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Old 08-01-2011, 01:00 AM   #1
dan
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Talking Lets publish the Wiki!

There is now a great opportunity to publish the wiki as a 'wiki-database' in the 2012 NAR annual database issue [1]!


Below are 'the details' from the previous email exchange with the editors of NAR. I've started a preliminary page for collaborative authorship of the paper here:

http://seqanswers.com/wiki/Publication/Paper_(NAR_2012)


So lets get writing! (Sorry for the short notice, 14 days and counting!!!)


Dan.

--- Details...

Dear Dan,

Thank you for your interest in the 2012 Nucleic Acids Research
database issue. Your proposal looks reasonable to me (don't know about
the reviewers) and I am glad to invite submission of your paper.

Please carefully read the instructions at the URL:
http://www.oxfordjournals.org/nar/fo..._database.html
Then go ahead and submit your manuscript by the August 15th deadline.
Please let me know in advance if you need a delay of a week or so.

Please note that we would ask you to include into your submission a
supplementary file with a short description of your database in
accordance with BioDBcore
(http://biocurator.org/biodbcore.shtml)standards (see the examples at
http://nar.oxfordjournals.org/conten...1/D7/suppl/DC1)

Best wishes,
Michael Galperin


On Fri, Jul 1, 2011 at 7:57 PM, Dan Bolser <dan.bolser@gmail.com> wrote:
> Dear Michael,
>
> Please find below a pre-submission inquiry for the description of a
> new wiki-database, SEQwiki (http://seqwiki.org).
>
>
> Sincerely,
> Dan Bolser.
>
> SEQwiki : A Wiki Database for High-throughput Sequencing Tools and Technologies.
>
> Dan Bolser, Keith Robison, Andreas Sjödin, Marcel Martin and Eric Olivares.
>
> In recent years, dramatic advances in sequencing technology have
> created unprecedented opportunities for biological discovery. At the
> same time, however, this rapidly advancing and complex field has
> created unprecedented challenges for data management and analysis. As
> a consequence, the development of scientific software and
> computational methods in the field is outpacing the speed of
> peer-reviewed publication and other traditional forms of information
> sharing.
>
> The SEQanswers forum (http://SEQanswers.com) was founded to address
> this gap; it facilitates the rapid dissemination of both wet-lab
> techniques and information regarding computational tools and analysis.
> The forum allows new tools, techniques and pipelines to be rapidly
> announced, tested and benchmarked within the community.
>
> SEQwiki (http://SEQwiki.org) is a Semantic MediWiki (SMW) site that is
> edited and updated by the members of the SEQanswers community. The
> wiki provides an extensive archive of categorized high-throughput
> sequencing analysis tools, technologies and providers.
>
> Wiki pages provide structured data for each tool, including data types
> and formats, capabilities, and provenance details as well as
> catalogues of links to publications and online resources. Users
> contribute both structured data and free text comments using a
> combination of standard wiki and SMW data entry. A search tool
> provides a simple means for finding information about particular
> tools, and structured data can be queried and presented as reports
> within the wiki.
>
> After two years, the SEQanswers community have created pages for over
> 400 unique software tools, with around 350 references and 500 web
> links. This effort has made the SEQwiki database the most
> comprehensive and detailed archive of high-throughput sequencing tools
> anywhere on the web. This community databases is an invaluable
> resource for the high-throughput sequencing.


--
--------------------------------------------
Michael Y. Galperin, PhD
Executive Editor, NAR Database Issue

E-mail: nardatabase@gmail.com
Phone: +1-301-435-5910
Fax: +1-301-435-7793
http://www.ncbi.nlm.nih.gov/Complete_Genomes
--------------------------------------------
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Last edited by dan; 08-01-2011 at 02:43 AM. Reason: Fixed the URL
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Old 08-01-2011, 01:04 AM   #2
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Of course, anyone who makes a significant contribution to the text will be listed as an author on the publication.
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Old 08-01-2011, 02:21 AM   #3
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Of course, anyone who makes a significant contribution to the text will be listed as an author on the publication.
How may I contribute if I want to ?
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Old 08-01-2011, 02:37 AM   #4
dan
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Quote:
Originally Posted by marcowanger View Post
How may I contribute if I want to ?
Ah! Sorry it wasn't clear! If you wan't to contribute, I suggest that you go to the wiki page for the paper:
http://seqanswers.com/wiki/Publication/Paper_(NAR_2012)

Then it's probably best to read the guidelines for authors (also linked there):
http://www.oxfordjournals.org/our_jo..._database.html

and then... start writing


You could write the Introduction, describing the growth in NGS tools and technologies, or the use of wikis, or the need for a database of tools, etc.

You could write a description of the contents and growth of SEQwiki, number and type of contributions / contributors, etc.

You could point out the strengths and weaknesses of the wiki and similar systems, etc.

etc...

