[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]

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)

;-)

[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.

[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]

Thanks. This is great!

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

[adaptivegenome]

Here it is "Success case studies (word)"

Thanks. This is great!

[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)"

[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]

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.

[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.

[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.

[Joann]

"Reading the genome" it is true, implies much more annotation past the initial raw dataset, which arrives in the form of reads--whether genomic or RNA, etc. Furthermore, there is much technical effort focused in this forum, and rightfully so, on the quality of the initial raw reads. One of the benefits of this forum is exposure to the many facets of the technology currently in the hands of many different investigators.

[marcowanger]

"most of us here) we are analyzing the data beyond mere reading".

Yet all do work that starts from the basic unit, which is the "read". This is a key feature of high through put sequencing and its analyses. And unmistakably demonstrated from a whole analysis of the posts on this forum.

sure, the "read" is the fundamental unit. Remember why the word "read" appear in the tagcloud is because it's frequently used. Usually in form of sequencing reads, how many reads mapped, unmapped reads, etc.

If it's used in the title "Reading the genome", then the word "read" is used in another context, which is not the original meaning used in the forum.

[Joann]

"most of us here) we are analyzing the data beyond mere reading".

Yet all do work that starts from the basic unit, which is the "read". This is a key feature of high through put sequencing and its analyses. And unmistakably demonstrated from a whole analysis of the posts on this forum.

[marcowanger]

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?

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).