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Crystal to Synchrotron and beyond… (managing the data in your home laboratory better)

Crystal to Synchrotron and beyond… (managing the data in your home laboratory better). Ian Berry e-HTPX Developer & BIOXHIT Working Group 1 Co-ordinator / Developer. Depositions in an ideal world…. How you processed the bioinformatics How you created the protein

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Crystal to Synchrotron and beyond… (managing the data in your home laboratory better)

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  1. Crystal to Synchrotron and beyond… (managing the data in your home laboratory better) Ian Berry e-HTPX Developer & BIOXHIT Working Group 1 Co-ordinator / Developer

  2. Depositions in an ideal world… • How you processed the bioinformatics • How you created the protein • How this protein crystallized • How the data were collected • How the data were processed • How the structure was solved / refined • Plus… • A summary of the failed experiments to get the final result!

  3. Working towards a coherent, seamless data management strategy in the Home Laboratory… • Able to populate it automatically (or at least very easily) so the users can continue to concentrate on the science! • Able to upload automatically to deposition sites easily. Are there any gaps? Possibly!

  4. Data Processing & Structure Solution Pipelines PIMS (Protein Production) Where does everything fit? CollectionDB Crystallization e-HTPX Synchrotron

  5. Where are we now? • PIMS • talks tomorrow! • Crystallization • BIOXHIT-funded extension to PIMS • 3 developers – OPPF, NKI & EMBL Grenoble) • Due Autumn 2007 (with test versions from the start of summer 2007) • ISPyB • Project now run by ESRF • Being installed and adapted for Diamond

  6. e-HTPX – Current Status • The e-HTPX Portal v1.0 is being tested and available for demonstrations (please talk to me afterwards if you would to have a go!) • The e-HTPX Message Model v1.3 is available and is being used by York and Oxford to submit sample information to ISPyB. • XIA2 release 0.2.5 available • MrBUMP being used • ISPyB now adopted / adapted by Synchrotrons

  7. e-HTPX - The future… • Data Reduction Portal due for release May 2007 • e-HTPX Message Model v2.0 is under development – making the XML more generic and have a wider applicability than just ESRF (i.e. Diamond) • e-HTPX Portal to be enhanced, extended and renamed “Trip Management” and merged with PIMS/BIOXHIT Crystallization developments • Web Services will be made more generic (currently using Apache Axis) • Promote the “Speaks e-HTPX” paradigm!

  8. Speaking e-HTPX • If we have a common format for communicating between things, it does not matter how we store them at either end… • E.g. in crystallization, local DB needs to know where in the store the plate is kept, but the synchrotron only needs to know how the drop was set up. • So as long as each side “speaks e-HTPX” then they can communicate. • e-HTPX is proposing a set of XML Standards for communicating Crystallographic data between sites (and can be used for programs)

  9. Data Processing & Structure Solution Pipelines PIMS (Protein Production) Home Lab View ?? PIMS BIOXHIT CCP4 / BIOXHIT CollectionDB Crystallization e-HTPX Can anyone help?!

  10. OPPF Jon Diprose Robert Esnouf Stephen Graham Karl Harlos Dave Stuart e-HTPX Graeme Winter Colin Nave Asif Akram Ludovic Launer Martin Walsh Michael Gleaves BIOXHIT Diederick de Vries Gael Seroul Tassos Perrakis Josan Marquez Acknowledgements

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