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e-HTPX: A User Perspective

Robert Esnouf, University of Oxford. e-HTPX: A User Perspective. The e-HTPX Research Challenge. Managing the processes along the protein crystallography pipeline: Remote user managing a complete experiment

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e-HTPX: A User Perspective

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  1. Robert Esnouf, University of Oxford e-HTPX: A User Perspective

  2. The e-HTPX Research Challenge • Managing the processes along the protein crystallography pipeline: • Remote user managing a complete experiment • Target selection, protein production, crystallization, data collection, structure solution, deposition • Exchange of data between laboratories, synchrotrons, computational resources, etc… • Development sites: SRS, EBI, York, Oxford, BM14 • Test sites: Oxford, York, Glasgow, (St Andrews’)

  3. Potential benefits of e-HTPX • Growing problems in protein crystallography: • Higher throughput, automation, distributed working, data volumes, better structure solution methods • ESRF JSBG beam lines 74MB images, 1s exposures • Need secure, universal data exchange • Standardized data model, single sign on, universal naming • Compute power • Automated data analysis against structure/sequence DBs • Current PX interest mainly limited to compute resources and small clusters (MrBUMP)

  4. e-HTPX e-Research Requirements • e-HTPX is primarily a (meta-)data management & data exchange problem: • Administration: single sign on, access rights, roles • Computation: small clusters (real-time data reduction) • Data sharing & integration: standardization & unique naming • Workflow: ‘expert’ data collection software • Collaboration tools: reporting, project management

  5. Getting Users to Adopt e-HTPX • Structural biology community is not necessarily computer literate • Focus more on understanding complex biology • No local software installation / complex certificates • Portal must offer real benefit in terms of experiment automation, access to remote services or simplifying data management/archiving • Error prevention by exchanging metadata and using barcoding intelligently • Integrated access to tools and resources

  6. Lessons from e-HTPX at Oxford • Strengths • Managing multi-researcher experiments • Highly automated crystallization management • ‘Champion’ driving developments at BM14 • Weaknesses • Balance of flexible data model & simple UI • Usefulness constrained by level of automation • Added burden/restriction on experimental freedom • Coping with rates of diffraction data acquisition

  7. BM14 at the ESRF, Grenoble

  8. Future Plans for e-HTPX • Merging e-HTPX with other developments • Widespread adoption of data exchange standards • Crystallization management interface  PiMS • e-HTPX Portal/Hub linked to PiMS (merged?) • ISPyB now ESRF-wide standard experiment log • DNA needs improving but desperately needed • MrBUMP now part of CCP4 suite • Diamond natural focus for synchrotron automation

  9. Take home messages • Crystallography is an experimental science • The e is much less important than the Science and must be invisible to the user • A simple tool addressing a well defined problem is much more likely to be taken up • Uptake guaranteed if Diamond data management is addressed • Need science champions to get over adoption ‘transition state’ • Low data volume but high complexity& variability

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