[marcowanger]

I posted some text suggestions and a partial outline of a direction similar to what Dan suggested.

I actually think that the paper might be better as a traditional journal article rather than a letter to Science/Nature that might not get picked for publishing. Something along the lines of the BioStar paper, except instead of screenshots perhaps some informative information gleamed from the posts over the years.

What do you think of something like Genome Biology or Genome Medicine? I know one of the editors at Genome Medicine and I think there could be interest for a paper like this.

Just a thought.

Thank you genericforms, (my personal feeling) Is Genome Medicine relevant to this MS? I would rather go to Genome Biology..But, as you raise Genome Medicine, I think we are all willing to consider it. Maybe ask him/her in email first? We can always Try PLoS ComBio.

BTW, if we send letter to Sci/Nature, the process will be quick. Cut and paste into the system, wait for 2 weeks. If they accept it, then there will be. No pain .... We can always start expanding the whole stuff immediately after we submit the short letter.

[adaptivegenome]

Yes, you are right as long as Science/Nature does give feedback. From what I saw on this site, it looked like if you write a letter to the editor they may or may not publish and they don't always give feedback?

I agree Genome Biology is probably a more general fit. I thought of Genome Medicine because I think they are interested in technologies and methods that will accelerate our understanding of genomes. PLOS Comp is fine too but they just published Biostar... another option is Bioinformatics, but that might appear as if we are focusing on the informatics part only...

[marcowanger]

Yes, you are right as long as Science/Nature does give feedback. From what I saw on this site, it looked like if you write a letter to the editor they may or may not publish and they don't always give feedback?

I agree Genome Biology is probably a more general fit. I thought of Genome Medicine because I think they are interested in technologies and methods that will accelerate our understanding of genomes. PLOS Comp is fine too but they just published Biostar... another option is Bioinformatics, but that might appear as if we are focusing on the informatics part only...

Yes, they say if they don't publish within 2 weeks, then you can consider your letter dead.

Well, it is always fine to file pre-submission inquiry first. At this moment, I think we can concentrate on the short letter to Sci/Nature first.

After we submit it and (touch wood) no good news come in 2 weeks, then we can email multiple journals that includes Genome Bio, Genome Med, PloS Comp Bio, etc.

Bioinformatics seems to lack editorial section.

Any other suggestions?

[maubp]

At this moment, I think we can concentrate on the short letter to Sci/Nature first.

Good plan.

[Joann]

Why do I SEQanswers?

And why do X number of other scientists find themselves here as well? Because SEQanswers represents the heartbeat and pulse of next generation genetic sequencing. We understand that genetic sequences are the bottom line in biology, the astoundingly vast Periodic Table of the living world. Through these logs I can trace and observe the tensions arising between the limits of biological wet lab methodologies and the abstract netherworld of computational application and all of its promise.

Why do you SEQanswers?

[marcowanger]

And why do X number of other scientists find themselves here as well? Because SEQanswers represents the heartbeat and pulse of next generation genetic sequencing. We understand that genetic sequences are the bottom line in biology, the astoundingly vast Periodic Table of the living world. Through these logs I can trace and observe the tensions arising between the limits of biological wet lab methodologies and the abstract netherworld of computational application and all of its promise.

Why do you SEQanswers?

I believe everyone has their own reason to be here. But the common thing is that we know

SEQanswers represents the heartbeat and pulse of next generation genetic sequencing

Keith Robinson has explained a bit too. See http://omicsomics.blogspot.com/2011/...ands-down.html

[robs]

Should we decide on a deadline for the letter? How about the end of this week?

What we still need:
1) number of "active" users/members
2) future directions

What would be nice to have:
1) a keyword analysis on posts to determine what the hot topics were in 2007, 2008, 2009, 2010, and 2011
2) average number of users contributing to a discussion
3) site stats (e.g. site views per day)

[ECO]

Should we decide on a deadline for the letter? How about the end of this week?

What we still need:
1) number of "active" users/members
2) future directions

I can get these numbers tonight, and Marco has an answer to future directions as part of the NAR paper i believe.

What would be nice to have:
1) a keyword analysis on posts to determine what the hot topics were in 2007, 2008, 2009, 2010, and 2011
2) average number of users contributing to a discussion
3) site stats (e.g. site views per day)

This is harder, as I'm not a MySQL expert. If someone wants to hop on google chat or skype and help me with queries, it shouldn't be too bad to make a tag cloud or similar for #1. #2 i'd have to think about how to query to get, and #3 is easy from Google Analytics.

[marcowanger]

I can get these numbers tonight, and Marco has an answer to future directions as part of the NAR paper i believe.



This is harder, as I'm not a MySQL expert. If someone wants to hop on google chat or skype and help me with queries, it shouldn't be too bad to make a tag cloud or similar for #1. #2 i'd have to think about how to query to get, and #3 is easy from Google Analytics.

The Future Directions in the NAR paper focused on the wiki development, I believe there are much more that can be talk on the forum itself.

[robs]

The Future Directions in the NAR paper focused on the wiki development, I believe there are much more that can be talk on the forum itself.

It might still be useful to give us some directions for the letter. Would you be willing to add something along those lines to the letter?

[robs]

This is harder, as I'm not a MySQL expert. If someone wants to hop on google chat or skype and help me with queries, it shouldn't be too bad to make a tag cloud or similar for #1. #2 i'd have to think about how to query to get, and #3 is easy from Google Analytics.

Thanks for taking a lead on this. Please make sure to apply a filter to not include things from introductions, literature watch, jobs, and the news section (and any others that are not really discussion topics).

"tag cloud" reminds me of wordle (http://www.wordle.net/). Maybe we can combine this with some timeline. If you can upload the tag/topic counts (with dates) somewhere, then we can play around with visualizations.

[adaptivegenome]

Yes, they say if they don't publish within 2 weeks, then you can consider your letter dead.

Well, it is always fine to file pre-submission inquiry first. At this moment, I think we can concentrate on the short letter to Sci/Nature first.

After we submit it and (touch wood) no good news come in 2 weeks, then we can email multiple journals that includes Genome Bio, Genome Med, PloS Comp Bio, etc.

Bioinformatics seems to lack editorial section.

Any other suggestions?

Honestly, I am really thinking if Science/Nature does not work out, we should go for Genome Medicine or Genome Biology as a Commentary with one figure. I personally would be excited to see this in Genome Medicine but both are great journals.

[adaptivegenome]

I can get these numbers tonight, and Marco has an answer to future directions as part of the NAR paper i believe.



This is harder, as I'm not a MySQL expert. If someone wants to hop on google chat or skype and help me with queries, it shouldn't be too bad to make a tag cloud or similar for #1. #2 i'd have to think about how to query to get, and #3 is easy from Google Analytics.

Since I troubled you guys with the suggestion, I would be happy to be responsible for figuring out hot topics for 2007 to now...

[marcowanger]

Since I troubled you guys with the suggestion, I would be happy to be responsible for figuring out hot topics for 2007 to now...

thanks you genericforms

[robs]

I can get these numbers tonight, and Marco has an answer to future directions as part of the NAR paper i believe.

I just checked and there was no update on the letter since my last changes yesterday. Will you be able to put those numbers in the letter sometime today? Do you need help with anything?