[adaptivegenome]

Sorry to be behind on the cloud. I was out of town and returned just yesterday. Will try to have some up tomorrow and will also share raw data with robs and macrowanger in case they have some suggestions. I think we should definitely make all the figures because if the letter is not accepted, I think this paper would fit nicely with Genome Medicine and there it will not be subject to the same restrictions.

[marcowanger]

Sorry to be behind on the cloud. I was out of town and returned just yesterday. Will try to have some up tomorrow and will also share raw data with robs and macrowanger in case they have some suggestions. I think we should definitely make all the figures because if the letter is not accepted, I think this paper would fit nicely with Genome Medicine and there it will not be subject to the same restrictions.

That ia great, looking forward to seeing the tag cloud. Genome Medicine is always an option ;-)

[adaptivegenome]

That ia great, looking forward to seeing the tag cloud. Genome Medicine is always an option ;-)

I know one of the editors there who I am sure will enjoy this paper. The collaborative analysis and sharing of genome data was a big point of interest at the recent CSHL Personal Genomes meeting.

[robs]

I improved the first figure and added some context to the letter text.

I also added some word count data to the gdoc. It basically shows that the most used words do not change over time and the top 20 are the same from 2008 to 2011. Not sure if it still makes sense to create a word cloud over time.

Maybe we can use a different statistic. The forum search tags might show some different trend. We just need to get the data from ECO and play around with it.

What else do we need for the letter? Could we agree on a deadline? Maybe the end of this week? We are working on this for a while now and I don't want to continue working on the letter forever (there are always things that can be changed).

[adaptivegenome]

It is interesting that you mention the lack of trending terms because in building iterative clouds where I keep removing common words I have been really unable to find anything either. It not surprising as it might be there no obvious major shifts in topics.

I think a deadline has to be set but also it is hard for me to follow the many versions of the paper. Is the one "final" rough draft that can be circulated in WORD format or via Gdocs? OR even on the wiki... It would be nice to have 1 spot we can see the entire paper as it currently stands.

I improved the first figure and added some context to the letter text.

I also added some word count data to the gdoc. It basically shows that the most used words do not change over time and the top 20 are the same from 2008 to 2011. Not sure if it still makes sense to create a word cloud over time.

Maybe we can use a different statistic. The forum search tags might show some different trend. We just need to get the data from ECO and play around with it.

What else do we need for the letter? Could we agree on a deadline? Maybe the end of this week? We are working on this for a while now and I don't want to continue working on the letter forever (there are always things that can be changed).

[marcowanger]

I improved the first figure and added some context to the letter text.

I also added some word count data to the gdoc. It basically shows that the most used words do not change over time and the top 20 are the same from 2008 to 2011. Not sure if it still makes sense to create a word cloud over time.

Maybe we can use a different statistic. The forum search tags might show some different trend. We just need to get the data from ECO and play around with it.

What else do we need for the letter? Could we agree on a deadline? Maybe the end of this week? We are working on this for a while now and I don't want to continue working on the letter forever (there are always things that can be changed).

Robs, I agree that we shouldnt wait for anytime longer. I love deadline. If the word use doesnt change dramatically (alsp observed by genericforms), we might need to ask ECO for the forum tag (becoz its's tagged by the one who post, may be different from the real keyword used)

Cant wait seeing the figures...

[marcowanger]

It is interesting that you mention the lack of trending terms because in building iterative clouds where I keep removing common words I have been really unable to find anything either. It not surprising as it might be there no obvious major shifts in topics.

I think a deadline has to be set but also it is hard for me to follow the many versions of the paper. Is the one "final" rough draft that can be circulated in WORD format or via Gdocs? OR even on the wiki... It would be nice to have 1 spot we can see the entire paper as it currently stands.

Genericforms, i will do it ASAP.

The current version scatterd in the wiki draft #3 and gdoc in draft#2. I will reconsile both as final draft. I need some time..

[adaptivegenome]

No rush. And if robs and others agree, I would say it would be reasonable to assign a deadline of 1 week from the day that you reconcile the final document. This should be plenty of time for everyone to make final comments. Someone will also then have to collect real names for all the authors, affiliations, etc. and do all the administrative stuff necessary to get the paper out!

[robs]

Genericforms, i will do it ASAP.

The current version scatterd in the wiki draft #3 and gdoc in draft#2. I will reconsile both as final draft. I need some time..

I switched to editing the wiki draft #3 version a while ago and did not do anything (except adding the figures) to the gdoc. I would suggest to either use draft #3 and I can add the figure or move everything to a new gdoc.

[robs]

No rush. And if robs and others agree, I would say it would be reasonable to assign a deadline of 1 week from the day that you reconcile the final document. This should be plenty of time for everyone to make final comments. Someone will also then have to collect real names for all the authors, affiliations, etc. and do all the administrative stuff necessary to get the paper out!

The real names and affiliations can be found on the wiki under "Signers". We can get the remaining information such as emails when we reach the deadline.

[adaptivegenome]

I switched to editing the wiki draft #3 version a while ago and did not do anything (except adding the figures) to the gdoc. I would suggest to either use draft #3 and I can add the figure or move everything to a new gdoc.

It would be great to setup a new GDoc. We could add finishing touches and then just export the GDoc to WORD and be ready to send it out. I REALLY like your figures btw.

[robs]

It would be great to setup a new GDoc. We could add finishing touches and then just export the GDoc to WORD and be ready to send it out. I REALLY like your figures btw.

Thanks!

I like gdoc too because of the comments, but I am fine with whatever you choose.

[robs]

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

Nucleic Acids Res. 2011 Nov. doi: 10.1093/nar/gkr1058

Jing-Woei Li, Keith Robison, Marcel Martin, Andreas Sjödin, Björn Usadel, Matthew Young, Eric C. Olivares and Dan M. Bolser

more

Btw, congrats to the SEQwiki paper.

[marcowanger]

Please edit on the #Final draft, from now on. Thanks.

http://seqanswers.com/wiki/Publicati...Draft_.23Final

[maubp]

Is that meant to be a quote from Heng Li in the opening paragraph? What's going on with the less than sign and only a closing quote?