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Old 08-01-2011, 12:57 PM   #21
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Quote:
Originally Posted by marcowanger View Post
How about parse the info from google scolar or ISI web of knowledge?
Yeah, that would be perfect. If the info can be put behind an api, I can then use the External Data Extension to pull the counts into the wiki and query them. Unfortunately, I don't know of an api for either.
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Old 08-01-2011, 05:07 PM   #22
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Quote:
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Yeah, that would be perfect. If the info can be put behind an api, I can then use the External Data Extension to pull the counts into the wiki and query them. Unfortunately, I don't know of an api for either.
I think a python script is available around for GS already:

http://www.icir.org/christian/scholar.html

We just need to stich it to work with the wiki system.

Last edited by marcowanger; 08-01-2011 at 05:09 PM. Reason: clarify the purpose of the script
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Old 08-01-2011, 05:57 PM   #23
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Why do you guys care ??????

When I was an undergraduate in India, email was new thing and only one professor in the whole university had email access. So, he received emails for everyone and printed them in papers in front of his office. We had to sort through reams of paper to find out anything useful.

If you enjoyed that story, I can also tell you about riding a horse-buggy in Haridwar (a small town near the Himalayas).
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Old 08-01-2011, 06:14 PM   #24
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Smile please clarify

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Originally Posted by samanta View Post
Why do you guys care ??????

When I was an undergraduate in India, email was new thing and only one professor in the whole university had email access. So, he received emails for everyone and printed them in papers in front of his office. We had to sort through reams of paper to find out anything useful.

If you enjoyed that story, I can also tell you about riding a horse-buggy in Haridwar (a small town near the Himalayas).
May you elaborate more, I do not really get what you mean
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Old 08-01-2011, 06:16 PM   #25
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Quote:
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Why do you guys care ??????

When I was an undergraduate in India, email was new thing and only one professor in the whole university had email access. So, he received emails for everyone and printed them in papers in front of his office. We had to sort through reams of paper to find out anything useful.

If you enjoyed that story, I can also tell you about riding a horse-buggy in Haridwar (a small town near the Himalayas).
To answer your question, I care because I benefit from the forum from the first day of my graduate study. I learn and keep track of papers from here (the generous persons who share their insight of paper and the authors who promote their tools and the newsbots). When I have gained so much from here, I think it is time to give back something.

And people here are nice too.

Last edited by marcowanger; 08-01-2011 at 06:36 PM. Reason: language editing
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Old 08-01-2011, 10:24 PM   #26
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To answer your question, I care because I benefit from the forum from the first day of my graduate study. I learn and keep track of papers from here (the generous persons who share their insight of paper and the authors who promote their tools and the newsbots). When I have gained so much from here, I think it is time to give back something.

And people here are nice too.

I am not doubting the power of this forum, but the power of Nucleic Acids Research. My original comment was written to suggest that paper journals are the horse buggy technology now

Why do we need endorsement from them? Just my take.....
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Old 08-02-2011, 12:37 AM   #27
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I am not doubting the power of this forum, but the power of Nucleic Acids Research. My original comment was written to suggest that paper journals are the horse buggy technology now

Why do we need endorsement from them? Just my take.....
Just my thought, to change the system, we must to be in the system. Everyone knows there is problem in peer review system. But it is probably the best way it works *for now*. If what the direction of PLoS ONE is working on is right, a community driven post-publication review system and metric by paper itself not grossly by a journal. But well, PLoS ONE still gets an impact factor (IF). I think that is because authors need IF, and PLoS needs good authors. Just symbiosis. But still PLoS ONE is going to achieve its goal. A community driven NGS wiki has more to do than now, but nevertheless SEQwiki is an excellent start (Thanks Eric and Dan). I think many of us have benefited from their effort. But if we want to bring SEQWiki to more audience, we need papers to target those who only read and believe in papers. When more audiences are aware of SEQwiki, more community effort is available to curate the ever growing resources. I think that is a good cycle.
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Old 08-02-2011, 12:53 AM   #28
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Talking A post-publication package review site?

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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?
We can follow the rules and write the most concise descriptions of SEQwiki.
2k words is easy. But we need to think about the figure.

But the most important point is that, we need future direction of SEQwiki, merely categorizing the packages will not be sustainable. I think we need a community review system. For example, let people write in respective pages their main criticism on a package (Not about practical side, e.g. error file opening). Or why it is so great. I think that is what we long for, a post publication review system.

