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dan
10-05-2011, 12:55 PM
During the review of the SEQwiki paper (http://seqanswers.com/wiki/Publication/Paper_(NAR_2012)/Reply), an important point was raised by the reviewers: the SEQanswers forum has yet to be published, and deserves a good publication.

Why don't we write a letter to Science or Nature about SEQanswers?

The project has already been 'informally' cited dozens of times (http://seqanswers.com/wiki/Papers_Referencing_SEQanswers) in the literature, so why not write a nice summary for everyone to cite?

The proposal is to use the wiki to collaboratively draft a letter to Science (http://www.submit2science.org/ws/begin.asp) or Nature (http://mts-nature.nature.com/cgi-bin/main.plex?form_type=display_auth_instructions) (see: wiki:Publication/Letter_for_SEQanswers (http://seqanswers.com/wiki/Publication/Letter_for_SEQanswers)), with each contributor adding their name to the paper. The final list of authors will be ranked according to (democratically determined) contribution to the final text.

Please contribute (and sign the letter) here (http://seqanswers.com/wiki/Publication/Letter_for_SEQanswers)!

Meta paper discussion should stay on this thread (wiki sucks for discussion).

marcowanger
10-05-2011, 11:01 PM
How long will we aim?

Personally, I think we should keep it short.

ulz_peter
10-05-2011, 11:43 PM
Publishing SeqAnswers for being able to cite it "formally" is a great idea.
I second the opinion of marcowanger to keep it quite short.

andreas.sjodin
10-06-2011, 12:53 AM
I also think we should aim to keep it short and that it is a great idea. At least if we are going for a letter. An alternative would to write a more extensive "application note" describing the features but that would require much more work.

maubp
10-06-2011, 02:10 AM
Do we want to mention that SeqAnswers also acts as a useful forum for helping users with problems using NGS tools (sometimes leading to useful bug reports for the tool developers)? Or would that just encourage more of this - which wouldn't be such a bad thing except it can drown out other more important threads, like file format changes etc.

ulz_peter
10-06-2011, 02:16 AM
I think thats a good idea, as most of the threads in Seqanswers are indeed related to usage questions

marcowanger
10-06-2011, 02:19 AM
Do we want to mention that SeqAnswers also acts as a useful forum for helping users with problems using NGS tools (sometimes leading to useful bug reports for the tool developers)? Or would that just encourage more of this - which wouldn't be such a bad thing except it can drown out other more important threads, like file format changes etc.

Maubp, you raised an important point. Helping users with tools selection and bug report and improvement is an important "function" of this forum(IMO). In fact we. have written a bit in the introduction part, maybe we need to stress it more.

maubp
10-06-2011, 02:30 AM
OK, I've added a bit of text along those lines.

Peter

maubp
10-06-2011, 02:32 AM
Also, is it worth thinking about an option for real names in forum profiles (http://seqanswers.com/forums/showthread.php?t=13411) at this point?

dan
10-06-2011, 02:34 AM
I also think we should aim to keep it short and that it is a great idea. At least if we are going for a letter. An alternative would to write a more extensive "application note" describing the features but that would require much more work.

That's what I was thinking too... anyone know the guidelines for 'letters' to Science or Nature? Lets stick to one guideline or the other.

fkrueger
10-06-2011, 02:42 AM
I also think that SEQanswers is an incredibly useful knowledgebase all around NGS and its bioinformatics applications. I especially love its instantaneous character and the (usually) extremely short reaction times of experts and developers in the fields to all sorts of questions, ranging from biological questions to discussion/usage of various bioinformatic tools to bug reports or feature requests. For many questions I have and had in the past, SEQanswers has become my first port of call to look for solutions or help.

ulz_peter
10-06-2011, 02:44 AM
Any suggestions for the future directions part?

ulz_peter
10-06-2011, 02:45 AM
found in Science Homepage:

How to Submit a Letter to the Editor

Letters to the Editor are selected for publication that are pertinent to material published in Science or that discuss problems of general interest. Letters may be reviewed. Those selected for publication are intended to reflect the range of opinions received. The author of a paper in question is usually given an opportunity to reply.

Letters are not routinely acknowledged. Full addresses, signatures, and daytime phone numbers should be included. Letters should be brief (300 words or less) and may be edited for reasons of clarity or space. They may appear in print and/or on the World Wide Web. Letter writers are not consulted before publication.

ETHANol
10-06-2011, 02:48 AM
I think the future directions section is interesting. Just some ideas on what could be mentioned there:
1) The addition of a wet lab protocols wiki
2) As the size of the community increases, what are measures that can be implemented to keep the ratio of good information high to bad information? Perhaps the addition of energetic application specific moderators. This by the way it should be mentioned in the text that the ratio of good information to bad is really high on this forum.
3) Something else that might be cool is if there was some way to 'like/+1' threads and a section with the most popular threads. Might make browsing more efficient for causal readers.

ulz_peter
10-06-2011, 02:53 AM
I think the future directions section is interesting. Just some ideas on what could be mentioned there:
1) The addition of a wet lab protocols wiki
2) As the size of the community increases, what are measures that can be implemented to keep the ratio of good information high to bad information? Perhaps the addition of energetic application specific moderators. This by the way it should be mentioned in the text that the ratio of good information to bad is really high on this forum.
3) Something else that might be cool is if there was some way to 'like/+1' threads and a section with the most popular threads. Might make browsing more efficient for causal readers.

I like the idea of the wetlab protocol wiki. That should be feasible with bioinformatic analysis guidelines as well (like the RNA Analysis manual).

So not only a list of available softwares (like the SeqWiki)but how to use them...

However, I think we should separate the Forum from the Wiki for the letter, as the Wiki is getting published already, am I right?

andreas.sjodin
10-06-2011, 03:13 AM
I think wet lab protocols are better hosted at OpenWetWare.

Adding a section of small "example code snippets" to each software in the SEQwiki would be great. Should be added to wanted features in the SEQwiki.

I think it is better to mainly concentrate on the SEQanswer Forum in the letter.

marcowanger
10-06-2011, 03:20 AM
I think wet lab protocols are better hosted at OpenWetWare.

Adding a section of small "example code snippets" to each software in the SEQwiki would be great. Should be added to wanted features in the SEQwiki.

I think it is better to mainly concentrate on the SEQanswer Forum in the letter.

Agree that openwetware works better for wet lab protocols. And in fact there are some software walkthrough in SEQwiki already. Snippet would be great

dan
10-06-2011, 03:24 AM
I also think that SEQanswers is an incredibly useful knowledgebase all around NGS and its bioinformatics applications. I especially love its instantaneous character and the (usually) extremely short reaction times of experts and developers in the fields to all sorts of questions, ranging from biological questions to discussion/usage of various bioinformatic tools to bug reports or feature requests. For many questions I have and had in the past, SEQanswers has become my first port of call to look for solutions or help.

I think you speak for a lot of users. Please go ahead and write this in the letter if you agree :-D

dan
10-06-2011, 03:27 AM
However, I think we should separate the Forum from the Wiki for the letter, as the Wiki is getting published already, am I right?

Yup, the point of the letter is to focus on the forum, and hopefully publish before the wiki (coming out in January).

flxlex
10-06-2011, 03:43 AM
There is some (considerable?) overlap between the bioinformatics forum at SeqAnswers, and biostar.stackexchange.com. Perhaps we should acknowledge that, and comment that SeqAnswer is targeting a wider audience than just those analyzing data using bioinformatic tools?

marcowanger
10-06-2011, 03:46 AM
Yup, the point of the letter is to focus on the forum, and hopefully publish before the wiki (coming out in January).

For the letter, I think it would be suitable for SCIENCE letter (<400 words) and NATURE correspondence. Both are meant to be short. So, let's write everything first and pick the most significant points to keep.

marcowanger
10-06-2011, 03:51 AM
There is some (considerable?) overlap between the bioinformatics forum at SeqAnswers, and biostar.stackexchange.com. Perhaps we should acknowledge that, and comment that SeqAnswer is targeting a wider audience than just those analyzing data using bioinformatic tools?


Sure it may seems to be. I think both SEQ and Biostar are great, and we should definitely acknowledge Biostar in the letter. However, one particular strong point in SEQ Bioinformatics Section is the freedom granted to users to announce their tools, which fostered much discussion beyond question-and-answer style in Biostar. IMO, Biostar does a better job in Q&A. So, both sites serve different purposes.

andreas.sjodin
10-06-2011, 04:02 AM
There is some (considerable?) overlap between the bioinformatics forum at SeqAnswers, and biostar.stackexchange.com. Perhaps we should acknowledge that, and comment that SeqAnswer is targeting a wider audience than just those analyzing data using bioinformatic tools?

I think this a good selling point. The SeqAnswers has a wide community of both wet-lab and computer biologists.

flxlex
10-06-2011, 04:11 AM
Sure it may seems to be. I think both SEQ and Biostar are great, and we should definitely acknowledge Biostar in the letter. However, one particular strong point in SEQ Bioinformatics Section is the freedom granted to users to announce their tools, which fostered much discussion beyond question-and-answer style in Biostar. IMO, Biostar does a better job in Q&A. So, both sites serve different purposes.