I'm planning to devote a few hours to the manuscript over the coming weeks too, so feel free to wade in
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Old 08-01-2011, 02:39 AM   #5
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I just checked the guidelines, and it seems the format is quite 'free':

Quote:
Authors should produce a brief description of their database. Again, this description should concentrate on the factual content of the database and provide sufficient information so that the reader can easily access and obtain information from the database. New submissions to NAR are typically 4-5 printed journal pages in length, but authors are urged to be succinct in their writing.
What can we cram in 4 pages? 2000 words and one figure?
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Old 08-01-2011, 02:46 AM   #6
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Quote:
Originally Posted by dan View Post
I just checked the guidelines, and it seems the format is quite 'free':



What can we cram in 4 pages? 2000 words and one figure?
Sounds interesting, let's pour some time in it .
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Old 08-01-2011, 06:02 AM   #7
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Originally Posted by marcowanger View Post
Sounds interesting, let's pour some time in it .
I find I do not have permission to edit the page

"You do not have permission to edit this page, for the following reason:
The action you have requested is limited to users in the group: Users."

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Old 08-01-2011, 06:05 AM   #8
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Originally Posted by marcowanger View Post
I find I do not have permission to edit the page

"You do not have permission to edit this page, for the following reason:
The action you have requested is limited to users in the group: Users."



That's weird, are you logged in on the forum when you visit the wiki?

Can you edit any pages (try a 'null edit' on a random page).


Cheers,
Dan.
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Old 08-01-2011, 06:07 AM   #9
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Talking

Oh, I found I tried to edit before logging on.

Thanks for telling me.

Marco

Quote:
Originally Posted by dan View Post
That's weird, are you logged in on the forum when you visit the wiki?

Can you edit any pages (try a 'null edit' on a random page).


Cheers,
Dan.
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Old 08-01-2011, 06:26 AM   #10
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Originally Posted by marcowanger View Post
Oh, I found I tried to edit before logging on.

Thanks for telling me.

Marco

as far as I can tell from looking at the code, you should be able to login to the forum or the wiki, but I found that wiki login fails.
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Old 08-01-2011, 06:26 AM   #11
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The wiki login is disabled...
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Old 08-01-2011, 06:30 AM   #12
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as far as I can tell from looking at the code, you should be able to login to the forum or the wiki, but I found that wiki login fails.
Thanks. Now I am able to edit in wiki, at least in discussion page
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Old 08-01-2011, 07:26 AM   #13
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Default Suggest

My suggestion is to compile the number of times the SEQanswers forum and/or wiki has been cited to date in published peer reviews and journal articles--both main text and bibliographically--and mention this in the NAR article background material. I know Eric has a collection of these, but let me know if additional searching would be helpful at this point.
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Old 08-01-2011, 07:46 AM   #14
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Originally Posted by Joann View Post
My suggestion is to compile the number of times the SEQanswers forum and/or wiki has been cited to date in published peer reviews and journal articles--both main text and bibliographically--and mention this in the NAR article background material. I know Eric has a collection of these, but let me know if additional searching would be helpful at this point.
A good reference to start with http://seqanswers.com/forums/showthread.php?t=3107
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Old 08-01-2011, 09:17 AM   #15
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One thing I'd really like to do is the reverse, for each reference in seqwiki, query an api to return the number of times that reference is cited, then list tools by their number of citations. This would be much better than the current (rather silly) ranked listing of tools.
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Old 08-01-2011, 10:21 AM   #16
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Originally Posted by dan View Post
One thing I'd really like to do is the reverse, for each reference in seqwiki, query an api to return the number of times that reference is cited, then list tools by their number of citations. This would be much better than the current (rather silly) ranked listing of tools.
Certainly, then it's really the prominence of the tool in the field rather than the number of view count, which can be artificially jack up.
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Old 08-01-2011, 10:24 AM   #17
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Originally Posted by marcowanger View Post
A more complete thread

And the wiki.
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Old 08-01-2011, 10:27 AM   #18
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Quote:
Originally Posted by dan View Post
One thing I'd really like to do is the reverse, for each reference in seqwiki, query an api to return the number of times that reference is cited, then list tools by their number of citations. This would be much better than the current (rather silly) ranked listing of tools.
How about parse the info from google scolar or ISI web of knowledge?
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Old 08-01-2011, 10:45 AM   #19
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Apparently the list should be twice bigger.
It's going to be more and more difficult to keep track with all these citations!
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Old 08-01-2011, 11:11 AM   #20
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Quote:
Originally Posted by steven View Post
Apparently the list should be twice bigger.
It's going to be more and more difficult to keep track with all these citations!
It is, and some more http://seqanswers.com/forums/showpos...33&postcount=9

Last edited by marcowanger; 08-01-2011 at 11:36 AM.
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