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Automation from a user perspective

Automation from a user perspective. Dr. J.P. Turkenburg York Structural Biology Laboratory. Overview. YSBL and how we work Role of e-HTPX in automation of diffraction experiment. York Structural Biology Laboratory. 8 PIs ~45 post-docs + support ~20 students

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Automation from a user perspective

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  1. Automation from a user perspective Dr. J.P. Turkenburg York Structural Biology Laboratory CCP4 Developers Meeting YSBL User experience

  2. Overview • YSBL and how we work • Role of e-HTPX in automation of diffraction experiment CCP4 Developers Meeting YSBL User experience

  3. York Structural Biology Laboratory • 8 PIs • ~45 post-docs + support • ~20 students • 3 X-ray generators with 3 detectors • ~25 days of ESRF time annually in BAG • requires 280 fte daysannually CCP4 Developers Meeting YSBL User experience

  4. Traditional approach to a typical ‘crystal’ experiment • Find suitable cryo (home source) • Find ‘single’ crystal (home source) • Store (ideally) 3 best crystals • Transport to synchrotron (with paper-trail) • Retest on beamline (enlightening!) • Collect data on best crystal (ideally) CCP4 Developers Meeting YSBL User experience

  5. Typical ESRF trip • 24 or 48 hours of beamtime • 3-4 people • 2 days travelling • 50-80 crystals • 15-25 projects • => data collection on other people’s crystals CCP4 Developers Meeting YSBL User experience

  6. Problems with ‘manual’ approach • Tracking samples • Testing crystals • Tracking results (+writing reports) • Time (people) CCP4 Developers Meeting YSBL User experience

  7. Aims and wishes More of the same: • Greater efficiency in terms of time and samples • Fewer people Allows more of: • Sample testing • Different data collections for same project • ‘Worse’ crystals All experiments and results tracked CCP4 Developers Meeting YSBL User experience

  8. Sample tracking & beyondor: how we do it now • e-HTPX project: ‘Sample tracker’ CCP4 Developers Meeting YSBL User experience

  9. Mar Research EU SPINE Standard Sample Holders and Vials: • Full spec at http://www.spineurope.org • Design based on Hampton Magnetic Crystal Cap and Vial System • Anti-icing lock, moat • 22mm fixed total length (18mm pins) • Ten character ID code • DataMatrix on the cap base • Clear code near to DataMatrix or rim of cap All York BAG projects now use these sample holders We use a USB handheld barcode reader connected to a PC in the X-ray room Hampton CCP4 Developers Meeting YSBL User experience

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  13. About 100 projects now in the database CCP4 Developers Meeting YSBL User experience

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  17. Must-have features • Multi-user • Simultaneous access by users • Privileges • Communication with ISPyB • Accessible from all computers in a lab • Searching/sorting • Soon: integration with Actor in home-lab CCP4 Developers Meeting YSBL User experience

  18. Effects on research work in YSBL • Everyone has switched to pins with barcode • All users now use e-HTPX hub • More crystals tested per project • More projects done • Fewer crystals lost? Not more! • Fewer people needed? CCP4 Developers Meeting YSBL User experience

  19. Hot off the press • Remote access to ID14-1 Friday 9 March 2007 • NoMachine into a linux box www.nomachine.com ?? • ssh –X into beamline computer • Start MXCube and DNA (two 17” screens) • Start adxv and ftp on second computer • Next slides: pictures CCP4 Developers Meeting YSBL User experience

  20. Acknowledgments • Sam Hart, X-ray technician, YSBL • Paul Young, YSBL • ESRF/BM14/EMBL/DNA/e-HTPX/SPINE/BIOXHIT……: lots of people CCP4 Developers Meeting YSBL User experience

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  24. (James Holton: 2346 datasets collected on one beamline, 48 depositions in PDB) CCP4 Developers Meeting YSBL User experience

  25. YSBL use of ESRF: scientific results • Last 2-year BAG review (March 2006) • 35 ESRF trips • > 30 MAD/SAD • > 400 single wavelength datasets 82 publications 96 PDB depositions CCP4 Developers Meeting YSBL User experience

  26. Form with essential information for experimenters about samples CCP4 Developers Meeting YSBL User experience

  27. Typical productivity for one trippre-automation • 48 hours ID14-4 • Projects from 5 PIs • 55 crystals tested/used • 30 datasets (4 MAD, i.e. 18+4x3) • >10,000 images CCP4 Developers Meeting YSBL User experience

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  30. Once at the ESRF….. • Load samples into sample changer • Get DNA to read barcodes and get sample info • Select samples to screen (per project) • Crystal loaded, centred (user input) • 2 test images • Indexing • Strategy!! (lifetime) • Collect (+process?) CCP4 Developers Meeting YSBL User experience

  31. ISPyB • Sample information at synchrotron (from eHTPX) • Details of diffraction experiments (testing & data collection) CCP4 Developers Meeting YSBL User experience

  32. ISPyB welcome page CCP4 Developers Meeting YSBL User experience

  33. Barcode in image filename. No more confusion! CCP4 Developers Meeting YSBL User experience

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  36. ISPyB info for a crystal CCP4 Developers Meeting YSBL User experience

  37. DNA results CCP4 Developers Meeting YSBL User experience

  38. ID14-2 24hrs 3Feb2007 16bunch CCP4 Developers Meeting YSBL User experience

  39. Are we happy? CCP4 Developers Meeting YSBL User experience

  40. What next? • More reliable! Miles better, but not there yet • DNA: more automated or more options? • Remote data collection ? (1 yorkie?) • Data collection service? • Real-time processing • Smaller teams? CCP4 Developers Meeting YSBL User experience

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