Courageous Cantaloupe

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** Add ...  
** Add ...  
* Free and open source software in use at PGP:
* Free and open source software in use at PGP:
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** https://trac.scalablecomputingexperts.com/wiki/Trait-o-matic Trait-o-matic]  
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** [https://trac.scalablecomputingexperts.com/wiki/Trait-o-matic Trait-o-matic]  
** [https://trac.scalablecomputingexperts.com/wiki Free Factories]
** [https://trac.scalablecomputingexperts.com/wiki Free Factories]
* Other free and open-source software of interest:
* Other free and open-source software of interest:
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** [http://www.ubuntu.com/cloud Ubuntu Cloud]  
** [http://www.ubuntu.com/cloud Ubuntu Cloud]  
** [http://www.eucalyptus.com/ Eucalyptus]
** [http://www.eucalyptus.com/ Eucalyptus]
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===PeoplePower and StatusUpdate===
===PeoplePower and StatusUpdate===

Revision as of 15:14, 30 November 2009

Image:PGP_template4.jpg

About        Projects        Publications        PersonalGenomes@Home        Public Data        FAQ        Updates (12/23)


March 2010, third public data release through ProteomeCommons.org's Tranche Network

Contents

Collaborators


Content

PeoplePower and StatusUpdate

AL:

  • collect all data on Orchestra /groups/pgp/
    • PGP4 now available
  • process data with GAP1.3.2, Swift, MAQ
  • BOINC application
    • read documentation, download and use
    • correspond with David Anderson
  • keep track of published/accepted data
    • in touch with Jay Lee


AWZ:

  • Software
  • BOINC application
    • David Anderson suggested we start by using the mailing lists.
    • He is mostly focused on Bossa and I can't help wonder if we should be focused on Bossa ourselves. It would be very impressive to have our community of volunteers helping to populate a database of genetic variants by culling the literature and performing other tasks. See http://stardustathome.ssl.berkeley.edu/ for an example of the sort of project that Bossa is intended to facilitate. Also see Amazon's Mechanical Turk

BKG:

  • BOINC application
    • read documentation, download and use
    • document progress at PGP and BOINC


BES:

  • Tranche upload
  • fold Tranche up-/download tools into BOINC application



Data Processing

AL: I have processed the following data with GAP1.3.2 and Swift:


Processed:
PGP1: PGP1_37_003
PGP2: PGP2_37_002
PGP3: PGP3_35_003
PGP4: PGP4_43_002
PGP5: PGP5_44_002
PGP8: PGP8_51_002, PGP8_37_001
PGP9: PGP9_43_003
PGP10: PGP10_41_003


Open:
PGP7_44_004
PGP8_51_006
PGP9_51_003, PGP9_51_007


Notes:
PGP5_44_002 stacks 95-100 could not be processed with Swift. Nava implemented a bug fix to Swift, needs rerun with latest Swift version.
PGP9_43_003 stacks 1,2 .fastq and .nonpf missing, need rerun
PPG6: Do not process, redacted.


Data location:
Complete Swift results including raw intensity files and reads are at /boinc-dev-scractch/PGP*
Complete RunFolders from GAP1.3.2 are at /boinc-scratch/RunFolder*

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