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ISPyB

Bio Struct BioSAXS meeting May 22, 23 2012. ISPyB. From your sample to your data analysis: how to track every step of your experiment in a database. An example with ISPyB for MX experiments. Solange Delageniere ESRF/TID/MIS. Contents. What is ISPyB ?

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ISPyB

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  1. Bio Struct BioSAXS meeting May 22, 23 2012 ISPyB From your sample to your data analysis: how to track every step of your experiment in a database. An example with ISPyB for MX experiments Solange Delageniere ESRF/TID/MIS ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  2. Contents • WhatisISPyB? • Tracking, experiments, samples, data flows… • Features : how canitbeadapted to BioSaxs ? • Architecture • How doesit help? • Ongoing Evolutions ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  3. What is ISPyB? • ISPyB: Information System for Protein CrystallographYBeamlines • Laboratory Information Management System (LIMS) for protein crystallography experiments on synchrotron beamlines • Web based interface • Access • http://ispyb.esrf.fr • To log-in: ESRF experimentnumber and password • Whereisitusedat the ESRF? • ID14-1, ID14-4 • BM29 verysoon ! (BioSAXS) • ID23-1, ID23-2, ID29 • BM14 I SPY on Beamlines ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  4. Sample tracking and Data Flow ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  5. History • 2001-2005: Pxweb • Python/Zope, MySql • JSBG Project (ESRF/EMBL) • Experimentlogging for MXPressusers (FX users) • 2005-2011: ISPyB • Java/Struts/Jboss, Mysql • ESRF/Spine/Bioxhit and BM14/MRC/eHTPX collaboration • Pxweb features + new features + Dewar Tracking • 2009: Collaboration withDiamond (code sharing) ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  6. ISPyB in 2012 • Important upgrade • ISPyB data model extensions (Autoprocessing, EDNA) • Jboss server 6.0, EJBs3 • Web services to communicatewith BLC (MXCube) • Verynear future • ISPyB for MASSIF : • ISPyB for BioSaxs • Project management • Scientistproject leader : Elspeth Gordon • Software project leader : Solange Delageniere • Meeting and videoconferencewithDiamond Light Source • Development forge • http://forge.epn-campus.eu/projects/ispyb ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  7. ISPyB Features & Modules • Experiment Management • Sample Management • ExperimentRecording • Search and Reporting • Ready for BioSaxs? • To becustomizedfor BioSaxs ? • To bedeveloped for BioSaxs ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  8. Experiment Management Ready • Items: • Proposals • Sessions (date, beamline, local contact) • Lab Contacts (email, address,..) • Proteins (approvedsamplesheets) • Features: • Data retrievedfrom the User Portal (SMIS) • Edit Lab Contact Card ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  9. Lab Contacts Ready Search Edit Select ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  10. To be customized Sample Management • Items: • Shipments (set of dewars) • Dewars (barcode, couriertrackingnumber) • Containers (barcode) • Samples (barcode, proteinacronym, crystalform,…) • Features: • Online shipment description • Shipment description upload (Excel file) • Dewar Tracking ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  11. Ready Creating Shipments Shipment Description (Excel) Shipment Creation Dewar Labels (sending, return) ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  12. Ready Dewar Tracking ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  13. Experiment Recording • Items: • Session info (date, beamlinename, operator,…) • Experimentparameters (wavelength, energy, detector distance,…) • Beamlineparameters (name, beam transmission, beam size,…) • Crystal snapshots • Images (thumbnails, link to real images) • Data Analysis / EDNA results (characterisation & strategy, mosflm.log, pointless.log,…) To be customized To be developed ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  14. To be developed Data Collections Data Collections of a Session ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  15. To be customized Data Collections Parameters & Results Image thumbnails (image wall) Crystal Snapshots Data Analysis reports XRF Spectrum Edge Scan ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  16. To be developed Search and Reporting • Search • Data Collection (protein, sample, experiment date,…) • Proteins • Samples • Reports • Pdf, Word, Csv ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  17. To be developed Ranking samples Ranked Samples Sample Screening DNA/EDNA Characterisation Sample Ranking & Selection Data Collect … ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  18. Ready Reporting for ManagersDashboard ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  19. To be customized ISPyB Data Model ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  20. ISPyB Technology • Pure Web Interface • Java • Jboss Application Server (Ejb) • Struts (MVC Web Application Framework) • MySql / Oracle Database • Communication with User Portal (SMIS) via Web Services • Communication with BCM and EDNA • Through web Services ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  21. How does it help? • Users • Prepare Experiment at home (and not waste time at the beamline) • Remote tracking by colleagues at home while the experiment is performed • Process experiment results back into the Home LIMS • Long term tracking of experiments (stored in the database) • Communication between Users and ESRF Staff • Dewar description (beamline, local contact, user address) • Sample description (description, bar-code, location, known unit cell dimensions, space group, diffraction plans, comments) • Operator comments on data collections ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  22. How does it help? • Management and Operations • Dashboards for monitoring operations • Statistics on how experiments are carried out • Screenings/Full data collections ratio,… • Figures on feature usage (training, interface improvement…) • Figures on data throughput (Data Collection Pipeline optimization) • Safety • Green/yellow/red samples depending on the level of risk • Sample location thanks to the Dewar Tracking ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  23. Ongoing Evolutions • Playback Centring and Grid Scanning integration • Data presentation (by project or acronym instead of sessions) • MASSIF project • ISPyB for BioSaxs ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  24. UPBL10 / MASSIF and ISPyB • Current Workflow: Sequential Data Collection Pipeline • Receiving dewars • [ [ Screening / Online Data Analysis ]* / Ranking / Data Collection ]* • Returning dewars ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  25. UPBL10 / MASSIF and ISPyB • Sample Sorting (*1) • Depends on sample description (size, mounting,…) • Depends on beamline workload • Screening Automation and Data Analysis (*2) • More reliant on information from the user (composition…) • Grid Scanning and Sample Centering results • Data Storage (images, characterisation and strategy) ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  26. ISPyB For BioSAXS • Features: • Sample tracking, experiment management and recording, search and reporting and web interface as for MX beamlines • Developments: • Experimentrecording: data model and GUI extensions for BioSAXS • Other modules: as itis in ISPyB or withsmall customisations • Link with MX experiments and SANS experiments… ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  27. Thanks to… Questions… ISPyB - Bio Struct BioSAXS meeting 22 May 2012

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