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Old 11-02-2011, 10:23 AM   #161
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Quote:
Originally Posted by ECO View Post
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.
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Old 11-02-2011, 04:18 PM   #162
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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.
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Old 11-02-2011, 04:20 PM   #163
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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...
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Old 11-02-2011, 07:03 PM   #164
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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
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Old 11-03-2011, 09:34 AM   #165
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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?
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Old 11-03-2011, 09:38 AM   #166
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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?
Hi Robs, seems the latest ver is #3 located at the wiki page

http://seqanswers.com/wiki/Publicati...for_SEQanswers

I started moving content from Gdoc back to the wiki
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Old 11-03-2011, 11:14 AM   #167
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Hi Robs, seems the latest ver is #3 located at the wiki page

http://seqanswers.com/wiki/Publicati...for_SEQanswers

I started moving content from Gdoc back to the wiki
I think, we should decide on one place to work on the letter. Otherwise, it will be too confusing and you end up merging things together. I like the comment feature in the Google docs and think that the version there is in much better shape than the Draft #3 in the wiki.
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Old 11-04-2011, 02:22 AM   #168
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I think, we should decide on one place to work on the letter. Otherwise, it will be too confusing and you end up merging things together. I like the comment feature in the Google docs and think that the version there is in much better shape than the Draft #3 in the wiki.
Yes, robs, we should stick to one place.
But some prefer gdoc (myself) and some the wiki. It is always hard to choose among various platform to write together....

Anyway, as the latest ver is being pasted as #3, I think we should respect the change (it's not done by me). Yes, we then have to do additional work to merge things together. I feel ok with it.. I can help merging things back.

I do like the structure of the #3 though, it's more than description or promotion of SEQanswers. Rather it let readers to think about the change of forms of scientific communicaiton, something at least complement to journals.

I suggest to stick to the wiki editing.
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Last edited by marcowanger; 11-04-2011 at 02:22 AM. Reason: fix typo
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Old 11-04-2011, 03:58 PM   #169
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I like it too. It is coming along nicely!
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Old 11-04-2011, 09:45 PM   #170
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I like it too. It is coming along nicely!
cool. Keep up the pace.
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Old 11-05-2011, 11:25 AM   #171
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I merged a few more things from the gdoc and the wiki into the draft #3. There are some good things in the long version that I think would fit quite well into the letter draft.

Any news yet on the tag cloud data?
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Old 11-05-2011, 05:28 PM   #172
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As I had mentioned earlier, I am happy to assemble that figure if someone gives me access to the post data.
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Old 11-05-2011, 09:16 PM   #173
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As I had mentioned earlier, I am happy to assemble that figure if someone gives me access to the post data.
genericforms. For this issue, you ask ECO or dan

I think we need to query the mysql db ...not familiar with vbulletin system personally
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Old 11-05-2011, 09:18 PM   #174
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Originally Posted by robs View Post
I merged a few more things from the gdoc and the wiki into the draft #3. There are some good things in the long version that I think would fit quite well into the letter draft.

Any news yet on the tag cloud data?
Thanks. Let's merge them and see how it goes.

Quote:
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)
Just to bump it it. We still need 3): To be provided by ECO.

1) & 2): need to ask people with mysql access
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Old 11-05-2011, 09:42 PM   #175
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I am clearly overcommitted elsewhere to work on these queries, sorry for dropping that ball...unfortunately there is no easy way (that I know of, but happy to take suggestions) to give read-only access to the db for people to play with queries. If you have suggestions let me know...I don't know vBulletin's tables well enough to put together the requisite queries.... :/
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Old 11-06-2011, 04:29 AM   #176
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I am clearly overcommitted elsewhere to work on these queries, sorry for dropping that ball...unfortunately there is no easy way (that I know of, but happy to take suggestions) to give read-only access to the db for people to play with queries. If you have suggestions let me know...I don't know vBulletin's tables well enough to put together the requisite queries.... :/
Rather than grant access to the DB can you simply dump every post to a text file and share that? We can work from the text file to capture the necessary data.
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Old 11-06-2011, 05:09 AM   #177
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The perfect example to illustrate how this community enable interactions among developers. (http://seqanswers.com/forums/showthread.php?t=15200)
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Old 11-06-2011, 04:59 PM   #178
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You know, I really liked the GDoc approach to collaboratively editing the document. Unless someone objects I would recommend we migrate back especially when we have a more mature draft and are simply refining words and phrases.

macrowanger, I agree the BWA/Bowtie thread has been very educational (at least for me!). Perhaps it is worth emphasizing that the key developers of the tools used for nextgen are members of SeqAnswers.
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Old 11-06-2011, 05:31 PM   #179
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Rather than grant access to the DB can you simply dump every post to a text file and share that? We can work from the text file to capture the necessary data.
Yup, got the sqldump shared in google docs...it's 40MB...send me an email and I'll share it with you, along with the schema.
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Old 11-06-2011, 05:35 PM   #180
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Thanks ECO. I sent you a private message with my contact details.
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