[adobrovic]

Good idea

I came across this forum accidentally while surfing, then forgot about it, and have now rediscovered it. It is so much better than comparable forums in LinkedIn which are close to useless. It would be good for everyone in this area to know about it.

[dan]

Here they are for everyone to look at:

Awesome! Hmm... Apparently I have to write more than one word...

[adaptivegenome]

I agree. I certainly would not use the images as a big figure. Too messy. But I will play around and see if I can extract anything interesting...

[robs]

Thanks for generating the tag clouds. It's kind of hard to find interesting trends that might be worth mentioning in the letter. If you could try to pick a few tags and generate some line charts over time then it might be easier to select some interesting trends or tags.

When I parsed the data, I converted everything to lower case to prevent counting e.g. Bowtie, bowtie and BOWTIE as three different words. Then I removed all the common English words that occurred in the top 50 list and generated the wordle. This might increase the size of some interesting words in your tag clouds.

Looking at the figures, we probably won't be able to put the tag cloud as a big figure. Maybe reducing the number of words (in wordle under Layout), or selecting a few and generating the cloud for those might be better. Especially if we want to add it to another figure, the top 20-30 words are probably the most that can still be read.

It might also be interesting to use phrases instead of single words. (You can upload pre-counted phrases under Advanced in wordle.) This might distinguish "read" from "I need to read" and "sequencing read".

[adaptivegenome]

Okay so spent some time looking at the data by date and by keyword frequency. There is clearly room to improve the analysis by omitting more of the common words, alternate versions of the same word, etc. but I have attached images for each quarter year since 2008. There are some trends I can see... for example in early 2008 there were terms like "capture" and "nimblegen" and these became less frequent later. There are also some interesting trends looking at terms like BWA, MAQ, and BOWTIE.

The images are not quantitative but we can use them to visually detect possible trends and then follow up by counting the occurrence of the terms in each dataset if we want to test for sure whether terms go in and out of fashion and also whether some terms become more prevalent than others.

So this is a first pass and I welcome comments/suggestions...

Here they are for everyone to look at:

http://www.genericforms.com/2008Q1.pdf

http://www.genericforms.com/2008Q2.pdf

http://www.genericforms.com/2008Q3.pdf

http://www.genericforms.com/2008Q4.pdf

http://www.genericforms.com/2009Q1.pdf

http://www.genericforms.com/2009Q2.pdf

http://www.genericforms.com/2009Q3.pdf

http://www.genericforms.com/2009Q4.pdf

http://www.genericforms.com/2010Q1.pdf

http://www.genericforms.com/2010Q2.pdf

http://www.genericforms.com/2010Q3.pdf

http://www.genericforms.com/2010Q4.pdf

http://www.genericforms.com/2011Q1.pdf

http://www.genericforms.com/2011Q2.pdf

http://www.genericforms.com/2011Q3.pdf

http://www.genericforms.com/2011Q4.pdf

[ulz_peter]

oh, that's a pretty good reason...

[marcowanger]

Why not leave this sentence (which is from long version of first draft), or at least the first half.:

However, the rate at which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field rapidly becoming known for 'big data'.

Because it is 95% identical to the wiki paper....is good to rewrite it

[marcowanger]

hi guys,
sorry for not looking into that for quite a while. The final draft looks very promising and the figures do look good as well.

I think the argument inside the <> is way too clumsy (I don't think mentioning an example here is helping the text).Especially connsidering the 300 word limit. This is still the plan right? Or did I miss something?

Apart from that, good work guys!!

I dont mean to include the example, i just mean to write an argument using that logic

[ulz_peter]

Why not leave this sentence (which is from long version of first draft), or at least the first half.:

However, the rate at which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field rapidly becoming known for 'big data'.

[ulz_peter]

hi guys,
sorry for not looking into that for quite a while. The final draft looks very promising and the figures do look good as well.

I think the argument inside the <> is way too clumsy (I don't think mentioning an example here is helping the text).Especially connsidering the 300 word limit. This is still the plan right? Or did I miss something?

Apart from that, good work guys!!

[marcowanger]

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?

I think that part needs a rewrite. things in <> are the ideas not the actual writing to be included.

[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?

[marcowanger]

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

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

[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.

[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.