I tried to add something to the letter along these lines.

marcowanger
10-06-2011, 04:17 AM
I tried to add something to the letter along these lines.

Thanks flxlex

marcowanger
10-06-2011, 04:58 AM
One caution for Nature Correspondence:

A Correspondence is usually signed by no more than three authors; this is because Correspondence is a forum for readers' reactions, not for statements by organizations or groups of individuals.

andreas.sjodin
10-06-2011, 05:06 AM
Then I think we need to skip the Nature Correspondence alternative

marcowanger
10-06-2011, 05:37 AM
Then I think we need to skip the Nature Correspondence alternative

Andreas, agree.

suryasaha
10-06-2011, 05:47 AM
The letter should make an effort to address PI's in the audience to make them point their students and post docs to this forum, especially if they are newbies. It will help, if metrics like the average time for response and % of answered queries were included, to present the effectiveness of the forum to non-users.

colindaven
10-06-2011, 06:16 AM
I think funding is an important issue. Who funds SeqAnswers ? I think if I remember rightly there was some mention one of the admins was at Pac Bio. How is advertising handled and the site supported ?

I personally do not think there is a lot of bias due to advertising etc, but some who do not know the community may be more skeptical.

Also, what are the guidelines on commercial software plugs, and should this be mentioned ?

marcowanger
10-06-2011, 06:23 AM
I think funding is an important issue. Who funds SeqAnswers ? I think if I remember rightly there was some mention one of the admins was at Pac Bio. How is advertising handled and the site supported ?

I personally do not think there is a lot of bias due to advertising etc, but some who do not know the community may be more skeptical.

Also, what are the guidelines on commercial software plugs, and should this be mentioned ?

To briefly answer your question (as a ordinary registered member ONLY), the writing below was the initial writing for the SEQwiki manuscript.

ECO is the founder of the SEQanswers community. SEQanswers has advertising relationships with companies. All relationships between SEQanswers and sponsoring companies are explicitly listed in “About SEQanswers” (http://seqanswers.com/index.php?pageid=about). These companies have no role in operation of SEQanswers. SEQwiki does not host any sponsored content, and all the contributed text is available under a copyleft agreement. Discussion on SEQanswers forum and curation on SEQanswers wiki is based on the entity of an individual registered with an account.

For the commercial plug, I remember the company-user is tagged with "Registered Vendor" before they can advertise, and only in "Vendor Forum", so I don't see there is any problem.

ulz_peter
10-06-2011, 06:40 AM
The letter should make an effort to address PI's in the audience to make them point their students and post docs to this forum, especially if they are newbies. It will help, if metrics like the average time for response and % of answered queries were included, to present the effectiveness of the forum to non-users.

Maybe that's a nice catch for the future directions part

ulz_peter
10-06-2011, 06:44 AM
Just to inform you: LibreOffice tells me its (only letter text) already 472 words... without summary or future directions

marcowanger
10-06-2011, 06:46 AM
Just to inform you: LibreOffice tells me its (only letter text) already 472 words... without summary or future directions Ya, obviously the text are too clumsy for a letter. But let's forget about the word limitation for now and write as much as you can. We can always trim the content down when fitting the stuff into particular letter/opinion/perspective/etc:)

marcowanger
10-06-2011, 06:52 AM
I think the future directions section is interesting. Just some ideas on what could be mentioned there:
1) The addition of a wet lab protocols wiki
2) As the size of the community increases, what are measures that can be implemented to keep the ratio of good information high to bad information? Perhaps the addition of energetic application specific moderators. This by the way it should be mentioned in the text that the ratio of good information to bad is really high on this forum.
3) Something else that might be cool is if there was some way to 'like/+1' threads and a section with the most popular threads. Might make browsing more efficient for causal readers.

ETHANol, regarding the point 3), I think the current vbulletin board has already scored the discussion thread quite well (by view count, and time-of-reply). But I am inspired by your point. Why not add a "SHARE" button, just like other site? I am not sure if it can be easily implemented, but it would be good to share the good discussion thread.

marcowanger
10-06-2011, 07:55 AM
I think the overall idea is already there. We just need to make the wordings precise and simple. And less feel like an advertisement.

I would be impressed and visit the site if I read this correspondence.:)

simonandrews
10-06-2011, 10:04 AM
Also, is it worth thinking about an option for real names in forum profiles (http://seqanswers.com/forums/showthread.php?t=13411) at this point?

You can do that now. Eco turned on the ability to edit your profile tag (http://seqanswers.com/forums/showthread.php?t=13802) a few weeks ago.

ulz_peter
10-06-2011, 10:59 PM
I tried to create a first trimmed version of the letter. It now consists of 370 words. Someone stated a Science letter may have less than 400 words which would be ok then. To cut it down to 300 words is nearly impossible...

ulz_peter
10-07-2011, 02:46 AM
current status 337 words (thanks marcowanger)

andreas.sjodin
10-07-2011, 03:06 AM
I just saw this statement in the Science "Guidelines and Directions for Web Submission of Letters to the Editor"

Letters submitted, published, or posted elsewhere, in print or online, will be disqualified.

It will be interesting to see how they judge online community writing. However, it is a working document in progress and not really posted as a final document.

marcowanger
10-07-2011, 03:21 AM
Andreas, it should be fine. I will make the fimal version in google doc. As you have said, it is still a working draft.

marcowanger
10-07-2011, 10:17 AM
I have added all high impact journals that acknowledge SEQ* explicitly in their text to our letter to science. It looks nice!

marcowanger
10-07-2011, 10:31 AM
polished the language, the letter is ready to go! (IMO)

ulz_peter
10-07-2011, 10:33 AM
Great stuff, totally agree with the current version. References look great indeed.

ulz_peter
10-07-2011, 10:37 AM
As the current version only has 170 something words (without references of course), do we want to add some future directions parts?

marcowanger
10-07-2011, 10:39 AM
Peter, my fault. I also count the words after I posted "ready to go".....

Good to write some more things. And for a "letter", I think we need active voice rather than passive voice.

ulz_peter
10-07-2011, 10:47 AM
you're right active voice is probably better. I added the future directions part of the untrimmed letter, but it somehow interfers with the former paragraph...

marcowanger
10-07-2011, 10:52 AM
you're right active voice is probably better. I added the future directions part of the untrimmed letter, but it somehow interfers with the former paragraph...
Peter, sorry I deleted the Future Directions for now. I have emailed ECO for his advices on Future Directions.:)

ulz_peter
10-07-2011, 10:56 AM
good idea. Sorry for interfering.

He's probably the best man to address that question to...

marcowanger
10-07-2011, 10:58 AM
good idea. Sorry for interfering.

He's probably the best man to address that question to...

You are helping a lot, Peter. But for the Future directions, well, he has the say......:D

Let's think something else we may have missed now.....anything else?:)

marcowanger
10-07-2011, 11:01 AM
Just for information for all, some writings under the section "Content" are extracted directly from the SEQwiki MS, so that serves merely a background, shouldn't be copied and pasted into the letter.

ulz_peter
10-07-2011, 11:13 AM
I guess going into more detail will lead to other details neede to be mentioned, so for the overall picture the letter is great as it is now. Some hundred words for the future directions part and that's it I'd say.

Just one question:
We founded the SEQanswers (http://SEQanswers.com) to facilitate rapid dissemination of HTS
Isn't there a noun missing (like community or forum)? My English is too bad to judge if thats comprehensible...

ulz_peter
10-07-2011, 11:15 AM
so we mention:
the community
question and answer of bioinformatic tools
wet-lab parts
SEQanswers as knowledge base
papers already published mentioning SEQanswers

we've got the introduction and the future perspectives part is going to come...

So, I guess that's pretty much it

marcowanger
10-07-2011, 11:16 AM
I guess going into more detail will lead to other details neede to be mentioned, so for the overall picture the letter is great as it is now. Some hundred words for the future directions part and that's it I'd say.

Just one question:

Isn't there a noun missing (like community or forum)? My English is too bad to judge if thats comprehensible...

I think SEQanswers is a term that speaks itself. We may add community and make it the "SEQanswers community" ?

marcowanger
10-07-2011, 11:17 AM
just a kind of checklist:
Introduction

May you elaborate a bit? :)

ulz_peter
10-07-2011, 11:20 AM
oops, I think I should go to bed...

marcowanger
10-07-2011, 11:21 AM
oops, I think I should go to bed...

me too. 3:30am here

ulz_peter
10-07-2011, 11:23 AM
IMHO I'd add "community" just to emphasize the community character of the forum. (OK any forum has a kind of community character, but there's something special about that one, right?)

marcowanger
10-07-2011, 11:24 AM
IMHO I'd add "community" just to emphasize the community character of the forum. (OK any forum has a kind of community character, but there's something special about that one, right?)

right, "SEQanswers community" now:)

ulz_peter
10-07-2011, 11:32 AM
I guess that's it for the moment. Good work marcowanger (sorry for not knowing your real name) and thanks for the great engagement on that one.

