Difference between revisions of "Courageous Cantaloupe"

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* Raw images extended to include PGP2, PGP4
* Raw images from targeted capture experiments from PGP1-5,PGP7-10.
* PGP reads from GA Pipeline 1.0
* PGP reads from GA Pipeline 1.0, 1.3.2, Swift.
* PGP reads from GA Pipeline 1.3.2
* Alignment results and raw reads from all [http://snp.med.harvard.edu Trait-o-matic genomes]
* PGP reads from [http://sgenomics.org/swift/ Swift]
* Data from accepted [[PGP:Publications|Publications]]:
* Alignment results from [http://maq.sourceforge.net/maq-man.shtml MAQ]
** Add [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp383 Bioinformatics]...  
* Data from '''accepted''' [http://openwetware.org/wiki/PGP:Publications Publications]
** Add [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08211.html Nature]...
* [http://boinc.berkeley.edu/ BOINC] application
** Add [http://www.sciencemag.org/cgi/content/abstract/1181498 Science]...
* Software
** Add ...
** [http://wiki.github.com/xwu/trait-o-matic/download-installation Trait-O-Matic]
* Free and open source software in use at PGP:
** [http://www.usenix.org/events/usenix08/tech/full_papers/zaranek/zaranek_html/index.html Genomerator]
** https://trac.scalablecomputingexperts.com/wiki/Trait-o-matic Trait-o-matic]  
** [https://trac.scalablecomputingexperts.com/wiki Free Factories]
* Other free and open-source software of interest:
** [http://boinc.berkeley.edu/ BOINC] & [http://http://boinc.berkeley.edu/trac/wiki/BossaIntro BOSSA]
** [http://www.ubuntu.com/cloud Ubuntu Cloud]  
** [http://www.eucalyptus.com/ Eucalyptus]
** [http://www.eucalyptus.com/ Eucalyptus]

Revision as of 13:13, 30 November 2009

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



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 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:

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*