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Old 08-09-2011, 02:35 AM   #41
usad
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The technology section sounds like a good idea.
But parts of it is covered in the excellent field guide which has a companion web site as well.
http://www.molecularecologist.com/next-gen-fieldguide/

Concerning a redesign: unfortunately my skills are underdeveloped in the art &design area.
Cheers,
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Old 08-09-2011, 03:22 AM   #42
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It is great. It is more about running vs cost vs throughput comparison.

Then may we focus more on really technology part, e.g. fundamental tech. and the experiences in choose them, rather than just numbers. Surely, we also want link them from here.

Quote:
Originally Posted by usad View Post
The technology section sounds like a good idea.
But parts of it is covered in the excellent field guide which has a companion web site as well.
http://www.molecularecologist.com/next-gen-fieldguide/

Concerning a redesign: unfortunately my skills are underdeveloped in the art &design area.
Cheers,
Björn
usad, never mind. I don't have much art talent too. But editing the wiki should not be that art demanding. Let's throw some ideas in discussion page
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Old 08-09-2011, 10:46 AM   #43
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5 days to go. And we still have much to do.

1) Write it up. (urgent & important)

2) Any native speaker volunteer to check the language? (important)

3) QC and polish the Wiki

4) Write the focus review. This part is important but not the most urgent part.
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Old 08-09-2011, 10:53 AM   #44
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Thanks for pushing this Marco, you're doing a fantastic job!

1) Write it up. (urgent & important)

2) Any native speaker volunteer to check the language? (important)

Yes, I'll do that this evening.


3) QC and polish the Wiki

This is important, but I figure we've got a few days post submission until a reviewer lays eyes on the wiki, so we can pospone that in favour of writing up and fixing critical issues.


4) Write the focus review. This part is important but not the most urgent part.

This is obviously a lot of work, and also, if we are not careful, may overlap with the remit of Wikipedia (you'll not get far trying to compete with Wikipedia). So this needs to be clearly focused on technical pipelines for common analysis... In the wiki spirit, I think it's best to get something down for everything rather than making one item perfect... I'll add some queries to each topic to return the list of tools relevant to that topic.


I'll also collect some usage statistics from the database.


Thanks again for pushing, every project needs someone to keep things going! :-)

Dan.
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Old 08-09-2011, 11:09 AM   #45
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Wink

Quote:
This is obviously a lot of work, and also, if we are not careful, may overlap with the remit of Wikipedia (you'll not get far trying to compete with Wikipedia). So this needs to be clearly focused on technical pipelines for common analysis... In the wiki spirit, I think it's best to get something down for everything rather than making one item perfect... I'll add some queries to each topic to return the list of tools relevant to that topic.
We are capable to cheat here. Think the community resource SEQanswers forum gives us.
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Last edited by marcowanger; 08-09-2011 at 11:10 AM. Reason: fix the language
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Old 08-09-2011, 11:12 AM   #46
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Quote:
Yes, I'll do that this evening.
Thanks.

LOL. I think we are working 24h a day (on the wiki). It's 2:00am here now, and I gotta sleep.
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Old 08-09-2011, 11:53 AM   #47
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Yeah, I was up to 2am the other day updating the wiki software and trying to suck in citation counts. I went to bed and got up 20 mins later because I needed to check something wasn't taking the whole wiki offline!

Sleep well ;-)
Dan.
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Old 08-09-2011, 11:58 AM   #48
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Quote:
Originally Posted by dan View Post
Yeah, I was up to 2am the other day updating the wiki software and trying to suck in citation counts. I went to bed and got up 20 mins later because I needed to check something wasn't taking the whole wiki offline!

Sleep well ;-)
Dan.
still here updating the manuscript. Hope to finish something before bed.
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Old 08-10-2011, 04:04 AM   #49
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Is somebody still working on updating the citations?

Otherwise I will do it -the good old fashioned curator way.....

I added two citations of Nature Mags on the discussion page.
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Old 08-10-2011, 04:22 AM   #50
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Dear usad.

