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Toward the automation of biological structure determination Thomas Earnest

Toward the automation of biological structure determination Thomas Earnest Berkeley Center for Structural Biology Physical Biosciences Division Lawrence Berkeley National Laboratory. Manual mounting and alignment. micro-scope. cryostream. gripper. goniometer/ XYZ stage. collimator/

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Toward the automation of biological structure determination Thomas Earnest

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  1. Toward the automation of biological structure determination Thomas Earnest Berkeley Center for Structural Biology Physical Biosciences Division Lawrence Berkeley National Laboratory

  2. Manual mounting and alignment

  3. micro-scope cryostream gripper goniometer/ XYZ stage collimator/ beamstop dewar heater sample

  4. Crystal transport and handling sample cassette with magnetic base (puck) puck handling tools automounterdewar with 112 samples

  5. Crystal transport and storage Taylor-Wharton CP 100 dry shipping Dewar holds 7 pucks (112 samples)

  6. Automated Loop Alignment • Auto Focus if loop can’t be found (<10 sec) • Center Loop (2 sec) • Rotate 90 degrees (1 sec) • Center Loop (2 Sec) • Raster using low-dose x-rays to maximize diffraction, thus centering xtal

  7. This system is installed and operational on BL 5.0.1, 5.0.2, 5.0.3 Under construction for HHMI BL 8.2.1 Also under construction for beamlines at NSLS, CHESS, and APS SER-CAT

  8. Beamline software DCS: Hutch Tab

  9. Beamline Software DCS: Scan Tab

  10. Beamline software DCS: Track Tab

  11. Autonomous agents as real-time, • adaptive controllers of • Data collection • Data processing • Analysis • Process flow • Information analysis • ROBOHUTCH CYBERHUTCH

  12. user priority Data collection on best crystal: Mounting/Collecting/Unmounting score strategy Automated screening / data collection Collaboration between BCSB and CCI (P. Adams, Nick Sauter) • Crystal mounting • Centering • Screening • Rescreen • Unmounting

  13. Xtal / User db

  14. sensors environment ? agent actuators Autonomous agents

  15. Autonomous Agents Definition: “An autonomous agent is a system situated within and a part of an environment that senses that environment and acts on it, over time, in pursuit of its own agenda and so as to effect what it senses in the future.” Franklin & Graesser, 1996 “Is it an Agent, or just a Program?” Proc. of 3rd Int. Workshop on Agent Theories

  16. situated within and a part of an environment • beamline, automounter, computational control • senses that environment • optical system, encoders • acts on it • mount crystal • move goniometer, detector • take data • pursuit of its own agenda • collection of highest-quality data as fast as possible • structure determination • effect what it senses in the future • knowledge base updating and influencing future actions

  17. Carl Cork Bob Nordmeyer John Taylor Earl Cornell Gyorgy Snell Bioinstrumentation Jeff Dickert Brian Greensmith Azer Dauz Nick Sauter Toni Borders Paul Adams Anthony Rozales CCI Jon Spears BCSB NIH/NIGMS, DOE/OBER, Agouron Institute

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