Best place to share data?

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Doug
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Best place to share data?

Postby Doug » Mon Apr 15, 2013 1:43 pm

A coworker of mine needs to deposit their data in a public database. It looks like Chorus isn't operational yet and Tranche has never worked for me in the past. What is currently the best place to put it?

Thanks.
"If we knew what we were doing it wouldn't be research." -AE

Biomarker
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Share data

Postby Biomarker » Mon Apr 15, 2013 9:48 pm

Hi Doug,

ADrive http://www.adrive.com/ is the place where you can deposit about 50 GB of data for free. But i guess with paid membership you can store more.

Cheers,
:)

achimt
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Postby achimt » Mon Apr 15, 2013 11:57 pm

Hi Doug,

proteomeXchange (http://www.proteomexchange.org/mission) looks quite feasible (for datasets that are not suitable for the conversion into prideXML one can do partial submissions, which are quite similar to what you were able to do on TRANCHE).

Hope this helps,
Achim

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Doug
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Postby Doug » Tue Apr 16, 2013 7:58 am

Thanks guys. As this question seems to come up a lot I wanted to share some of the responses I got from twitter as well.

@SharedProteomic At the moment, probably PASSEL https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Submit?_subtab=2

@SharedProteomic see the 2 ProteomeXchange options here, one for SRM, one for shotgun proteomexchange.org/submission

@attilacsordas @SharedProteomic have I missed something but what has happened to PRIDE?
"If we knew what we were doing it wouldn't be research." -AE

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Doug
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Postby Doug » Tue Apr 16, 2013 7:59 am

I believe my coworker is going with Peptide Atlas. I will find out how it goes and report back.
"If we knew what we were doing it wouldn't be research." -AE

Craig
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Postby Craig » Tue Apr 16, 2013 11:38 am

Just one more option, it might be worth giving Tranche another try. I have heard and in my experience it has been working better lately. And when Chorus is up I believe they intend to migrate over all the Tranche data so you shouldn't have to worry about it then.

gadsouza
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Postby gadsouza » Wed Apr 17, 2013 11:30 pm

Hey Craig, I think you mean ProteomeCommons? (Tranche is a general file transfer protocol if I remember correctly, which PC use). If so they currently have only 2 servers online, from +20, so the vast majority of already available data there is still unavailable due to the fact it is saved in current offline servers. In addition, they are not taking any new upload until they transfer the service to a new site domain.

Gajanan
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Postby Gajanan » Thu Apr 18, 2013 1:37 am

You can upload ur data in PRIDE http://www.ebi.ac.uk/pride/

Craig
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Postby Craig » Thu Apr 18, 2013 5:39 pm

gadsouza, thanks for the update on ProteomeCommons/Tranche. I thought maybe you could upload to the few servers that were still online and downloading would be relatively robust even if not very distributed as was intended. There are probably better options though, as others have posted.


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