Michael.James.Clark
10-07-2011, 01:42 PM
I think this is fantastic. I added a few things and made a few cosmetic edits. Great job, and please let me help out.

I especially wanted to add reference to this paper (http://www.sciencemag.org/content/early/2011/07/13/science.1207745) (http://www.sciencemag.org/content/early/2011/07/13/science.1207745) and evidence that SeqAnswers serves as a resource to suit this modern Internet phenomenon of transactive memory and learning.

I think a bit of actual data is called for. I added a few requests in there that are very simple but bolster the statements that Seqanswers has significant impact on the community. I think ECO should be able to provide those.

(Sorry I totally missed pages 2 and 3 of this thread somehow. If I messed anything up in the draft on the wiki, sorry about that. Didn't realize you guys were done. I didn't touch the letter part.)

ECO
10-07-2011, 03:02 PM
I can definitely pull some stats from the backend of the forum, Google Analytics, and/or direct mysql queries.

Probably some basics on traffic growth, users, overall # of posts, time to first response...others?

marcowanger
10-07-2011, 06:35 PM
I think this is fantastic. I added a few things and made a few cosmetic edits. Great job, and please let me help out.

I especially wanted to add reference to this paper (http://www.sciencemag.org/content/early/2011/07/13/science.1207745) (http://www.sciencemag.org/content/early/2011/07/13/science.1207745) and evidence that SeqAnswers serves as a resource to suit this modern Internet phenomenon of transactive memory and learning.

I think a bit of actual data is called for. I added a few requests in there that are very simple but bolster the statements that Seqanswers has significant impact on the community. I think ECO should be able to provide those.

(Sorry I totally missed pages 2 and 3 of this thread somehow. If I messed anything up in the draft on the wiki, sorry about that. Didn't realize you guys were done. I didn't touch the letter part.)

Michael.James.Clark, I will integrate your changes in "CONTENT" into "Trimmed draft #1"

marcowanger
10-07-2011, 06:50 PM
Michael.James.Clark, I will integrate your changes in "CONTENT" into "Trimmed draft #1"

done:) .Now the side is one ECO

marcowanger
10-07-2011, 06:57 PM
I can definitely pull some stats from the backend of the forum, Google Analytics, and/or direct mysql queries.

Probably some basics on traffic growth, users, overall # of posts, time to first response...others?

And also answer to the questions in the #draft 1

The most common search terms leading to SEQanswers include [ECO might be able to put together a list/table of the most common search terms that lead from Google to SeqAnswers using Google Analytics if he has it set up here] and the site is regularly accessed from X countries all over the world [ECO might be able to provide a short table with typical hit counts from specific countries].
[edit]

1> Common search terms that lead viewer from Google to SEQ*
2> Countries visiting SEQ*

Michael.James.Clark
10-07-2011, 11:58 PM
Thanks for your hard work, Marco. :)

Joann
10-08-2011, 02:49 AM
I can definitely pull some stats from the backend of the forum, Google Analytics, and/or direct mysql queries.

Probably some basics on traffic growth, users, overall # of posts, time to first response...others?

How about some reference to the number and range of different countries (geographic localities) represented.

nilshomer
10-09-2011, 01:37 PM
Just saw this now, is this the current draft: http://seqanswers.com/wiki/Publication/Letter_for_SEQanswers?

maubp
10-09-2011, 01:47 PM
What is this bit about?
In parallel, SEQanswers is inviting a network of high profile bloggers to bring even more content to the site, thereby stimulating more vibrant discussion.
Peter

dan
10-09-2011, 02:38 PM
Just saw this now, is this the current draft: http://seqanswers.com/wiki/Publication/Letter_for_SEQanswers?

Yes, it is the current draft.

marcowanger
10-09-2011, 06:21 PM
What is this bit about?

Peter

Peter, as I have mentioned, I have emailed ECO for his future works on SEQanswers. Among all, some are relatively easier to do, including the invitation of bloggers and some others written in the current draft #1. As ECO has started contacting blogger, I assume this will be done soon, so I wrote it in the draft.

Peter, can you leave me your email, I think it is okay to forward the email. (correct me if I do not ;-))

ulz_peter
10-09-2011, 10:16 PM
Soory to come up with the word count again, but it is currently 361 (without the comments), and some of ECO's parts are still missing. Anything we could get rid of without losing the main message?

marcowanger
10-09-2011, 10:37 PM
Peter, dont worry, i will take care of it later

ulz_peter
10-09-2011, 10:40 PM
:)I bet you do!

andreas.sjodin
10-09-2011, 10:47 PM
Do we have an approximate deadline?

Lilith-Elina
10-09-2011, 11:05 PM
Do you need someone for proofreading? I love proofreading. :)

maubp
10-09-2011, 11:18 PM
Peter, as I have mentioned, I have emailed ECO for his future works on SEQanswers. Among all, some are relatively easier to do, including the invitation of bloggers and some others written in the current draft #1. As ECO has started contacting blogger, I assume this will be done soon, so I wrote it in the draft.
Oh OK - so its something happening now/soon. Thanks.

rglover
10-10-2011, 03:20 AM
Soory to come up with the word count again, but it is currently 361 (without the comments), and some of ECO's parts are still missing. Anything we could get rid of without losing the main message?

You could drop the "We reckon" at the start of paragraph 3. It's quite a casual couple of words and dropping it would make the "SEQanswers is uniquely positioned in the HTS field" more definitive and confident about the forum (plus drop 2 words from the count) :)

flxlex
10-10-2011, 03:29 AM
After not having seen this for a bit, I am wondering about the flow between the first two paragraphs. The one starting with "We noted that HTS" and the one starting "We founded the SEQanswers community": is it meant to reflect a historical flow? we noted this, so we started seqanswers? If so, a little bit of rewriting would make this clearer.

There is two times 'rapid' in the second sentence.

Why not start like this:
"Rapid technological advancements in High throughput sequencing (HTS) have outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field more and more becoming known for 'big data'. We founded SeqAnswers..." (or "SeqAnswers was founded...")

By now, that HTS enables new research is well know, or? Saves some words, too...

Joann
10-10-2011, 04:17 AM
Some thoughts on distilling the letter contents:
1. Most readers of Science already understand that HTS is out of the gate and thundering down the track.
2. By now it's a given that SEQanswers is and has been a key contributer--I have read countless thank-yous in posts. It is time to own the status.
3. There are a number of topics in the current trimmed letter that beg for even more elaboration but the route to this is full length articles. (students especially encouraged!) Covering these with just a few statistics does not do sufficient justice in introducing the forum to the general Science readership so these should be chosen wisely.

maubp
10-10-2011, 04:35 AM
You could drop the "We reckon" at the start of paragraph 3. It's quite a casual couple of words and dropping it would make the "SEQanswers is uniquely positioned in the HTS field" more definitive and confident about the forum (plus drop 2 words from the count) :)
Absolutely. Done, and removed the repetition of "involved" in the next sentence.

And I fixed another bit of odd grammar and removed a little more redundancy.

rglover
10-10-2011, 05:12 AM
Why not start like this:
"Rapid technological advancements in High throughput sequencing (HTS) have outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field more and more becoming known for 'big data'. We founded SeqAnswers..." (or "SeqAnswers was founded...")

I like that opening a lot and "SeqAnswers was founded" seems a much nicer fit.

Just done a quick edit of the SeqAnswers in google searches part to make it a little more succinct - word count now looks to be 346 approx.

marcowanger
10-10-2011, 05:09 PM
Do we have an approximate deadline?

ASAP once it's done.:)

marcowanger
10-10-2011, 05:30 PM
incorporated you idea. Thanks.:):)

After not having seen this for a bit, I am wondering about the flow between the first two paragraphs. The one starting with "We noted that HTS" and the one starting "We founded the SEQanswers community": is it meant to reflect a historical flow? we noted this, so we started seqanswers? If so, a little bit of rewriting would make this clearer.

There is two times 'rapid' in the second sentence.

Why not start like this:
"Rapid technological advancements in High throughput sequencing (HTS) have outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field more and more becoming known for 'big data'. We founded SeqAnswers..." (or "SeqAnswers was founded...")

By now, that HTS enables new research is well know, or? Saves some words, too...

marcowanger
10-10-2011, 05:33 PM
I like that opening a lot and "SeqAnswers was founded" seems a much nicer fit.

Just done a quick edit of the SeqAnswers in google searches part to make it a little more succinct - word count now looks to be 346 approx.

done. Now it reads (The SEQanswers community (http://SEQanswers.com/) was founded )

jcsites
10-10-2011, 08:24 PM
Totally agree.

robs
10-10-2011, 09:28 PM
I just returned from my vacation and think that it is a great idea to write the letter (I have a manuscript in review mentioning seqanswers myself and a reference would be nice).

