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“Database” usage and requirements for CCP4 automation

“Database” usage and requirements for CCP4 automation. Projects at Daresbury. HAPPy - experimental phasing DJR, PE, EJD, CCB XIA-DPA - dataprocessing (other) GW (DNA) BMP - molecular replacement RK, MDW (NDS) CCP4i PJB Data storage WY, PJB. Tracking. Persistence.

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“Database” usage and requirements for CCP4 automation

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  1. “Database” usage and requirements for CCP4 automation CCP4 database meeting

  2. Projects at Daresbury • HAPPy - experimental phasing • DJR, PE, EJD, CCB • XIA-DPA - dataprocessing (other) • GW (DNA) • BMP - molecular replacement • RK, MDW (NDS) • CCP4i • PJB • Data storage • WY, PJB CCP4 database meeting

  3. Tracking Persistence Current state of affairs Project Job Fact Project_id Name Job_id Name Name_id Fact • Database or filesystem • Individual or central • Security models Dingbat dingbat_id dingbat CCP4 database meeting

  4. (Loose) Storage Requirements • Tracking (Jobs) - ccp4i, HAPPy • Data types • Knowledge base - ccp4i • Object persistence - GW • Templates and protocols - eHTPX External view Project Control CCP4 database meeting

  5. Job Tracking • Workflow view • Database or filesystem • Track progress • ccp4i gives good example CCP4 database meeting

  6. HAPPy view • Nodes (actions) • Type: Job, Fork, Decision, Start, End (Container) • Status: Success, Failed, Killed, Running • Time stamps • Human readable notes • Designed to work with ccp4i database. CCP4 database meeting

  7. Data tracking • Meta data (describe file) • URI • Wavelength • Cell • Column names • Source and usage CCP4 database meeting

  8. Knowledge base • Small amounts of data -> xml files, otherwise database • Project and pipeline independent • mmcif definitions at deposition end • Datamodel (?) • HA positions and statistics • x, y, z, occ, anon_occ, b • Sequence • Solvent fraction • MR models CCP4 database meeting

  9. Persistent Objects (databucket) • Project specific (unless common) • Store local state • object orientated database (ZODB) • dingbats • .xml file • HAPPy has HAPPy state object • always in memory • current state and history • persistence required for restart CCP4 database meeting

  10. Protocols and Templates • User preferences • Pathways / Workflow CCP4 database meeting

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