Courageous Cantaloupe

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** [ Free Factories]
** [ Free Factories]
* Other free and open-source software of interest:
* Other free and open-source software of interest:
** [ BOINC] & [http:// BOSSA]  
** [ BOINC] & [ BOSSA]  
** [ Ubuntu Cloud]  
** [ Ubuntu Cloud]  
** [ Eucalyptus]
** [ Eucalyptus]

Current revision


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

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




PeoplePower and StatusUpdate


  • 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


  • 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 for an example of the sort of project that Bossa is intended to facilitate. Also see Amazon's Mechanical Turk


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


  • 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:

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

PGP9_51_003, PGP9_51_007

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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