[robs]

Robs, please check your email.

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

[marcowanger]

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

Thank you robs

[Joann]

FYI all posters to this thread and open access public forum

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]

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]

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]

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]

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]

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.

[robs]

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.

I think these are some very motivating words. Keep up the good spirit and we should get this done very soon.

I updated the figures. As for the demographic data, there was only one month available, so I couldn't do much with it. I put a new version of every figure in the gdoc. Feel free to comment on them or change the figure captions.

I think I will work on "SEQanswers - A Platform/Community for" over the weekend. It would be great if Marco, Dan, ECO or you could put some ideas for the "Outlook and Perspective" part, as I am not sure about the plan for SEQanswers for the next 2-3 years.

[adaptivegenome]

I think these are some very motivating words. Keep up the good spirit and we should get this done very soon.

I updated the figures. As for the demographic data, there was only one month available, so I couldn't do much with it. I put a new version of every figure in the gdoc. Feel free to comment on them or change the figure captions.

I think I will work on "SEQanswers - A Platform/Community for" over the weekend. It would be great if Marco, Dan, ECO or you could put some ideas for the "Outlook and Perspective" part, as I am not sure about the plan for SEQanswers for the next 2-3 years.

I will work on the two points I suggested and also per your suggestion I will work on the "Outlook and Perspective". Hopefully we can reassess the document early next week! Input from Dan and Eco and Marco would also be great.

[marcowanger]

I will work on the two points I suggested and also per your suggestion I will work on the "Outlook and Perspective". Hopefully we can reassess the document early next week! Input from Dan and Eco and Marco would also be great.

Then I would work on "The Need for an Open Science Platform" and "Success cases".

[Joann]

specific to the Genome Medicine journal and part of its editorial feedback

In now developing this article towards acceptance by Genome Medicine, it is useful to note that Genome Medicine is a journal dedicated to principles of open access science, which makes SEQanswers forum and this journal a joint force for open source platforms in the service of excellence in DNA sequencing technology, genomic science, and for their speedy and efficient implementations in the clinic.

Suggestion #1
With the demographic data, the existing figure 3 allows for easier visualization of the numbers. The illustration I envision to communicate the above concepts in more depth is as follows:

This illustration is composed as a simple diagram of a platform as a plane supported by 2 columns.

The plane (line) is represented by the underlined words:

OPEN ACCESS DNA SEQUENCING PLATFORMS (or words to that effect)

meaning current global support for open access principles (software, methods, database archives) happening at and represented by SEQanswers

Underneath this plane and supporting it are two columns composed of bricks of various sizes proportional to the visitor numbers. (Just split the bar in exisiting fig 3. down the middle.)
The right side column is made of only 2 bricks--by the numbers US and UK
The left side column of equal height and supporting the platform equally is composed of smaller sized bricks on down the list of countries and supported at the foundation by the numerous small bricks. I would like to include the name of all 130 countries on all 130 bricks of various sizes because I think it is very important to recognize and encourage the growth in global support for open access science as proven by each and every brick (large and small) participating in and supporting the open access platform at SEQanswers.

I realize would take a bit more work and complexity but speaks to the roles that everyone plays in support of open access principles and engendering same.

Suggestion #2
Of relevance to the clinician-scientist..this forum is a public open access discussion forum, therefore has evolved various layers of privacy protection. The key to this approach-- encourages discussion at a general level which then facilitates a broader application of solutions and information to possibly related issues that could arise in a different clinical research setting. In addtion to topic headings and search capacity the forum also provides a geographical handle to the network of experts that may provide advice and insight in the course of a sequencing project at a given clinical site.

[robs]

Suggestion #1
With the demographic data, the existing figure 3 allows for easier visualization of the numbers. The illustration I envision to communicate the above concepts in more depth is as follows:

This illustration is composed as a simple diagram of a platform as a plane supported by 2 columns.

The plane (line) is represented by the underlined words:

OPEN ACCESS DNA SEQUENCING PLATFORMS (or words to that effect)

meaning current global support for open access principles (software, methods, database archives) happening at and represented by SEQanswers

Underneath this plane and supporting it are two columns composed of bricks of various sizes proportional to the visitor numbers. (Just split the bar in exisiting fig 3. down the middle.)
The right side column is made of only 2 bricks--by the numbers US and UK
The left side column of equal height and supporting the platform equally is composed of smaller sized bricks on down the list of countries and supported at the foundation by the numerous small bricks. I would like to include the name of all 130 countries on all 130 bricks of various sizes because I think it is very important to recognize and encourage the growth in global support for open access science as proven by each and every brick (large and small) participating in and supporting the open access platform at SEQanswers.

I realize would take a bit more work and complexity but speaks to the roles that everyone plays in support of open access principles and engendering same.

I have trouble visualizing this based on your description. Would you (or someone else) be able to make a rough sketch and put it in the gdoc?
As for the bricks for each country, the relative size probably makes it impossible to have all bricks with the name of the country (considering countries with 40,000 and others with <10 visits). I also think that listing all countries I grouped under "Other" does not yield much additional information for the reader considering the additional amount of space we would use. Maybe your sketch can convince me otherwise. :-)