The term HTS might be ambiguous and should be introduced at its first use, even if it adds 2 additional words ( I changed that in the text along with other minor changes).

I am not sure about the restrictions for references, but you might want to restrict the list to the most important (highest impact factor?) ones.

"The most common search terms leading to SEQanswers include [...]"
I think, this would be in contrast with the broad range of topics covered by the forum.

"and the site is regularly accessed from X countries all over the world"
The mentioning of the more than 20,000 users and "targets a wide audience" should speak for itself and you might be able to cut some words here.

Second paragraph:
"with participation of many researchers" and "Many experts from well-established groups contribute extensively" seems to be a repetition.

Maybe you can specify who the "We" in "We also plan to seek" refers to (the site admins, the users, ... ?).

marcowanger
10-11-2011, 06:19 AM
I just returned from my vacation and think that it is a great idea to write the letter (I have a manuscript in review mentioning seqanswers myself and a reference would be nice).

The term HTS might be ambiguous and should be introduced at its first use, even if it adds 2 additional words ( I changed that in the text along with other minor changes).

I am not sure about the restrictions for references, but you might want to restrict the list to the most important (highest impact factor?) ones.

"The most common search terms leading to SEQanswers include [...]"
I think, this would be in contrast with the broad range of topics covered by the forum.

"and the site is regularly accessed from X countries all over the world"
The mentioning of the more than 20,000 users and "targets a wide audience" should speak for itself and you might be able to cut some words here.

Second paragraph:
"with participation of many researchers" and "Many experts from well-established groups contribute extensively" seems to be a repetition.

Maybe you can specify who the "We" in "We also plan to seek" refers to (the site admins, the users, ... ?).

HTS term: I wrote it because somehow maybe the full term was deleted when we rearranged the sentences. Thanks for adding it back

References: Yes, I selected only Nature, Plos Comput, and NAR? with sentences EXPLICITLY thanks SEQanswers for help. All papers (even Nature) with merely links are not included. Manually checked.

The rest: I will take a deeper look at it after the ICHG ...... thanks, I think your suggestions make sense to me ... Need to modify the writings

colindaven
10-11-2011, 07:20 AM
Hi Marco, robs comments seem good to me too. Instead of the last sentence some form of comment on future prospects might be appropriate.

Perhaps
"In future we aim to facilitate access of information to new users by providing summary pages with links and summaries of various important topics and continue to provide a platform for discourse among isolated groups of experts in many different countries."

"active, strong and sizeable" might be shortened to "active and influential" ?

marcowanger
10-11-2011, 07:23 AM
Hi Marco, robs comments seem good to me too. Instead of the last sentence some form of comment on future prospects might be appropriate.

Perhaps
"In future we aim to facilitate access of information to new users by providing summary pages with links and summaries of various important topics and continue to provide a platform for discourse among isolated groups of experts in many different countries."

"active, strong and sizeable" might be shortened to "active and influential" ?

Agree.

The "active, strong and sizable" term is quoted from reviewer #2's comment to the SEQwiki paper:D, maybe we can shorten it to "active and influential", but "influential" seems to bold to ourselves?

robs
10-11-2011, 10:47 AM
I made a few more changes to shorten the text and remove some of the redundancy. Take a look and see if you are ok with the changes. Without the last sentence (the stats), it would be 289 words now.

Some more comments:

1) The reviewers might ask for the number of active users instead of registered users
2) If you want to make it more useful for students, then you could consider a slightly longer article with more content in an open-access journal such as PLoS Computational Biology (in case the science letter doesn't work out)
3) The last paragraph needs some editing to have a better flow between the first and second sentence
4) I would like to see some future directions at the end as well (maybe collindaven's suggestion, but replace "we" with "seqanswers")

marcowanger
10-11-2011, 12:38 PM
Robs, perhaps we should consider submitting to PloS comput bio. is there perspective/review type of paper we can submit?

Guess what, let's see current issue of PloS comp bio, the editorial is "ten rules to seek help from online communities"

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

Shall we respond? I think we should.

I made a few more changes to shorten the text and remove some of the redundancy. Take a look and see if you are ok with the changes. Without the last sentence (the stats), it would be 289 words now.

Some more comments:

1) The reviewers might ask for the number of active users instead of registered users
2) If you want to make it more useful for students, then you could consider a slightly longer article with more content in an open-access journal such as PLoS Computational Biology (in case the science letter doesn't work out)
3) The last paragraph needs some editing to have a better flow between the first and second sentence
4) I would like to see some future directions at the end as well (maybe collindaven's suggestion, but replace "we" with "seqanswers")

marcowanger
10-11-2011, 12:41 PM
This paper is written by Wikigenes member, it is ALSO edited collaboratively at wiki. Go for it!

Robs, perhaps we should consider submitting to PloS comput bio. is there perspective/review type of paper we can submit?

Guess what, let's see current issue of PloS comp bio, the editorial is "ten rules to seek help from online communities"

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

Shall we respond? I think we should.

robs
10-11-2011, 01:31 PM
If you are worried about the number of authors in a nature publication, you could try to submit it as an editorial instead (http://www.nature.com/nrmicro/journal/v7/n4/full/nrmicro2119.html).

In order to decide where to send it to, we need to figure out if someone has contacts to the editor of the respective journal. If you want to submit to Science or Nature, this might be fastest way to get it out or get feedback for interest in the article. If you consider PLoS, I should be able to help out with contacts.

Based on the selected journal, we should take a look at similar letters/editorial/etc. and modify the text based on that. Going forth and back between a short and long text will just waste time.

So, who knows some editors?

robs
10-11-2011, 01:34 PM
One more thing we should start thinking about are the publication charges. Will the SEQanswers site admin cover those from the advertisements, or will it be split between the authors, etc.

marcowanger
10-11-2011, 01:37 PM
One more thing we should start thinking about are the publication charges. Will the SEQanswers site admin cover those from the advertisements, or will it be split between the authors, etc.

For the SEQwiki paper, the SEQanswers admin has promised to cover it. For this letter/paper, we may ask again. But don't worry about it for now and write it first. I think whiter it is funded by admin or not won't change our plan.:)

marcowanger
10-11-2011, 01:41 PM
Ya, anyone know some editors?

Originally we planned for science/nature letter type. As you said, their response I'd fast, so why not write for it first? (as it is already almost a finished draft)

In parallel, may Robs you help contact PloS's editor?

Thanks.


If you are worried about the number of authors in a nature publication, you could try to submit it as an editorial instead (http://www.nature.com/nrmicro/journal/v7/n4/full/nrmicro2119.html).

In order to decide where to send it to, we need to figure out if someone has contacts to the editor of the respective journal. If you want to submit to Science or Nature, this might be fastest way to get it out or get feedback for interest in the article. If you consider PLoS, I should be able to help out with contacts.

Based on the selected journal, we should take a look at similar letters/editorial/etc. and modify the text based on that. Going forth and back between a short and long text will just waste time.

So, who knows some editors?

robs
10-11-2011, 02:35 PM
I wrote the editor of PLoS Computational Biology and asked if he would support our letter. Let's see what his response is.

One more thing I was missing is a title. Any suggestions?

marcowanger
10-11-2011, 05:09 PM
Robs, may you send us the letter draft telling us how it ia written first?

robs
10-11-2011, 05:26 PM
When I wrote "letter", I was referring to the one everyone is working on. If you were asking about something else, can you maybe rephrase your question?

marcowanger
10-11-2011, 08:15 PM
When I wrote "letter", I was referring to the one everyone is working on. If you were asking about something else, can you maybe rephrase your question?

OK robs, I understand what you mean.

Why not send the text to Science / Nature first?

In case they reject, we can transform it as the preliminary inquiry for PLoS Comput Editiorial:)

marcowanger
10-11-2011, 08:15 PM
The reason, the newbies into HTS are not always computer nerd :D .Remember the target audience

OK robs, I understand what you mean.

Why not send the text to Science / Nature first?

In case they reject, we can transform it as the preliminary inquiry for PLoS Comput Editiorial:)

robs
10-12-2011, 07:59 AM
This decision is totally up to you. It just sounded like you want me to contact the PLoS Editor and ask him about their interest in a article about SEQanswers. (Btw, they said they will take a look at the letter.) Also, PLoS is an open-access publisher and I am not sure if Science offers open-access.

I removed the last sentence with the stats and added a modified version of collindaven's suggestion for future directions. Take a look at it and see if you agree (especially ECO).
Otherwise, it should be in reasonable shape to be considered for review and if you get ECO's ok, then you should go ahead and submit it to a journal.

ulz_peter
10-12-2011, 08:12 AM
I removed the last sentence with the stats and added a modified version of collindaven's suggestion for future directions. Take a look at it and see if you agree (especially ECO).
Otherwise, it should be in reasonable shape to be considered for review and if you get ECO's ok, then you should go ahead and submit it to a journal.

I'm a bit unhappy with "SEQanswers aims" and "SEQanswers continues" as it is not clear for me who you are talking about (admins, users, community as a whole...).

