[marcowanger]

Rob, it is still peer-reviewed. So really there is almost no point to query the editor unless you are concerned the article is completely inappropriate for the journal. The most you can hope to get is "this article will not be immediately rejected..."

If we are lucky sometimes we get a few extra tips on how to get the article in... like with the Genome Medicine editor who gave us some good advice...

That is good, what specific advice Genome Med editor told us? Maybe I have forgotten them already

[adaptivegenome]

Rob, it is still peer-reviewed. So really there is almost no point to query the editor unless you are concerned the article is completely inappropriate for the journal. The most you can hope to get is "this article will not be immediately rejected..."

If we are lucky sometimes we get a few extra tips on how to get the article in... like with the Genome Medicine editor who gave us some good advice...

[robs]

So I would say we that we should make a final decision no later than next Friday. Knowing the journal will help us also put finishing touches and finalize the paper as well as format it.

Does the submission go through review or is it solely the decision of the editor?

[robs]

3+5) Breaking the article into different sections is good. Sometimes it is not a bad idea to have all people to work on the same thing. Just give and take. The finalized version probably is a consensus to "almost" everyone, language tends to be more polished...And the bad, slower progress...

I think that if we have people work on different parts initially, they will be more detailed. After that, everyone should edit those.

[adaptivegenome]

I think as we have finalized the perspectives/community pages. We should have known. I bet we cannot finish in 7 working days (counting from the day we submit the inquiry) . If they don't reply within a week (count working day). Then we have every reason to believe they are not interested.

So I would say we that we should make a final decision no later than next Friday. Knowing the journal will help us also put finishing touches and finalize the paper as well as format it.

[marcowanger]

What is the final deadline we will give the journals before we pick one?

I think as we have finalized the perspectives/community pages. We should have known. I bet we cannot finish in 7 working days (counting from the day we submit the inquiry) . If they don't reply within a week (count working day). Then we have every reason to believe they are not interested.

[adaptivegenome]

1) Maybe just moving them further away from the current draft? I think it's good to keep track of what we have written. And the changes between versions.

3+5) Breaking the article into different sections is good. Sometimes it is not a bad idea to have all people to work on the same thing. Just give and take. The finalized version probably is a consensus to "almost" everyone, language tends to be more polished...And the bad, slower progress...

What is the final deadline we will give the journals before we pick one?

[marcowanger]

1) I find it confusing to have all the different versions in the wiki article. Could we merge the old long version, the other draft and the current version into a single one and remove the rest?

3+5) Can we try to separate the article into parts that different people work on. I think, the progress will be better and different people concentrate on specific aspects instead of adding things to the same thoughts already there.

1) Maybe just moving them further away from the current draft? I think it's good to keep track of what we have written. And the changes between versions.

3+5) Breaking the article into different sections is good. Sometimes it is not a bad idea to have all people to work on the same thing. Just give and take. The finalized version probably is a consensus to "almost" everyone, language tends to be more polished...And the bad, slower progress...

[marcowanger]

In an earlier post, I mentioned that I wrote the Editor of PLoS CB and he seemed to be interested. I could ask him again to take a look at the current version.

Thanks. Please let him know we submitted it at "Nov 24 2011 12:19PM"

The status as displayed in the system is "Submission being processed"

[adaptivegenome]

1) I find it confusing to have all the different versions in the wiki article. Could we merge the old long version, the other draft and the current version into a single one and remove the rest?

3+5) Can we try to separate the article into parts that different people work on. I think, the progress will be better and different people concentrate on specific aspects instead of adding things to the same thoughts already there.

I think we need to move to GDoc again since eventually this document will be exported and uploaded to the journal. We should start formatting the document, add a title page, etc. so it can be ready to go. Actually I am hoping this will happen quickly as editors expect submissions shortly after expressing interest. We should have something ready in the next week or two. We need to set a hard deadline and this will also help get things moving.

I also agree it would help to break the paper up a little and maybe include an extra section or two now that we have a little more space.

Your figures are great. I do agree with others that it might look better to remove the raw data points. Other than that they are awesome.

[robs]

1> For now, I have assembled the content of the letter as the abstract.

3> Let's finalize the content before migrating to the Gdoc.

5> good work so far. We need to concentrate on the main text now.

1) I find it confusing to have all the different versions in the wiki article. Could we merge the old long version, the other draft and the current version into a single one and remove the rest?

3+5) Can we try to separate the article into parts that different people work on. I think, the progress will be better and different people concentrate on specific aspects instead of adding things to the same thoughts already there.

[robs]

4> We still need robs to remove the raw data points in figure 2

That is easily done. Where should I put the new version?
Do you need any other plots? If we submit a longer article, maybe a figure with a bigger tag cloud would fit now.

[robs]

I did it the difficult way (submit through the automated system)

I have made sure it's "presubmission"

There is no drop-down list to select article type, so I write explicitly in the cover letter.

PLoS Biology: Community Pages / Perspectives
PLoS CompBio: Perspectives only (no community pages or similar)

In an earlier post, I mentioned that I wrote the Editor of PLoS CB and he seemed to be interested. I could ask him again to take a look at the current version.

[adaptivegenome]

Sounds good. Looking forward to the responses.

[marcowanger]

Nice. Did you just email the editors of PLOS? Or did you actually submit through the automated system?

I did it the difficult way (submit through the automated system)

I have made sure it's "presubmission"

There is no drop-down list to select article type, so I write explicitly in the cover letter.

PLoS Biology: Community Pages / Perspectives
PLoS CompBio: Perspectives only (no community pages or similar)