SEQanswers

Go Back   SEQanswers > Site News > Site Feedback/Suggestions



Similar Threads
Thread Thread Starter Forum Replies Last Post
Minimum Criteria to Publish ChIP-seq data ETHANol Epigenetics 7 12-04-2011 04:35 AM
Lets publish the Wiki! dan Wiki Discussion 108 09-07-2011 09:10 AM
SEQanswers mentioned for the second time in a major journal ECO Site Announcements 3 08-01-2011 08:51 AM
Jim Watson in Excruciating Detail: 454/Baylor Publish Complete Genome Sequence ECO Literature Watch 1 04-16-2008 02:43 PM
Welcome to SEQanswers.com! ECO Site Announcements 0 10-28-2007 03:59 PM

Reply
 
Thread Tools
Old 11-12-2011, 06:22 PM   #201
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

To save you the search for the gdoc link:
https://docs.google.com/document/d/1.../edit?hl=en_US
robs is offline   Reply With Quote
Old 11-12-2011, 08:20 PM   #202
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Hi robs, great work. figure 1 is super nice, i see the new discussion(i suppose it means a thread?) still get steady increases after these years. While there are a slight drop /steady trend in the number of posts per month. Hey, on second thought I think the drop is due to bad curve fitting, the overall trend is still increasing. The rapid dropping in time between questions and answers support such argument. Obviously when ppl ask a question, normally they open a new post and thus the increase of new discussion.

For figure 2, the raw data points for time between Q&A looks a bit messy. Should we hide them?
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-12-2011, 08:24 PM   #203
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Robs, remember to keep the data file and the scripts for graph generation. We still dont know if we have to change the color scheme or anything to suit journal's requirement. Great graphs!
__________________
Marco

Last edited by marcowanger; 11-12-2011 at 08:27 PM. Reason: fix typo
marcowanger is offline   Reply With Quote
Old 11-12-2011, 08:31 PM   #204
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Regarding the tag cloud, I think genericforms are having it done soon. Because there are already 2-3 figures potentially useful, I rather focus on the text. Just to avoid duplication of effort. Frankly, can we use all figures? Is there any #figures limitation? I think all these three would be worthwhile to be published. Thank you again robs!
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-13-2011, 12:00 AM   #205
andreas.sjodin
Member
 
Location: Umeň, Sweden

Join Date: Apr 2009
Posts: 27
Default

I like the first figure too. The points should probably go away in second figure to make it less messy.
andreas.sjodin is offline   Reply With Quote
Old 11-13-2011, 01:27 PM   #206
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

Thanks for the comments.

I think, we can only add one figure for the letter (not sure though). I will wait until the tag cloud is done and maybe we can put all together into one figure.

If you have more ideas of what data might be interesting to plot, let me know and I will do my best to get the graph done.
robs is offline   Reply With Quote
Old 11-13-2011, 06:12 PM   #207
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Talking

Quote:
Originally Posted by robs View Post
Thanks for the comments.

I think, we can only add one figure for the letter (not sure though). I will wait until the tag cloud is done and maybe we can put all together into one figure.

If you have more ideas of what data might be interesting to plot, let me know and I will do my best to get the graph done.
Having these three would be fine enough I think...
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-13-2011, 07:41 PM   #208
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Quote:
Originally Posted by robs View Post
Thanks for the comments.

I think, we can only add one figure for the letter (not sure though). I will wait until the tag cloud is done and maybe we can put all together into one figure.

If you have more ideas of what data might be interesting to plot, let me know and I will do my best to get the graph done.
Just thinking overlaying the tag cloud into the second figure to replace the raw dots. What do you guys think?
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-13-2011, 09:02 PM   #209
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

Quote:
Originally Posted by marcowanger View Post
Just thinking overlaying the tag cloud into the second figure to replace the raw dots. What do you guys think?
If we want to make a single figure, then I would add the tag cloud data to the first one and ignore the second figure. We could keep the second figure for the longer version, if necessary. Or we can try to submit all figures that we will have at that point of submission and let them choose.
robs is offline   Reply With Quote
Old 11-14-2011, 09:51 PM   #210
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Smile

Quote:
Originally Posted by robs View Post
If we want to make a single figure, then I would add the tag cloud data to the first one and ignore the second figure. We could keep the second figure for the longer version, if necessary. Or we can try to submit all figures that we will have at that point of submission and let them choose.
Agree, it is good to have everything now.
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-15-2011, 05:39 PM   #211
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

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.
adaptivegenome is offline   Reply With Quote
Old 11-15-2011, 05:46 PM   #212
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Smile

Quote:
Originally Posted by genericforms View Post
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 ;-)
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-15-2011, 05:54 PM   #213
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

Quote:
Originally Posted by marcowanger View Post
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.
adaptivegenome is offline   Reply With Quote
Old 11-15-2011, 06:03 PM   #214
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

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 is offline   Reply With Quote
Old 11-15-2011, 06:15 PM   #215
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

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.



Quote:
Originally Posted by robs View Post
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).

Last edited by adaptivegenome; 11-15-2011 at 06:18 PM. Reason: typo
adaptivegenome is offline   Reply With Quote
Old 11-15-2011, 06:17 PM   #216
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Quote:
Originally Posted by robs View Post
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...
__________________
Marco

Last edited by marcowanger; 11-15-2011 at 06:22 PM. Reason: read genericforms's post after i make the post
marcowanger is offline   Reply With Quote
Old 11-15-2011, 06:20 PM   #217
marcowanger
Senior Member
 
Location: Hong Kong

Join Date: Dec 2008
Posts: 350
Default

Quote:
Originally Posted by genericforms View Post
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..
__________________
Marco
marcowanger is offline   Reply With Quote
Old 11-15-2011, 06:29 PM   #218
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default

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!
adaptivegenome is offline   Reply With Quote
Old 11-15-2011, 07:03 PM   #219
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

Quote:
Originally Posted by marcowanger View Post
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 is offline   Reply With Quote
Old 11-15-2011, 07:07 PM   #220
robs
Senior Member
 
Location: San Diego, CA

Join Date: May 2010
Posts: 116
Default

Quote:
Originally Posted by genericforms View Post
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.
robs is offline   Reply With Quote
Reply

Tags
publication

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:06 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO