Automation from a user perspective

Automation from a user perspective
Dr. J.P. Turkenburg York Structural Biology Laboratory 05/12/2018 CCP4 Developers Meeting YSBL User experience

CCP4 Developers Meeting YSBL User experience
Overview YSBL and how we work Role of e-HTPX in automation of diffraction experiment 05/12/2018 CCP4 Developers Meeting YSBL User experience

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 days annually 05/12/2018 CCP4 Developers Meeting YSBL User experience

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) 05/12/2018 CCP4 Developers Meeting YSBL User experience

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 05/12/2018 CCP4 Developers Meeting YSBL User experience

Problems with ‘manual’ approach
Tracking samples Testing crystals Tracking results (+writing reports) Time (people) 05/12/2018 CCP4 Developers Meeting YSBL User experience

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 05/12/2018 CCP4 Developers Meeting YSBL User experience

Sample tracking & beyond or: how we do it now
e-HTPX project: ‘Sample tracker’ 05/12/2018 CCP4 Developers Meeting YSBL User experience

EU SPINE Standard Sample Holders and Vials: Full spec at 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 Mar Research 05/12/2018 CCP4 Developers Meeting YSBL User experience

05/12/2018 CCP4 Developers Meeting YSBL User experience

This is an essential feature in a lab with many users and projects. We cannot allow users to accidentally edit each others information. Hierarchy allows PIs to see all projects belonging to their people. Only admin can access all data and add and remove holders from system etc. This also allows multiple users to input data on their own computer. Admin can gather this to put together all info for a synchrotron trip. 05/12/2018 CCP4 Developers Meeting YSBL User experience

About 100 projects now in the database 05/12/2018 CCP4 Developers Meeting YSBL User experience

Let’s look at a typical synchrotron trip and the info that is submitted to ISPyB 05/12/2018 CCP4 Developers Meeting YSBL User experience

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 05/12/2018 CCP4 Developers Meeting YSBL User experience

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? 05/12/2018 CCP4 Developers Meeting YSBL User experience

Hot off the press Remote access to ID14-1 Friday 9 March 2007 NoMachine into a linux box ?? ssh –X into beamline computer Start MXCube and DNA (two 17” screens) Start adxv and ftp on second computer Next slides: pictures 05/12/2018 CCP4 Developers Meeting YSBL User experience

Acknowledgments Sam Hart, X-ray technician, YSBL Paul Young, YSBL ESRF/BM14/EMBL/DNA/e-HTPX/SPINE/BIOXHIT……: lots of people 05/12/2018 CCP4 Developers Meeting YSBL User experience

(James Holton: 2346 datasets collected on one beamline, 48 depositions in PDB) 05/12/2018 CCP4 Developers Meeting YSBL User experience

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 05/12/2018 CCP4 Developers Meeting YSBL User experience

Form with essential information for experimenters about samples 05/12/2018 CCP4 Developers Meeting YSBL User experience

Typical productivity for one trip pre-automation
48 hours ID14-4 Projects from 5 PIs 55 crystals tested/used 30 datasets (4 MAD, i.e. 18+4x3) >10,000 images 05/12/2018 CCP4 Developers Meeting YSBL User experience

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?) 05/12/2018 CCP4 Developers Meeting YSBL User experience

ISPyB Sample information at synchrotron (from eHTPX) Details of diffraction experiments (testing & data collection) 05/12/2018 CCP4 Developers Meeting YSBL User experience

ISPyB welcome page 05/12/2018 CCP4 Developers Meeting YSBL User experience

Barcode in image filename. No more confusion! 05/12/2018 CCP4 Developers Meeting YSBL User experience

ISPyB info for a crystal

DNA results 05/12/2018 CCP4 Developers Meeting YSBL User experience

ID hrs 3Feb bunch 05/12/2018 CCP4 Developers Meeting YSBL User experience

Are we happy? GOOD BAD eHTPX sample tracking multi-user Interface not too user friendly ISPyB pre/post experiment info login; info once home (links) DNA can be v. fast strategy not as good as me….. sample changer saves time samples safe reliability issues ‘system’ capabilities ‘communication’ 05/12/2018 CCP4 Developers Meeting YSBL User experience

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? 05/12/2018 CCP4 Developers Meeting YSBL User experience

Automation from a user perspective

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