Managing crystallization experiments within PIMS

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13 Νοε 2013 (πριν από 3 χρόνια και 9 μήνες)

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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)


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
xtal
PIMS.


What does it do?


Crystallization and protein production data can be
closely integrated in a PIMS database. Alternatively, the
xtal
PIMS user interface can be adapted to work with
existing crystallization databases.


xtal
PIMS GUI

xtal
PIMS 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
xtal
PIMS will
work at sites with multiple different robotic
systems.

For v1.0

Planned (probably for v2.0)


Veeco Systems


Formulatrix Systems


Bruker Crystal Farm


ThermoFisher


BioTOM


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 18
th

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 /
xtal
PIMS


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
xtal
PIMS.


In an ideal world,
xtal
PIMS 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

Demo

Demo

Demo

Demo

Demo

Demo