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Old 12-02-2011, 03:18 PM   #341
robs
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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.
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Old 12-02-2011, 03:58 PM   #342
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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.
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Old 12-03-2011, 05:54 AM   #343
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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".

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Old 12-03-2011, 06:00 PM   #344
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Default 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.

Last edited by Joann; 12-03-2011 at 06:08 PM. Reason: spelling, clarity
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Old 12-03-2011, 06:46 PM   #345
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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. :-)
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Old 12-03-2011, 06:48 PM   #346
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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.
I think this would nicely fit in the paragraph "Implications of SEQanswers for the Scientific Community and the medical field". Would you be able to fit it in there?
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Old 12-04-2011, 03:14 AM   #347
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I think this would nicely fit in the paragraph "Implications of SEQanswers for the Scientific Community and the medical field". Would you be able to fit it in there?
The material is available just for that purpose. However I have looked at the comments/response by the list of journal editors so far and am concerned about submitting new material in a paper along side previous original material (that I and many other helped to construct on the forum site for the purpose of our forum note supplemental to the wiki effort). At a certain point it would be wasting new editors' time given the accumulated reponses we received from their editorial colleagues. Remember, lots of journal editors are volunteers also.

Now the focus must shift away from depending on the previous text at all (which while very representative of the forum but unfortunately cannot be re-used, it seems) and towards effectively abstracting, summarizing and commenting on all the new material generated especially since Nov. 15.

On the figure 3 construct: the scale of course depends on the amount of space alloted for the image and at a certain point, the representation will go off scale. Around the visual point where the bricks are too small to read, I would insert a link to the expanded list, even if provided as a supplemental content. If there had been more equal representation, in theory, there would be 65 names on each of the two columns which would not be out of the question, scale-wise. I personally know that the post from Paraguay was valid, because I answered it so I am assuming that other posts have been screened and monitored for validity. The purpose is to continue to help create inroads to doing open access science as part of the global picture.
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Old 12-04-2011, 10:50 AM   #348
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The material is available just for that purpose. However I have looked at the comments/response by the list of journal editors so far and am concerned about submitting new material in a paper along side previous original material (that I and many other helped to construct on the forum site for the purpose of our forum note supplemental to the wiki effort). At a certain point it would be wasting new editors' time given the accumulated reponses we received from their editorial colleagues. Remember, lots of journal editors are volunteers also.
Could you please explain what "purpose" you mean and what "original material" you are referring to?

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Originally Posted by Joann View Post
Now the focus must shift away from depending on the previous text at all (which while very representative of the forum but unfortunately cannot be re-used, it seems) and towards effectively abstracting, summarizing and commenting on all the new material generated especially since Nov. 15.
We worked on many different versions/drafts. What is the "previous text"?

Quote:
Originally Posted by Joann View Post
On the figure 3 construct: the scale of course depends on the amount of space alloted for the image and at a certain point, the representation will go off scale. Around the visual point where the bricks are too small to read, I would insert a link to the expanded list, even if provided as a supplemental content. If there had been more equal representation, in theory, there would be 65 names on each of the two columns which would not be out of the question, scale-wise. I personally know that the post from Paraguay was valid, because I answered it so I am assuming that other posts have been screened and monitored for validity. The purpose is to continue to help create inroads to doing open access science as part of the global picture.
Supplementary files are allowed for a correspondence in Genome Medicine, so we could think about how to present that data in detail as supplement.
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Old 12-04-2011, 10:57 AM   #349
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Supplementary files are allowed for a correspondence in Genome Medicine, so we could think about how to present that data in detail as supplement.
Rob, you are correct in that we could submit supplementary files, but really I think we are getting a bit too big here. Let's just focus on the key sections we have for now and bring the paper as close to completion as possible. I am working on my part. Then we can see what is missing. Although I am not intensely opposed to supplemental data, I think it is a bit much for such a short and simple correspondence.

Last edited by adaptivegenome; 12-04-2011 at 10:58 AM. Reason: typo
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Old 12-04-2011, 04:04 PM   #350
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Previous original material (content) published in NAR on Nov 15 covering the forum SEQanswers cannot be resubmitted for publication in any of the journals approached that do not consider publishing previously published material. See the list of journals discussed in previous posts.