And just to make sure: you wanted to post it in the content part to have it checked before posting it in the trimmed letter, right?

robs
10-12-2011, 08:32 AM
I assumed that we are working on the letter draft and must have missed the part where it says that we should only modify the content part. Sorry for that.

I think, the SEQanswers community "continues to provide a platform for discourse" and not just the admin or just the users. I also took a look at the alternative suggestions under "Future Directions" and they sound more like a summary than future directions. I personally feel that we need something that wraps everything up at the end and leaves the reader motivated to go and give SEQanswers a try. I don't think that statistics will do that, but future directions might be able to.

ulz_peter
10-12-2011, 09:31 PM
Hi robs,
THat was a misunderstanding. I just noted that you edited the Content part only and left the trimmed letter part, and I was asking if that was on purpose.

I agree concerning the future directions, although some statistics would fit in nicely as well (but maybe not at the end...)

marcowanger
10-12-2011, 09:38 PM
Robs, yes. Preliminary inquirey to PLoS editor is certainly. My only concern is that Nature/Science Correspondence does not permit the submitted thing to be "appeared" elsewhere.

Then, I propose use

(1) The one in "CONTENT" as the inquiry letter to PLoS Compu Bio.

And

(3) The "Trimmed letter" as the letter to Nat/Sci

do you think it is within Nature/Sci permission? (they are not the same anyway)

This decision is totally up to you. It just sounded like you want me to contact the PLoS Editor and ask him about their interest in a article about SEQanswers. (Btw, they said they will take a look at the letter.) Also, PLoS is an open-access publisher and I am not sure if Science offers open-access.

I removed the last sentence with the stats and added a modified version of collindaven's suggestion for future directions. Take a look at it and see if you agree (especially ECO).
Otherwise, it should be in reasonable shape to be considered for review and if you get ECO's ok, then you should go ahead and submit it to a journal.

usad
10-13-2011, 05:14 AM
Hi Marco

sorry I was busy the last few days. I reckon concerning Nature/Science allowing that, we could argue that we worked on this together. In theory it would be open like this, but it would be an interesting case. And none of these rules are set in stone.....

Also in the current trimmed draft there are a lot of what seqanswers is going to do, but that can always sound "overpromising" to the reviewers.

So I would potentially change the wording of SEQanswers is inviting a network of high profile bloggers to bring even more content to the site, thereby stimulating more vibrant discussion.

To include that we already have some bloggers posting here. (Unless you mean bloggers, that are also known beyond the natural sciences)

Cheers,
Björn

robs
10-14-2011, 04:41 PM
@marcowanger

I would probably send the short letter to Science and wait for their reply. They usually get back to you within a week and maybe we get some additional feedback on the letter.
If Science is not interested, we should work on a longer version for PLoS CB and ask editors for support before we even submit it. This way, we might be able to get feedback faster.

robs
10-14-2011, 04:57 PM
How about this for the final statement:

SEQanswers will continue to provide a platform for open discourse, allowing the rapid dissemination of knowledge and emerging issues to scientists all over the world.

marcowanger
10-14-2011, 05:04 PM
Hi robs. Let's give ECO a job to submit the letter after we finished the letter.

BTW, for Science correspondence, they said they won't give you reply. I remember you can consider your correspondence failed if they dont publish it within a certain period of time.

Letters should be 300 words or less and should discuss an item published in Science in the past 3 months or matters of general interest to our readership. Letters are not acknowledged upon receipt. Whether published in full or in part, Letters are subject to editing for clarity and space.

robs
10-14-2011, 05:05 PM
The Science submission site states that "Letters are subject to editing for clarity and space". Maybe, someone could ask ECO to take a look at it and give some feedback. I actually don't think that there will be many changes coming soon and whoever is going to submit it should set a deadline for people to make changes to the letter.

robs
10-14-2011, 05:08 PM
BTW, for Science correspondence, they said they won't give you reply. I remember you can consider your correspondence failed if they dont publish it within a certain period of time.

That's why it would be nice to have a connection to one of the editors. What is the "certain period" you are willing to wait?

(Sorry for the slight disconnect between the last post and your post. We probably wrote that at the same time.)

ECO
10-14-2011, 05:16 PM
This and the final revisions of the SEQwiki paper are on my weekend and monday morning train to-do list! :D

marcowanger
10-16-2011, 06:21 PM
Thank you so much ECO:)

This and the final revisions of the SEQwiki paper are on my weekend and monday morning train to-do list! :D

ulz_peter
10-19-2011, 02:15 AM
Hi guys,

Any news about the letter? Did the monday morning train give you a little inspiration ECO?

marcowanger
10-19-2011, 04:42 AM
Just my opinion, I think at this stage the letter may seems too subjective and sounds like an advertisement to others. Although the idea should stay the same, we may need to convey the idea in a more objective way.

But anyway, let's wait for Eric's reply first. Thanks Peter for pushing this.

marcowanger
10-21-2011, 09:26 AM
probably one more thing to write in the letter

Company announce up-coming software changes (matter to ALL bioinformaticians) in SEQanswers

Link: http://seqanswers.com/forums/showthread.php?t=8895

robs
10-21-2011, 10:14 AM
How about:
An increasing number of companies use SEQanswers to announce new software releases and upcoming changes to their commercial software tools.

If there is enough space left, maybe we can add something about conferences as well. (Something along the lines of: conferences are discussed before and after the event, helping other people to choose the most suitable conferences for their research.)

marcowanger
10-27-2011, 11:10 PM
Dear all,

Please note the papers that appear in Oct issue of PLoS Comp Bio

1> BioStar http://dl.dropbox.com/u/4125508/Community.Science/BioStar.pdf
2> "10 simple rules to get help from online community - by Wikigenes writing group"
http://dl.dropbox.com/u/4125508/Community.Science/Wikigenes.writing.pdf

ulz_peter
10-28-2011, 12:17 AM
Hi Marco,

Now that I read those articles I wonder if SeqAnswers wouldn't deserve a full publication just as the BioStar paper...
OK there's the time problem with regard to the publication to the Wiki, but that's already gonna be kind of close.

maubp
10-28-2011, 12:20 AM
Dear all,

Please note the papers that appear in Oct issue of PLoS Comp Bio

1> BioStar http://dl.dropbox.com/u/4125508/Community.Science/BioStar.pdf
2> "10 simple rules to get help from online community - by Wikigenes writing group"
http://dl.dropbox.com/u/4125508/Community.Science/Wikigenes.writing.pdf

Full titles for anyone searching (note Ten not 10);

Parnell et al. (2011) "BioStar: An Online Question & Answer Resource for the Bioinformatics Community"
http://dx.doi.org/10.1371/journal.pcbi.1002216

Dall'Olio et al. (2011) "Ten Simple Rules for Getting Help from Online Scientific Communities"
http://dx.doi.org/10.1371/journal.pcbi.1002202

marcowanger
10-28-2011, 12:46 AM
Hi Marco,

Now that I read those articles I wonder if SeqAnswers wouldn't deserve a full publication just as the BioStar paper...
OK there's the time problem with regard to the publication to the Wiki, but that's already gonna be kind of close.

i think SEQanswers still deserve, this is quite different from research paper...

dan
10-28-2011, 01:20 AM
Any timeline for submitting the letter? Sorry I've not been involved, I've been swamped with other work.

Has anyone volunteered to handle submission?

Cheers,

marcowanger
10-28-2011, 01:27 AM
Any timeline for submitting the letter? Sorry I've not been involved, I've been swamped with other work.

Has anyone volunteered to handle submission?

Cheers,

i think probably I can. :)

robs
10-30-2011, 06:05 PM
Why not try the letter to Science and if that doesn't work we can extent the article to full length with more details. If we split up the parts, we might be able to get this done within 1-2 weeks. Just a thought.

marcowanger
10-30-2011, 06:59 PM
Why not try the letter to Science and if that doesn't work we can extent the article to full length with more details. If we split up the parts, we might be able to get this done within 1-2 weeks. Just a thought.

Cool, good to have great guys like you. And Peter as well.

Here you go

https://docs.google.com/document/d/12lpMJxg-7HlYNXjjNrHMNu8-JwREXkkoNrfI0W3OpJc/edit?hl=en_US

Edit it.

Just a few reminders to all (including myself of course:))

1> Be concise
2> Remember to take the publication of BioStar paper into account (appreciation) :)
3> Differentiation. We are not only Q&A site.:D
4> No buzz words

ulz_peter
10-30-2011, 10:39 PM
Sorry but what do you mean with "buzz" words?

ulz_peter
10-30-2011, 11:08 PM
just in case someone is wondering: I am the "Anonymous" who did the changes, but when I am logging in, Google changes the language to Thai...

Azazel
10-31-2011, 02:09 AM
I just read the draft(s), I am referring to the longer version. Two points:

1.) "...incorporating all of the myriad platforms currently in use..." this sounds way to exaggerated. You can count the sequencing platforms available on the fingers of your two hands, that's not exactly a myriad. Even if you take a look at the different flavours of sequencing (se, pe, RNA-Seq, 5' biased variants...) they are not that many really. I would remove that paragraph entirely.

