[robs]

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?

[Joann]

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.

[robs]

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?

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"?

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.

[adaptivegenome]

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.

[Joann]

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.

[Joann]

fact check on demographic data, please

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!

[adaptivegenome]

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...

[marcowanger]

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

[adaptivegenome]

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.

[robs]

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.

[robs]

Can someone explain why all the changes that I made over the weekend were removed?

[Joann]

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.

[marcowanger]

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)

[adaptivegenome]

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.

[robs]

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.