Difference between revisions of "Software Group progress report for 2010"

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(Production)
(Production (Stuart, Gail, Ben, Mike C))
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#During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.
 
#During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.
 
#Worked on testing and install of Amigo 1.8 (required 64bit OS for clucene-based searching)
 
#Worked on testing and install of Amigo 1.8 (required 64bit OS for clucene-based searching)
 +
#Made several upgrades to GAF filtering script
 +
#* update from GAF 1.0 -> 2.0
 +
#* added the following feature_types
 +
#** gene_product
 +
#** polypeptide
 +
#* added the following evidence codes: IMR, IRD
 +
#* added qualifier 'rapid_divergence'
 +
# Put in place filter-paint-associations.pl script
  
 
=== Schema Overhaul ===
 
=== Schema Overhaul ===

Revision as of 10:30, 23 November 2010

Management

Annotation Support

Database

Production (Stuart, Gail, Ben, Mike C)

  1. Rebuilt goweb-dev (not replaced)
    • Upgraded OS from RH 32-bit -> RH 64bit
    • Upgraded mysql from 4.1 -> 5.1
  2. Replaced GO loading machine
    • (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks
    • (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)
      • sucessfully testing loading on claret.
      • have also done initial testing on load-qfo replacement for loading sequences into godb
  3. Ordered 2 machines to replace GO frontends, goweb1/goweb2
    • Anticipated that these machines will be into production by the end of 2010.
  4. During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.
  5. Worked on testing and install of Amigo 1.8 (required 64bit OS for clucene-based searching)
  6. Made several upgrades to GAF filtering script
    • update from GAF 1.0 -> 2.0
    • added the following feature_types
      • gene_product
      • polypeptide
    • added the following evidence codes: IMR, IRD
    • added qualifier 'rapid_divergence'
  7. Put in place filter-paint-associations.pl script

Schema Overhaul

Schema Overhaul

SHAHID TO FILL IN

(this may belong in a separate report - add here for now anyway)

Annotation QC

 AMELIA TO FILL IN

AmiGO

Website

AMELIA - ANYTHING HERE?

Workflow Support

  • Created a basic GO_Galaxy_Environment
    • integrated map2slim
    • integrated slim-creator
    • integrated enrichment tools
      • GO TermFinder
      • Ontologizer

MOOSE libraries

AMELIA TO FILL IN

Reference Genome Support

RefG in AmiGO

  • Loading Trees (SVEN)
    • Matching IDs
      • Currently ~64% of of the ids are being matched after the new QFO load.
      • Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.
    • Report Pages
      • 2. Date selected for concurrent annotation: Have data, obtaining write access to GO cvs
      • 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is


MARY TO FILL IN

Paint

SUZI TO FILL IN

Ontology Support

TermGenie

See Compositional_Term_Submission_Tool

  • Created initial prototype, in use by ontology group and annotators

OBO-Edit

See

AMINA TO FILL IN

Transition to OWL

See Transition_to_OWL