2.) The current wording downplays the level of discussion on SEQanswers. The overall level of discussion is higher, and much more specific than many posts that I have read on BioStar. In particular I find this strange: "It is a source of information to beginners of all types and backgrounds, from high school interns to MBA's". This is simply not correct, one needs to have a fairly good background to even *understand* what most question on SEQanswers are about, let alone know the solution.

Instead, I would emphasize that SEQanswers addresses grad students, post-docs and senior researchers who ask and answer about problems of technical relevance, with the aim of finding solutions to progress their research. Also it should be stressed that many of the posters who answer, are the actual authors of the tools they answer about - this is important!

P.S.: I wouldn't want to be on the list of authors I think, because if this *really* gets published in Science I would feal cheap for getting a co-authorship on a Science publication so easily, so I am just commenting here my ideas for improvement and if you like it, please feel free to apply to the text.

maubp
10-31-2011, 02:34 AM
I just read the draft(s), I am referring to the longer version. Two points:

1.) "...incorporating all of the myriad platforms currently in use..." this sounds way to exaggerated. You can count the sequencing platforms available on the fingers of your two hands, that's not exactly a myriad. Even if you take a look at the different flavours of sequencing (se, pe, RNA-Seq, 5' biased variants...) they are not that many really. I would remove that paragraph entirely.

2.) The current wording downplays the level of discussion on SEQanswers. The overall level of discussion is higher, and much more specific than many posts that I have read on BioStar. In particular I find this strange: "It is a source of information to beginners of all types and backgrounds, from high school interns to MBA's". This is simply not correct, one needs to have a fairly good background to even *understand* what most question on SEQanswers are about, let alone know the solution.

Instead, I would emphasize that SEQanswers addresses grad students, post-docs and senior researchers who ask and answer about problems of technical relevance, with the aim of finding solutions to progress their research. Also it should be stressed that many of the posters who answer, are the actual authors of the tools they answer about - this is important!
I thought we were focusing on the shorter one and the end now, "Trimmed letter: Draft #1", but those are good points regarding the longer version and I agree with them.

ulz_peter
10-31-2011, 02:54 AM
The trimmed version and the Google Doc version do not contain these paragraphs.

I think we should now focus on the Google Doc version.

andreas.sjodin
10-31-2011, 05:41 AM
I modified the wiki page to get people to start using the Google document

marcowanger
10-31-2011, 05:54 AM
I modified the wiki page to get people to start using the Google document

thanks Andreas

marcowanger
10-31-2011, 06:42 AM
just in case someone is wondering: I am the "Anonymous" who did the changes, but when I am logging in, Google changes the language to Thai...

I think you have to login to gmail first? Otherwise it shows u as anonymous....

marcowanger
10-31-2011, 06:47 AM
Sorry but what do you mean with "buzz" words?

Peter, I just personally think the current version is still too "advertisement" like.....lingering how to improve. And well, google ranking does not always reflect popularitu, it can be result of search engine optimization....We should focus on how the forum benefit the community as a whole....the idea is already there...

marcowanger
10-31-2011, 07:00 AM
Peter, I just personally think the current version is still too "advertisement" like.....lingering how to improve. And well, google ranking does not always reflect popularitu, it can be result of search engine optimization....We should focus on how the forum benefit the community as a whole....the idea is already there...

The draft #2 looks good to me.

robs
10-31-2011, 11:12 AM
The first two paragraphs look good, but the last one needs some more editing and content. We used about 200 words for the first two paragraphs and have enough left to add more things.

marcowanger
10-31-2011, 07:20 PM
The first two paragraphs look good, but the last one needs some more editing and content. We used about 200 words for the first two paragraphs and have enough left to add more things.

Differentiation of ourself from BioStar / More on unique FUNCTIONs served by this community / Usage success case.

For usage success case, I have a document for that. I previously prepared it for reviewer...i can find it out and paste it here for reference. It is by no means complete, please add more if you know any..:)

robs
10-31-2011, 07:54 PM
I added some more details to the second paragraph.

As for the use cases, I think the list of publications [2-13] provide sufficient examples.

I think we should try to add some future directions in the last paragraph. Maybe something along the lines of the BioStar "Outlook and Perspectives" part. I will try to add this tomorrow.

marcowanger
10-31-2011, 08:01 PM
I added some more details to the second paragraph.

As for the use cases, I think the list of publications [2-13] provide sufficient examples.

I think we should try to add some future directions in the last paragraph. Maybe something along the lines of the BioStar "Outlook and Perspectives" part. I will try to add this tomorrow.

Agree to certain extent, indeed the references are strong support of the community but we should explicitly describe how briefly. Just too vague to say the community has helped a lot of ppl without even telling the reader how speficically.

marcowanger
10-31-2011, 08:07 PM
For the "Outlook and perspective". Thanks for that

dan
11-01-2011, 07:53 AM
OK, it reads good, but I'd emphasize the 'success' of the platform, which has been driven by the developing technology and the 'information gap' in other media....

i.e.

* NGS takes off.
* Information about NGS becomes crucial asset for everyone.
* Publication / education / conferences / etc. can't keep up.
* Along comes a forum, and takes off in a big way.
** Used in various ways... by various experts...
* Finally:

A forum isn't a traditional scientific medium, but the 'perfect storm' of rapid development in the field, rapid application in the lab, and the slow pace of 'traditional' methods of scientific communication made the forum an ideal communication method for scientists...

As it stands, the paper is like... we made a forum... the forum is big... it is used ... the end.

The key points are the novelty and the success of the site in the scientific arena. People posting results on a forum is unprecedented in recent years, but is exactly what science is about, sharing information.

I don't see the fascination with BioStar. If you start mentioning other projects, the list could be endless. The point of the letter is to emphasize how new and interesting the SEQanswers community is, mentioning the many citations it has already received, how widely used it is, and the cutting edge discussions and announcements that it hosts. e.g. BGI, EBI, NCBI, etc.

Putting the forum in the context of all others projects is a bigger work. Here we need to put the site in the broadest possible context, but nothing else. IMHO.

i.e. If I'm an astrophysicist reading about SEQanswers, what do I want to know? Why am I interested in this project? Do I care because it breaks new ground in building a community around a new field? Or because it's similar to something called BioStar?


Just my 2p.

Dan.

marcowanger
11-01-2011, 08:03 AM
Thank you Dan for the direction of the letter we have to aim.



OK, it reads good, but I'd emphasize the 'success' of the platform, which has been driven by the developing technology and the 'information gap' in other media....

i.e.

* NGS takes off.
* Information about NGS becomes crucial asset for everyone.
* Publication / education / conferences / etc. can't keep up.
* Along comes a forum, and takes off in a big way.
** Used in various ways... by various experts...
* Finally:

A forum isn't a traditional scientific medium, but the 'perfect storm' of rapid development in the field, rapid application in the lab, and the slow pace of 'traditional' methods of scientific communication made the forum an ideal communication method for scientists...

As it stands, the paper is like... we made a forum... the forum is big... it is used ... the end.

The key points are the novelty and the success of the site in the scientific arena. People posting results on a forum is unprecedented in recent years, but is exactly what science is about, sharing information.

I don't see the fascination with BioStar. If you start mentioning other projects, the list could be endless. The point of the letter is to emphasize how new and interesting the SEQanswers community is, mentioning the many citations it has already received, how widely used it is, and the cutting edge discussions and announcements that it hosts. e.g. BGI, EBI, NCBI, etc.

Putting the forum in the context of all others projects is a bigger work. Here we need to put the site in the broadest possible context, but nothing else. IMHO.

i.e. If I'm an astrophysicist reading about SEQanswers, what do I want to know? Why am I interested in this project? Do I care because it breaks new ground in building a community around a new field? Or because it's similar to something called BioStar?


Just my 2p.

Dan.

dan
11-01-2011, 08:52 AM
Thank you Dan for the direction of the letter we have to aim.

Just my opinion. Feel free to aim in any direction, but the above is what I suggest ;-)

Cheers,

marcowanger
11-01-2011, 08:58 AM
Just my opinion. Feel free to aim in any direction, but the above is what I suggest ;-)

Cheers,

You raised an important point everyone has to remember during writing.

If I'm an astrophysicist reading about SEQanswers, what do I want to know? Why am I interested in this project?

nilshomer
11-01-2011, 03:44 PM
Check out the Biostar (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002216) paper.

dan
11-01-2011, 06:04 PM
Check out the Biostar (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002216) paper.

Yeah, I really should.

Here is a rough stab at a new version (just to add to the mix):
http://goo.gl/WL8lE

dan
11-01-2011, 06:19 PM
Check out the Biostar (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002216) paper.

