BIRCH/Database Development

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Project data from different labs will be integrated into a unified database, hosted at the Genome Canada Bioinformatics Platform at the University of Calgary.

BIRCH/Database Development/Schema design

BIRCH/Database Development/Implementation plan

BIRCH/Database Development/Interfaces and clients

TODO

Setup COE

• obtain database account on COE01 and create new database "MGCB2db" or something like that
• COE software
  • determine what software to install on COE01
  • ask Daryl to install the software
• Do research into GUI clients for MySQL that run on Solaris DONE - see BIRCH/Database Development/Interfaces and clients
• Ask Daryl to configure remote access to MySQL
  • preferred umanitoba.ca domain - requires SSL
  • if unable to:
    • albacore.cs.umanitoba.ca
    • gaia.cc.umanitoba.ca
    • moon.cc.umanitoba.ca
    • antares.cc.umanitoba.ca
    • deneb.cc.umanitoba.ca
    • mira.cc.umanitoba.ca
    • merak.cc.umanitoba.ca
    • toliman.cc.umanitoba.ca

Create example database

• Create MySQL tables from:
  • BirchDB - look at this one first
    • File object - For files let it either be local or http-based
  • ACEBF
    • Author - rename as person
    • Species has genome, genome has genes
    • Gene
    • Isolate- rename as Strain
• Write out a schema with 5 or 6 classes and a few fields in each class
• Implement schema
• Populate database
• Consult with microbiologists on where to go from here