1. Genome Medicine wishes to consider different material of excellence not previously published but only in the form and context of an entire manuscript. The strongest data and material not previously published consists of the proof of robust open acess participation from 130 countries, namely the complete listing of countries in some form. One importance of this data is that it will create a baseline from which to measure future growth and direction of open access participation in the field so it is significant data now and an important base for future metrics concerning science policy.

2. It is also a requirement to include (new) content addressing medical/clinical research.

This content (1 and 2) forms the central new material of a publishable and currently unpublished communication from the SEQanswers forum. It should serve as the main focus rather than fitting it around material similar to that already published and that we have now learned is unsuitable in the opinion of a number of journals approached in the wake of the NAR publication.

The completion of this new material and its publication can be achived more or less quickly depending on the number of resubmissions of the new material that end up being necessary.
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Old 12-05-2011, 10:16 PM   #351
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Default fact check on demographic data, please

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I updated the figures. As for the demographic data, there was only one month available, so I couldn't do much with it.
The information on forum demographics actually appears to be inclusive 2007-October, 2011. Could I get a quick confirmation for this? Also whether all the single location posts have been pre-monitored as valid. If not can someone review each of the single location posts for this purpose? This would need to be done before the final SEQanswers manuscript is submitted, however informally it appears that they could indeed be valid, and if so, nice work ECO and monitors!
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Old 12-06-2011, 02:11 PM   #352
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Guys, I forgot to ask. Did we submit an inquiry to PLOS Comp Bio? I know Marco had mentioned that journal previously but I cannot remember if we ruled it out or if an inquiry was sent...

Last edited by adaptivegenome; 12-06-2011 at 02:13 PM. Reason: typo
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Old 12-06-2011, 03:01 PM   #353
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Guys, I forgot to ask. Did we submit an inquiry to PLOS Comp Bio? I know Marco had mentioned that journal previously but I cannot remember if we ruled it out or if an inquiry was sent...
I did submit the inquiry on 24th Nov. The status as of yesterday is still "with editor".......so, let's forget about it
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Old 12-06-2011, 03:06 PM   #354
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I did submit the inquiry on 24th Nov. The status as of yesterday is still "with editor".......so, let's forget about it
Ok, sounds good. I was just checking to be sure we examined all the options before deciding upon Genome Medicine.
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Old 12-06-2011, 07:33 PM   #355
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The information on forum demographics actually appears to be inclusive 2007-October, 2011. Could I get a quick confirmation for this? Also whether all the single location posts have been pre-monitored as valid. If not can someone review each of the single location posts for this purpose? This would need to be done before the final SEQanswers manuscript is submitted, however informally it appears that they could indeed be valid, and if so, nice work ECO and monitors!
Maybe we have different sources. The data I was referring to was from Google Analytics and only contained Oct 2011.
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Old 12-06-2011, 07:40 PM   #356
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Can someone explain why all the changes that I made over the weekend were removed?
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Old 12-07-2011, 02:02 AM   #357
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Maybe we have different sources. The data I was referring to was from Google Analytics and only contained Oct 2011.
I was referring to the country list on the spread sheet Marco sent, which appears to me to be a cumulative list, but maybe it is not, which is why I asked for clarification. Site activity analysis, that would reasonably be a month's worth of data, right? Not four years.

As far as the material under the open access topic heading, I would prefer to publish the cumulative list of countries as a benchmark. At the present time I have been successful locating datasets from other studies of open access information communication that would allow comparisons of global participation and would like to include this info as they are quite favorable.

I posted a reference (and pdf) over the weekend on a recent publishing industry survey that indicates researchers world wide have the most difficulty accessing (open and closed formats) the very type of scholarly/professional material that is regularly posted on this forum.
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Old 12-07-2011, 07:45 PM   #358
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Can someone explain why all the changes that I made over the weekend were removed?
You can view the change log in wiki (history) & GDoc (under file--> file revision)
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Old 12-07-2011, 07:49 PM   #359
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Can someone explain why all the changes that I made over the weekend were removed?
I saw that Joann removed some of my edits. I restored some of them. You might look to see if your revisions were removed around the same time. Think it was the 6th.

Last edited by adaptivegenome; 12-07-2011 at 07:50 PM. Reason: typo
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Old 12-07-2011, 09:55 PM   #360
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I saw that Joann removed some of my edits. I restored some of them. You might look to see if your revisions were removed around the same time. Think it was the 6th.
Seems like Joann removed mine as well. I assumed that the removal of my edits was by accident and added them again.
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