[adaptivegenome]

Sure.

Keypoint: Write about Open Science, collaboration, how collective intelligence work. Joann is right, we need to demonstrate some cases for that. Please read the BioStar's paper to see how they describe the success case. We can learn from them (how to write).

I agree. SeqAnswers is a success story and although we originally wanted to put together a letter in Science/Nature that simply advertised the existence of the forum, with our new target journals and article format, the focus should change slightly towards an argument for open science, collaboration, etc.

And that is how our draft currently reads. It is coming along nicely.

[adaptivegenome]

I don't quite see why these words have to appear in the forum for being able to use them in the title. Anyways, I agree that the word "reading" might lead to a wrong perception of the article, as (at least most of us here) we are analyzing the data beyond mere reading.

Do you guys think we should start expanding the article already?

Yes. We have discussed the title enough! There are some good title suggestions on the Wiki page but now we need to advance the text. Marco says we need 800 to 3000 words. I would say if we assembled a brief commentary of about 1500 words and two figures from Rob, we would have a good document to submit.

We will also need a brief abstract and we can then submit. All of this needs to be assembled in a single document so as soon as everyone feels comfortable, we should migrate back to GDoc or something like that since eventually we will produce a document file anyways that gets submitted.

[marcowanger]

Yes. We have discussed the title enough! There are some good title suggestions on the Wiki page but now we need to advance the text. Marco says we need 800 to 3000 words. I would say if we assembled a brief commentary of about 1500 words and two figures from Rob, we would have a good document to submit.

We will also need a brief abstract and we can then submit. All of this needs to be assembled in a single document so as soon as everyone feels comfortable, we should migrate back to GDoc or something like that since eventually we will produce a document file anyways that gets submitted.

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

2> 800-3000 words is the impression I got from Genome Bio/Med journal correspondence type paper. I do agree 1500 word with 2 figures is reasonable enough.

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

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

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

[marcowanger]

I agree. SeqAnswers is a success story and although we originally wanted to put together a letter in Science/Nature that simply advertised the existence of the forum, with our new target journals and article format, the focus should change slightly towards an argument for open science, collaboration, etc.

And that is how our draft currently reads. It is coming along nicely.

Previously I have collected a not-so-exhaustive list of success cases in SEQanswers (that should be what Joann talks about). Those examples, IHO, are how people leverage collective intelligence to improve their works/tools.

I will go find it ...it is in my laptop..somewhere...

[marcowanger]

Previously I have collected a not-so-exhaustive list of success cases in SEQanswers (that should be what Joann talks about). Those examples, IHO, are how people leverage collective intelligence to improve their works/tools.

I will go find it ...it is in my laptop..somewhere...

Here it is "Success case studies (word)"

[adaptivegenome]

Here it is "Success case studies (word)"

Thanks. This is great!

[marcowanger]

Thanks. This is great!

Please be reminded. There are a lot more success cases. These examples just serve as a primer.

[Joann]

user-developer exchanges, and...

These are examples of user-developer exchange. What other topics might be included in the expanded article under consideration? Standards development, modification, replacement? (for example the role of Sanger sequencing) Jobs and career advice (i.e. where to do an internship?) Topics in personal genomics (especially relevant to focus on the medical application side)? Personalized trouble shooting on your project by the experts? (how often is the word "help" used) Approaches to experimental design? International database repositories? These also are all important aspects of the forum as a whole.

Perhaps the generation of a consensus topics list could sort these out and help authors manage content within their alloted word count while meeting the topic requirements of a targeted journal--while preserving an accurate representation of the SEQanswers forum.

[marcowanger]

These are examples of user-developer exchange. What other topics might be included in the expanded article under consideration? Standards development, modification, replacement? (for example the role of Sanger sequencing) Jobs and career advice (i.e. where to do an internship?) Topics in personal genomics (especially relevant to focus on the medical application side)? Personalized trouble shooting on your project by the experts? (how often is the word "help" used) Approaches to experimental design? International database repositories? These also are all important aspects of the forum as a whole.

Perhaps the generation of a consensus topics list could sort these out and help authors manage content within their alloted word count while meeting the topic requirements of a targeted journal--while preserving an accurate representation of the SEQanswers forum.

Joann. Yes, I know the list I sent out is far from complete. Any suggestion is welcome.

[marcowanger]

Status update:

1> Genome Medicine (positive feedback, see wiki for editor's reply)
2> Genome Biology (inquiry sent, 11-23-2011)
3> PLoS Biology (inquiry sent)
4> PLoS Computional Biology (inquiry sent)

;-)

[adaptivegenome]

Status update:

1> Genome Medicine (positive feedback, see wiki for editor's reply)
2> Genome Biology (inquiry sent, 11-23-2011)
3> PLoS Biology (inquiry sent)
4> PLoS Computional Biology (inquiry sent)

;-)

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

[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)

[adaptivegenome]

Sounds good. Looking forward to the responses.

[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.

[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.