[robs]

I tried to put some headings for the parts of the article that I think are important. Based on this, we should assign people to the different parts to add content.

Joann: If you have an idea for a different outline, could you please post it here or add it to the wiki?

[adaptivegenome]

I tried to put some headings for the parts of the article that I think are important. Based on this, we should assign people to the different parts to add content.

Rob, I like the headings you added.

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.

[marcowanger]

Rob, I like the headings you added.

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.

I just received the PloS Comp Bio manuscript ID yesterday

The PloS Biology should be in editor office for several days now.

[adaptivegenome]

I just received the PloS Comp Bio manuscript ID yesterday

The PloS Biology should be in editor office for several days now.

Great. Let's see what they say. I am particularly interested in feedback from PLOS Biology as it is a journal with broad topics and readership.

[Joann]

some ideas and content

A manuscript for Plos Biology would provide an opportunity to give a short introductory perspective to next gen sequencing that most here would feel redundant perhaps--but as representatives of the field to the rest of biology this is indeed a proper task for the forum. I would suggest simply noting the technical expansion from Sanger sequencing and also mention the corresponding growth (and struggles to house) in open access sequence databases world wide.

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. There are many important medicine informed posts here, one of the most interesting to me being a policy discussion on whole genome sequencing of He La cells for public reference, for example.
But this could also be the focus in an additional paper from the forum later on.


Finally, I think it is important to measure the fact of a strong global participation in the forum. Minimally, mention of the Wiki sequencing center map, (by means of the new Wiki citation in NAR) but ideally some additional identification of the locations of posters if this data can be harvested at some point. It is thrilling to post along with scientists working in Bulgaria and Cyprus as well as in Boston and China.

[robs]

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.

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]

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]

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]

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]

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]

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

This will be interesting to see.

[adaptivegenome]

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]

...geographical..global participation

Robs, please check your email.

Anyone want to produce a figure from the stats?

[adaptivegenome]

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]

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.