Courageous Cantaloupe

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

Collaborators

 * User:Andrea Loehr (PGP)
 * User:Alexander Wait Zaranek (PGP)
 * User:Brandon K. Grantham (PGP)
 * User:Bryan E. Smith (Tranche)

Content

 * Raw images from targeted capture experiments from PGP1-5,PGP7-10.
 * PGP reads from GA Pipeline 1.0, 1.3.2, Swift.
 * Alignment results and raw reads from all Trait-o-matic genomes
 * Data from accepted Publications:
 * Add Bioinformatics...
 * Add Nature...
 * Add Science...
 * Add ...
 * Free and open source software in use at PGP:
 * Trait-o-matic
 * Free Factories
 * Other free and open-source software of interest:
 * BOINC & BOSSA
 * Ubuntu Cloud
 * Eucalyptus

PeoplePower and StatusUpdate
AL: AWZ: BKG: BES:
 * 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 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
 * 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:

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*