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Managing crystallization experiments within PIMS. What is it?. BIOXHIT-funded extension to labPIMS Developed by: Ian Berry (OPPF, Oxford) Gael Seroul (EMBL, Grenoble) Diederick de Vries (NKI, Amsterdam) With lots of help from PIMS team (particularly Chris Morris and Bill Lin).
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What is it? • BIOXHIT-funded extension to labPIMS • Developed by: • Ian Berry (OPPF, Oxford) • Gael Seroul (EMBL, Grenoble) • Diederick de Vries (NKI, Amsterdam) • With lots of help from PIMS team (particularly Chris Morris and Bill Lin)
What does it do? • Organizes and manages all data relating to protein crystallization. • All images and data can be viewed using a standard web browser on any computer remotely over the web via a secure login. • Information about crystals can be transferred to synchrotron systems, such as ISPyB, based on the e-HTPX messaging model, and data about experiments on the beamline will be transferrable back to xtalPIMS.
What does it do? • Crystallization and protein production data can be closely integrated in a PIMS database. Alternatively, the xtalPIMS user interface can be adapted to work with existing crystallization databases. xtalPIMS GUI xtalPIMS GUI Business API PIMS DB Impl Business API OPPF PlateDB Impl Hibernate JPA PIMS DB OPPF PlateDB
Imager Integration • Design is independent of any particular set up, storage or imaging system, indeed xtalPIMS will work at sites with multiple different robotic systems. • Image Analysis – support for ALICE (and other image analysis programs) is built in to Image Processing part of Imager Integrations
Releases • v0.3 (Current release) – GUI on top of OPPF PlateDB – default crystal viewer in OPPF for the past two months (approx 22877 plates, 52530399 images and 372 users as of 18th March) • v0.4 (GUI/PlateDB) to be released soon… • v1.0 – GUI on top of PIMSDB – aiming for Mid April (BIOXHIT AGM), but still much development work & optimization to do! • v2.0 – Mid June (end of BIOXHIT) • v3.0 – anyone got any funding?!
Future Plans • Optimization screens: • Creation of optimization blocks from source condition using a standard pattern (e.g. OPPF) • Creation of optimization blocks from source condition using gradients • Creation of hand-crafted optimization screens • “Best Screens” • Using data mining, answer the question: for this protein with these features what 96 (or 192) conditions would provide me with the best chance of getting crystals in my initial sparse matrix screening?
Future Plans • Trip Management • Extension of e-HTPX Portal • Allow users to highlight crystal drops they would like to collect data for • These are summarised for management committee • Crystals are either approved, delayed for later trip or rejected • Crystals then available for mounting through integrated e-HTPX Portal / xtalPIMS • Data Collection data • Retrieved from ISPyB / Synchrotron data store using e-HTPX Message Model and stored in PIMS db, along with links to frames on local file store. • Data processing with XIA2 Portal • Further integration with CCP4 - Links to run CCP4 programs on local clusters / store results in PIMS DB / etc... Any ideas????!?!
Licencing • With PIMS moving from LGPL to a more restrictive licence, there is an effect on xtalPIMS. • In an ideal world, xtalPIMS will have the same licence so that they can be branded / “sold” as a bundle. • It is unclear (to me) how the association with BIOXHIT / NKI / EMBL through funding / development work will affect this… Different bits of paperwork say different things… do other BIOXHITers have any idea?
Demo xtalPIMS Demo