Right! I change my mind, excellent paper and looks like a great project (I didn't use it much yet). This should definitely be referenced, as it presents a lot of the arguments that we want to present in a very clear and thoughtful way.

adaptivegenome
11-02-2011, 05:39 AM
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.

marcowanger
11-02-2011, 05:56 AM
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
11-02-2011, 06:01 AM
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
11-02-2011, 06:10 AM
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
11-02-2011, 06:17 AM
At this moment, I think we can concentrate on the short letter to Sci/Nature first.
Good plan.

Joann
11-02-2011, 07:23 AM
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
11-02-2011, 07:27 AM
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/2011/05/forums-open-beats-closed-hands-down.html

robs
11-02-2011, 09:24 AM
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
11-02-2011, 09:30 AM
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
11-02-2011, 09:48 AM
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
11-02-2011, 10:17 AM
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
11-02-2011, 10:23 AM
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
11-02-2011, 04:18 PM
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
11-02-2011, 04:20 PM
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
11-02-2011, 07:03 PM
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
11-03-2011, 09:34 AM
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?

marcowanger
11-03-2011, 09:38 AM
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/Publication/Letter_for_SEQanswers

I started moving content from Gdoc back to the wiki

robs
11-03-2011, 11:14 AM
Hi Robs, seems the latest ver is #3 located at the wiki page

http://seqanswers.com/wiki/Publication/Letter_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.

marcowanger
11-04-2011, 02:22 AM
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.

adaptivegenome
11-04-2011, 03:58 PM
I like it too. It is coming along nicely!

marcowanger
11-04-2011, 09:45 PM
I like it too. It is coming along nicely!

cool. Keep up the pace. :)

robs
11-05-2011, 11:25 AM
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?

adaptivegenome
11-05-2011, 05:28 PM
As I had mentioned earlier, I am happy to assemble that figure if someone gives me access to the post data.

marcowanger
11-05-2011, 09:16 PM
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

marcowanger
11-05-2011, 09:18 PM
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.

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

ECO
11-05-2011, 09:42 PM
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.... :/

adaptivegenome
11-06-2011, 04:29 AM
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.

marcowanger
11-06-2011, 05:09 AM
The perfect example to illustrate how this community enable interactions among developers. (http://seqanswers.com/forums/showthread.php?t=15200)

adaptivegenome
11-06-2011, 04:59 PM
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.

ECO
11-06-2011, 05:31 PM
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. :cool:

adaptivegenome
11-06-2011, 05:35 PM
Thanks ECO. I sent you a private message with my contact details.

marcowanger
11-06-2011, 05:43 PM
ECO, sent you private message with email.

marcowanger
11-06-2011, 05:48 PM
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.

Key developer: agree. We definitely should emphasize that

Gdoc, wiki: worries expressed by members that there is no easy way to keep track of the changes. Well, I also prefer the gdoc approach. But as i said, I do not object on usong the wiki....

ECO
11-06-2011, 05:55 PM
You both have emails with shared docs!

marcowanger
11-06-2011, 05:57 PM
You both have emails with shared docs!

Thank you ECO.:)

adaptivegenome
11-06-2011, 06:01 PM
Thanks! Now comes the fun part...

marcowanger
11-06-2011, 06:06 PM
Thanks! Now comes the fun part...

Genericform, I am on travel now and cannot load/parse the gdoc. I will back you up. Let's discuss in email how we can share the work.:)

ECO
11-06-2011, 06:10 PM
Another collection shared with all the "easy" stats that are generated by vBulletin (users, threads, posts, activity / day). I'll add the Google Analytics update now also.

adaptivegenome
11-06-2011, 06:13 PM
Genericform, I am on travel now and cannot load/parse the gdoc. I will back you up. Let's discuss in email how we can share the work.:)

Sounds good. Send me a private message with your email and I will confer with you by email...

adaptivegenome
11-06-2011, 06:14 PM
Another collection shared with all the "easy" stats that are generated by vBulletin (users, threads, posts, activity / day). I'll add the Google Analytics update now also.

Thanks ECO!!

marcowanger
11-06-2011, 06:22 PM
Sounds good. Send me a private message with your email and I will confer with you by email...

Private msg with email address sent, please check.

ECO, thanks for the stat.

robs
11-07-2011, 08:54 AM
Private msg with email address sent, please check.

ECO, thanks for the stat.

I sent both of you my email address. Would be great if you could keep me in the loop with the graph.

marcowanger
11-07-2011, 09:00 AM
I sent both of you my email address. Would be great if you could keep me in the loop with the graph.

I got your email robs. Replied your PM. Do act quick:)

robs
11-07-2011, 10:04 AM
I got your email robs. Replied your PM. Do act quick:)

Thanks. Just waiting for ECO's reply.

robs
11-07-2011, 06:13 PM
Got the data. Thanks ECO!

adaptivegenome
11-08-2011, 01:04 PM
Another collection shared with all the "easy" stats that are generated by vBulletin (users, threads, posts, activity / day). I'll add the Google Analytics update now also.

ECO,

In the SQL dump you sent there are only 17 records for 2011. Can you confirm the data is complete or re-dump it?

marcowanger
11-09-2011, 11:29 PM
Added a draft of wiki paper describing the SEQanswers community.

2 purposes.

(1) avoid self-plagiarism, (2) give insights for the writing

robs
11-10-2011, 10:16 AM
I shifted a couple of things around and added some of the points into the text that were listed above. I think the text is getting in good shape, the only thing we still need is the figure and a few more stats.

This means: ECO, we need your help with the SQLdump. :-)

We might be over the word limit, but we can trim down the letter when we have added everything we want. (It will be easier to eliminate the weaker parts and select the most important ones.)

adaptivegenome
11-10-2011, 10:19 AM
This means: ECO, we need your help with the SQLdump. :-)


I have this. Email me and I can share it with you.

bioinfosm
11-10-2011, 01:48 PM
got really tied up for the past couple months, but this is very interesting, and can look to contribute.

I will start with scrolling through the thread, but feel free to PM me with any specifics..

robs
11-12-2011, 11:31 AM
I added two figures to the gdoc and would like to get your comments and suggestions.

How is the tag cloud coming along?

robs
11-12-2011, 06:22 PM
To save you the search for the gdoc link:
https://docs.google.com/document/d/12lpMJxg-7HlYNXjjNrHMNu8-JwREXkkoNrfI0W3OpJc/edit?hl=en_US

marcowanger
11-12-2011, 08:20 PM
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?

marcowanger
11-12-2011, 08:24 PM
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!

marcowanger
11-12-2011, 08:31 PM
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!

andreas.sjodin
11-13-2011, 12:00 AM
I like the first figure too. The points should probably go away in second figure to make it less messy.

robs
11-13-2011, 01:27 PM
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.

marcowanger
11-13-2011, 06:12 PM
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...:D

marcowanger
11-13-2011, 07:41 PM
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?

robs
11-13-2011, 09:02 PM
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.

marcowanger
11-14-2011, 09:51 PM
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.

adaptivegenome
11-15-2011, 05:39 PM
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
11-15-2011, 05:46 PM
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
11-15-2011, 05:54 PM
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
11-15-2011, 06:03 PM
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
11-15-2011, 06:15 PM
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
11-15-2011, 06:17 PM
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
11-15-2011, 06:20 PM
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
11-15-2011, 06:29 PM
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
11-15-2011, 07:03 PM
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
11-15-2011, 07:07 PM
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
11-15-2011, 07:10 PM
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
11-15-2011, 07:17 PM
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
11-15-2011, 07:18 PM
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 (http://nar.oxfordjournals.org/content/early/2011/11/15/nar.gkr1058.abstract)

Btw, congrats to the SEQwiki paper.

marcowanger
11-16-2011, 04:59 AM
Please edit on the #Final draft, from now on. Thanks.

http://seqanswers.com/wiki/Publication/Letter_for_SEQanswers#Letter:_Draft_.23Final

maubp
11-16-2011, 05:17 AM
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
11-16-2011, 05:47 AM
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.:)

ulz_peter
11-16-2011, 07:21 AM
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!!

ulz_peter
11-16-2011, 07:23 AM
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'.

marcowanger
11-16-2011, 07:28 AM
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:)

marcowanger
11-16-2011, 07:30 AM
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

ulz_peter
11-16-2011, 07:59 AM
oh, that's a pretty good reason...

adaptivegenome
11-16-2011, 07:14 PM
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

robs
11-16-2011, 08:10 PM
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
11-16-2011, 08:22 PM
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...

dan
11-19-2011, 09:08 AM
Here they are for everyone to look at:

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

adobrovic
11-19-2011, 03:27 PM
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.

marcowanger
11-20-2011, 07:17 AM
Hi all again,

Current initial effort is to publish SEQanswers in the form of letter to Science / Nature.

