Courageous Cantaloupe: Difference between revisions

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September 2009, second public data release through [https://proteomecommons.org/tranche/ ProteomeCommons.org's Tranche Network]<br/>
March 2010, third public data release through [https://proteomecommons.org/tranche/ ProteomeCommons.org's Tranche Network]<br/>


====Collaborators====
====Collaborators====
Line 15: Line 15:
===Content===
===Content===


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


===PeoplePower and StatusUpdate===
===PeoplePower and StatusUpdate===


'''AL:''' <br/>
'''AL:''' <br/>
*collect all data on Orchestra /groups/pgp/  
*collect all data on Orchestra /groups/pgp/  
** Andrew will make PGP4 available 05/20
** PGP4 now available
* process data with GAP1.3.2, Swift, MAQ  
* process data with GAP1.3.2, [http://sgenomics.org/swift/ Swift], [http://maq.sourceforge.net/maq-man.shtml MAQ]
* BOINC application
* [http://boinc.berkeley.edu/ BOINC] application
** read documentation, download and use
** read documentation, download and use
** correspond with David Anderson  
** correspond with David Anderson  
Line 44: Line 45:
'''AWZ:''' <br/>
'''AWZ:''' <br/>
* Software
* Software
* BOINC application
* [http://boinc.berkeley.edu/ BOINC] application
** contact David Anderson
** David Anderson suggested we start by using the mailing lists. 
<br/>
** He is mostly focused on [http://boinc.berkeley.edu/trac/wiki/BossaIntro 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 [https://www.mturk.com/mturk/welcome Mechanical Turk]
'''BKG:'''<br/>
'''BKG:'''<br/>
* BOINC application
* [http://boinc.berkeley.edu/ BOINC] application
** read documentation, download and use
** read documentation, download and use
** document progress OWW <br/>
** document progress at [http://openwetware.org/wiki/PGP_and_BOINC PGP and BOINC] <br/>
<br/>
<br/>
'''BES:'''<br/>
'''BES:'''<br/>
* Tranche upload
* [https://proteomecommons.org/tranche Tranche] upload
* fold Tranche up-/download tools into BOINC application  
* fold Tranche up-/download tools into [http://boinc.berkeley.edu/ BOINC] application  
<br/>
<br/>
===Data Processing===
'''AL:'''  I have processed the following data with GAP1.3.2 and Swift: <br/>
'''Processed:'''<br/>
PGP1: PGP1_37_003 <br/>
PGP2: PGP2_37_002 <br/>
PGP3: PGP3_35_003 <br/>
PGP4: PGP4_43_002 <br/>
PGP5: PGP5_44_002 <br/>
PGP8: PGP8_51_002, PGP8_37_001 <br/>
PGP9: PGP9_43_003 <br/>
PGP10: PGP10_41_003 <br/>
'''Open:''' <br/>
PGP7_44_004<br/>
PGP8_51_006<br/>
PGP9_51_003, PGP9_51_007 <br/>
'''Notes: '''<br/>
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. <br/>
PGP9_43_003 stacks 1,2 .fastq and .nonpf missing, need rerun <br/>
PPG6: Do not process, redacted.<br/>
'''Data location:'''<br/>
Complete Swift results including raw intensity files and reads are at /boinc-dev-scractch/PGP* <br/>
Complete RunFolders from GAP1.3.2 are at /boinc-scratch/RunFolder*

Latest revision as of 13:15, 30 November 2009

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


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

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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