should identify and sort these authors.

I am also going to start working on the final WORD/GDoc document that will contain a title, authors, keywords, abstract, etc. (all the sections and formatting we need) so that when the text is final, we can easily integrate it into the final document and submit.

I think we have a great story and I think that getting this paper out to Genome Medicine will be good for the journal and also great for the SEQanswers community.

[Joann]

Originally Posted by marcowanger

Robs, I have previously obtained such data. I will send it out

Would someone kindly e-mail me a copy of this dataset, also? Just PM and I will reply with the e-mail address. Thanks.