Science (http://www.sciencemag.org/site/feature/contribinfo/prep/gen_info.xhtml#commentary)
Commentary Perspectives:

We need to submit inquiry first. Ask (1) if interested and (2) more than 2 authors

Perspectives (up to 1000 words plus 1 figure) highlight recent exciting research, but do not primarily discuss the author's own work. They may provide context for the findings within a field or explain potential interdisciplinary significance. Perspectives commenting on papers in Science should add a dimension to the research and not merely be a summary of the experiments done in the paper. Although many of the Perspectives that comment on research published in Science are solicited, we welcome inquiries regarding new advances and fresh insights. As these are meant to express a personal viewpoint, with rare exceptions, Perspectives should have no more than two authors

Commentary Letters:
Any recent material about scientific community in Science?
Letters (up to 300 words) discuss material published in Science in the last 3 months or issues of general interest. Letters should be submitted online (www.submit2science.org). Letters are subject to editing for clarity and space. E-letters are online-only, 400-word contributions for rapid, timely discussion.

Nature (http://www.nature.com/nature/authors/gta/others.html):

Correspondence:
These items are 'letters to the Editor': short comments on topical issues of public and political interest, anecdotal material......A Correspondence is usually signed by no more than three authors; this is because Correspondence is a forum for readers' reactions, not for statements by organizations or groups of individuals.

Perspective:

Not sure how to submit.

Perspective articles are intended to provide a forum for authors to discuss models and ideas from a personal viewpoint. They are more forward looking and/or speculative than Reviews and may take a narrower field of view. They may be opinionated but should remain balanced and are intended to stimulate discussion and new experimental approaches.

Perspectives follow the same formatting guidelines as Reviews. Both are peer-reviewed and edited substantially by Nature's editors in consultation with the author.


There are some other possibilities, including PloS Comp Bio and genericforms suggested BMC Genome Medicine

PLoS Comp Bio: perspective

Perspectives in PLoS Computational Biology typically reflect an author's viewpoint on a particular development in science and how, based on current knowledge of the field and the progress in it, this development evidences or can lead to change in how science is conducted or interpreted. Perspectives are intended to be more prospective than retrospective but require sufficient background to place the points made in context. Perspectives are intended to invite debate and further comment as appropriate. The length is ideally around 2000 and limited to 2500 words. Suggestions for topics may be forwarded to ploscompbiol [at] plos.org and are usually handled by the Editor-in-Chief.

BMC Genome Medicine: Opinion / Correspondence

Opinion:
opinion articles are to provide systematic and substantial coverage of mature or emerging topics as well as a discussion of possibly controversial views, different models and theories in the field

Correspondence:
Correspondence items discuss material published in Genome Medicine or issues of exceptional interest to the broad readership of the journal. They are short, freely available, peer-reviewed articles and include data, guidelines, or policies for which free availability is a key consideration

What do you think?

marcowanger
11-20-2011, 07:29 AM
I think Genome Biology is suitable too

Correspondence articles (http://genomebiology.com/authors/instructions/correspondence):

Genome Biology publishes Correspondence articles on all aspects of political, scientific, and medical issues relating to genomic, post-genomic and genome-scale analyses, as well as to molecular, cellular, organismal or population biology studied from a genomic perspective.

Correspondence items discuss material published in Genome Biology or issues of general interest to the readership. They may be edited for clarity or length. Correspondence are short, freely available, peer-reviewed items of correspondence. They should describe material of exceptional interest to the broad readership of Genome Biology and include data, guidelines, or policies for which free availability is a key consideration. To contribute, contact the editors.

or Commentary Editorial (http://genomebiology.com/authors/instructions/commentaryeditorial)

The second form is more editorial in nature and covers an aspect of an issue that is relevant to the journal's scope. Examples of this type of Commentary - Editorial could be a discussion of the impact of new technology on research and treatment, or a discussion of changes in peer review or grant application procedures and their effect on research. By their nature, the second form of Commentary - Editorial articles is less frequent.

adaptivegenome
11-20-2011, 02:54 PM
I think that Genome Medicine and Genome Biology are great choices. PLOS CompBio is highly ranked but probably not a good target unless we focus the article on the informatics aspect to genomics. I think I already voted in favor of Genome Medicine...

And this is not necessarily a bad thing to do. Just commenting here. Informatics is definitely one of the primary discussion points on the board.

ulz_peter
11-20-2011, 09:53 PM
it seems that the Science commentary letter doesn't really fit for our problem...

Two things come to my mind: Do we want to adress the people who might cite SEQanswers because they use it or do we want to inform people who might have no idea what SEQanswers is about, that there is a place to exchange questions, ideas, experiments, etc. regardings HTS?

In the first case it doesn't really matter where we are trying to put it (regarding the possible readers) as it will be found, however if we would like to have people have a look at it, which are previously uninformed we should pick a Biology/medicine journal...

I personally would prefer the latter...

So my choice is for Genome Medicine or Genome Biology. You didn't state the limitations for publishing in one of those journals. Are there any regarding word count or number of authors?

marcowanger
11-20-2011, 11:29 PM
Invited ECO via PM for his opinion on this.

Dear Eric,

Approaching the final phase of preparation to publish SEQanswers, we need your opinion in choosing the appropriate journal.

Would you please leave your comment in http://seqanswers.com/forums/showthread.php?p=57405#post57405

Thanks.

With regards,
Marco

ulz_peter
11-20-2011, 11:41 PM
What do you think Marco?

marcowanger
11-20-2011, 11:47 PM
What do you think Marco?

I consider possibility.


original goal (1):
It seems either Nature / Science is hard. Unless we find some articles there that discuss community science. Then we can refer to that article and reply with what we have written.

If in case we find none, then (2):

I do not have personal preference. But of course, the wider the reader's base, the better. I think Genome Biology, Genome Medicine, PloS CompBio are both good choices.

Just leave the format or words limit alone first.

I suggest emailing the editors pre-inquiry emails. :)

ulz_peter
11-21-2011, 02:23 AM
So there is an article in Nature about community science:

Technology: The inspiration exchange

Chris Lintott

Nature, 478, 320–321 (20 October 2011) doi:10.1038/478320a

Published online
19 October 2011

Which is not too long ago, but there is the 3-author limit on the correspondence and I guess the letter doesn't really fit in the perspectives part. I'm looking for something similar in Science...

Joann
11-21-2011, 04:37 AM
Hi all,

For the section on implications--I could shorten it to:

"As the accelerated flow of technology development has dwarfted traditional peer reviewed information sharing, the computationally-abled HTS community has successfully connected itself by means of the electronic scientific forum, SEQanswers, since 2007."

The wonderful word data analysis give rise to a possible title:

"SeqAnswers, Reading Biological Sequences as a Community since 2007."

And I would like to see the letter in a general science journal such as Science because of its importance. Please submit and ask in the cover letter to waive the existing format.

adaptivegenome
11-21-2011, 05:37 AM
So my choice is for Genome Medicine or Genome Biology. You didn't state the limitations for publishing in one of those journals. Are there any regarding word count or number of authors?

Neither journal restricts authors and they are both open access journals so there would be a fee (depending on who submits the manuscript; and also this fee can be waived in some cases). An Opinion article would be 1500-3000 words which I think fits nicely for our topic. I would go for a shorter length (closer to 1500) and then go for more figures; particularly the two figures Rob came up with.

There are some other formats we could also shoot for, such as "Method" or "Database"; however given that the draft is more focused on showcasing a new way of doing science, I would think an "Opinion" would be a great format. A traditional "Review" format would be too long and I think ill-suited for our goals.

adaptivegenome
11-21-2011, 05:44 AM
Hi all,

For the section on implications--I could shorten it to:

"As the accelerated flow of technology development has dwarfted traditional peer reviewed information sharing, the computationally-abled HTS community has successfully connected itself by means of the electronic scientific forum, SEQanswers, since 2007."

The wonderful word data analysis give rise to a possible title:

"SeqAnswers, Reading Biological Sequences as a Community since 2007."

And I would like to see the letter in a general science journal such as Science because of its importance. Please submit and ask in the cover letter to waive the existing format.

I don't think that our paper will work in Science/Nature. But that is just my opinion. In addition to Genome Biology or Genome Medicine we could shoot for PLOS Biology which is both highly ranked and also widely read (not as much as Nature... but they could be sympathetic to our cause as they have obviously pushed for open science, etc.)

I agree with Marco we should simply send off presubmission inquiries to see who is interested. I would be willing to contact Genome Medicine if there is interest from everyone as I know someone people there...

BTW: Joann, I like that title. We might try for something a little more aggressive than "reading"... for example "decoding" or "interpreting", but it is a great title.

Joann
11-21-2011, 06:19 AM
Hi genericforms,
The title is strictly data based, upon some top word counts from the forum. As a generalist, I like to promote wider scientific exposure. Also, I am wanting to see exactly how many times the question "What's a paired-end read?" gets posted on the forum by a newbie.

adaptivegenome
11-21-2011, 06:26 AM
Hi genericforms,
The title is strictly data based, upon some top word counts from the forum. As a generalist, I like to promote wider scientific exposure. Also, I am wanting to see exactly how many times the question "What's a paired-end read?" gets posted on the forum by a newbie.

Clever title then!

ulz_peter
11-21-2011, 06:55 AM
Agree with genericforms: great title!!