Thanks.

1) A few days ago we have updated something here (http://seqanswers.com/forums/showthr...7828#post47828). Basically it is a manual search from Google Scholar. Obviously it can be automated. I am not sure if it's the most comprehensive list. Thanks for adding the Nat. Mag.

2) By the way, Usad may you update your profile in the wiki? Especially the real name, email and affiliation(s).


Quote:
Originally Posted by usad View Post
Is somebody still working on updating the citations?

Otherwise I will do it -the good old fashioned curator way.....

I added two citations of Nature Mags on the discussion page.
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Old 08-10-2011, 05:01 AM   #51
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Hi

I updated the profile already I will check though if it that went ok, thanks for the reminder.

I found 32 total publications in Google scholar or Pub Med central where I could get access and check the original paper and really found seqanswers (as in our forum or the wiki) mentioned in the main text and/or a main table . In addition Google scholar found two completely false positives and a lot of crud.

Also there were two book chapter I didn't have access to and thus couldn't check manually.

For now I put it here:
https://spreadsheets.google.com/spre...xGZ1E&hl=en_US

Cheers,
Björn

Last edited by usad; 08-10-2011 at 05:05 AM.
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Old 08-10-2011, 08:05 AM   #52
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Hi Usad, that is good. We may need cite the numbers and make them in supp. section. I saw some Database issue has supp.

Quote:
Originally Posted by usad View Post
Hi

I updated the profile already I will check though if it that went ok, thanks for the reminder.

I found 32 total publications in Google scholar or Pub Med central where I could get access and check the original paper and really found seqanswers (as in our forum or the wiki) mentioned in the main text and/or a main table . In addition Google scholar found two completely false positives and a lot of crud.

Also there were two book chapter I didn't have access to and thus couldn't check manually.

For now I put it here:
https://spreadsheets.google.com/spre...xGZ1E&hl=en_US

Cheers,
Björn
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Old 08-10-2011, 08:34 AM   #53
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Quote:
Originally Posted by usad View Post
Is somebody still working on updating the citations?

Otherwise I will do it -the good old fashioned curator way.....

I added two citations of Nature Mags on the discussion page.
I was planning to update the list on the wiki using the updated >2010 Scholar search, but I probably won't get to it until tonight or tomorrow.
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Old 08-10-2011, 09:42 AM   #54
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If you want to use my list be my guest (the false positives are removed) or east I head a look at all of them (see above for the google doc link)

Cheers,
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Old 08-10-2011, 11:22 AM   #55
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Talking Publication/Paper (NAR 2012)

It Is super awesome!!!!
Just today I realized about this opportunity and I am so busy right now, that I can not be part of it (plus the fact that my writing quality is so so... )
I am really happy to see that this "social" and valuable resources are recognized like that by the community!

Go ahead with the paper guys!
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Old 08-11-2011, 10:17 AM   #56
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Less than 90 hours to go. The content in the wiki will be freezed and I will start putting them into a doc. soon Hurry up guys.
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Old 08-11-2011, 10:24 AM   #57
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when will you freeze?
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Old 08-11-2011, 10:29 AM   #58
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The wiki will not actually be "freezed" actually. I just cannot synchronize the wiki and the doc, once I extract the content to a doc

Hey. I have another idea. How about making a google doc.

Surely I still have to prepare the references in Endnote and add in the citation at last (~24 hrs?) to play safe

then at ~18-12 hrs to due, I will send the doc to all authors. If no correction is done, then the doc will be sent to Dan for submission.
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Old 08-11-2011, 10:32 AM   #59
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for now, there are still a number of things to fix in the text. I will try my best. Any form of help is very much welcome.....
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Old 08-11-2011, 10:34 AM   #60
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Sounds more comfortable to me than the wiki, as I could make comments directly in the text (something I was missing yesterday)

And another high impact citation
The genome of the extremophile crucifer Thellungiella parvula
Nature genetics PubmedID 21822265

Cheers,
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