Managing crystallization experiments within PIMS

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• Managing crystallization experiments within PIMS

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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)

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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.

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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
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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

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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?!

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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?

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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????!?!

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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?

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Demo

• xtalPIMS Demo

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Demo
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Demo
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Demo
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Demo
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Demo
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Demo