Last edited by marcowanger; 08-02-2011 at 12:55 AM. Reason: Add topic sentence
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Old 08-02-2011, 01:00 AM   #29
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Anyone know why I always see 500 internal Server Error after I clicked the submit button in SEQwiki?
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Old 08-02-2011, 01:21 AM   #30
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We can follow the rules and write the most concise descriptions of SEQwiki.
2k words is easy. But we need to think about the figure.

But the most important point is that, we need future direction of SEQwiki, merely categorizing the packages will not be sustainable. I think we need a community review system. For example, let people write in respective pages their main criticism on a package (Not about practical side, e.g. error file opening). Or why it is so great. I think that is what we long for, a post publication review system.
Good point. I made a list of things that should be done to improve the wiki at some point. I'll try to dig that out and we can sift through it. The main problem is time... I'd love to be paid to work on SEQwiki full time, because there are loads of great features I'd love to add. However, the current system of academia demands that I publish papers to get grant funding before (or rather, if ever) I can do that.

About 500 errors, please pester ECO about that ;-) I see them too... They usually go away if you hit reload, but you know the one time that the problem will be bad is when the reviewers come to check our site...

I really like the figure you added BTW, it's a really nice demonstration of what we have currently.
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Old 08-02-2011, 02:57 AM   #31
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Dear Dan,

excellent initiative.

Wouldn't is also be a good idea to do some QC of the wiki and maybe add some summary pages for certain major tasks which would almost read like a mini review for the big (most used) tools and would point to comparisons?
e.g. for de-novo assembly it would provide a nice overview page of the two handful of most used tools, their strength and weaknesses, papers comparing these, ongoing challenges and pointers to results, general tips. Maybe some new comparison based on what is posted here (e.g. run time CPUs memory in real life) etc.pp. and finally make sure that wiki pages about the these major tools are maintained and up to date. (e.g. the allpaths site needs an urgent overhaul), as it is definitely maintained and as of late many recent papers using allpaths-lg obatined excellent results e.g. Schneeberger et al., 2011 PNAS.

From my side I think it would be tremendously useful to have
assembler de-novo
read mapper
stand alone scaffolder
SNP detection tools
....
(or rather it would have been several years ago....)

as nice task views.

But then I always think in manually through through ontologies, and maybe that is there. (But I can always ever find the click through software lists which just list the wiki pages). And maybe that wouldn't be in the spirit of the seqwiki.

Cheers,
Björn
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Old 08-02-2011, 03:04 AM   #32
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Thanks for your thoughts Björn,

These are good ideas, and most of them have been on my SEQwiki 'todo' list for some time. Please do kick this off on the wiki. The more people (and the more ways) people contribute there the better!
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Old 08-02-2011, 03:17 AM   #33
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Let's do it quick.
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Old 08-02-2011, 03:28 AM   #34
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Yeah I guess who proposes, volunteers....

I could probably contribute 1) de novo assembly and cover CLC, soap, Allpaths, Abyyss and sprinkle in a bit of velvet even though we don't have a lot of experience with the latter. And will QC the entries as I go along.

2) Scaffolding I could also do. But I only have first hand experience with Bambus and SSPACE which we managed to get to work with some success.

and
3) a bit about short read aligners.

However, I can only start this tomorrow afternoon, but could finish probably early next week.

Cheers,
Björn
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Old 08-02-2011, 04:25 AM   #35
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Björn,

You are a star!

What you propose sounds awesome!


Please don't hesitate to ask if you have any technical questions regarding the wiki. I'll do my best to help as much as I can!


I'll start another thread to help organize this effort :-)
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Old 08-02-2011, 05:09 AM   #36
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I can possibly contribute 1) short read aligners, 2) Variants Calling pipelines, 3) QC the threads... 4) writeup something

Thanks dan for organizing all these.

Marco

Last edited by marcowanger; 08-02-2011 at 05:29 AM.
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Old 08-02-2011, 05:21 AM   #37
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Great! On this topic, please see:
http://seqanswers.com/forums/showthread.php?p=47934
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Old 08-04-2011, 06:30 AM   #38
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10 days counting
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Old 08-08-2011, 06:15 PM   #39
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Countdown to 15th Oxford Time http://www.timeanddate.com/counters/...&sec=0&p0=1233
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Old 08-09-2011, 01:08 AM   #40
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LOL, thanks Marco. I'm sure we can do it!

Lets focus on writing rather than wiki editing, as the latter can be done post submission.

Does anyone volunteer to redesign the wiki home page? Currently it kinda sucks... I'll front up some money if ECO would like to hold a 'design a front page' competition ;-)

Also, I'd really like to add a section about 'technology' to store data about all the different machines available...
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