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ISPyB

TID Day June 8th, 2012. ISPyB. MX beamlines upgrade and ISPyB new features. Solange Delageniere ESRF/TID/MIS. ISPyB – TID Day – 8 June 2012. Contents. What is ISPyB ? Tracking , experiments , samples , data flows … Features How does it help?

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ISPyB

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  1. TID Day June 8th, 2012 ISPyB MX beamlines upgrade and ISPyB new features Solange Delageniere ESRF/TID/MIS ISPyB – TID Day – 8 June 2012

  2. Contents • WhatisISPyB? • Tracking, experiments, samples, data flows… • Features • How doesit help? • Ongoingevolutionslinked to the beamlines upgrade • UPBL10 - MASSIF (Massively Automated Sample Selection Integrated Facility) • BM 29 BioSaxs ISPyB – TID Day – 8 June 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 • The EYE of HORUS has a very specific meaning • Helps to see the invisible • Consists of 6 parts • The 6 senses • 6 doors to collect data • Egyptian fraction system to measure the world • (1/2, 1/4, 1/8, 1/16, 1/32, 1/64) I spy on Beamlines ISPyB – TID Day – 8 June 2012

  4. Where is ISPyB? • 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 ISPyB – TID Day – 8 June 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 – TID Day – 8 June 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 • Development forge • http://forge.epn-campus.eu/projects/ispyb ISPyB – TID Day – 8 June 2012

  7. Sample tracking and Data Flow ISPyB – TID Day – 8 June 2012

  8. ISPyB Features & Modules Shipment, dewars, containers, samples Dewar tracking Experiments management Samples management Experiments logging Search and reporting ISPyB – TID Day – 8 June 2012

  9. Experiments management • Link with the SMIS • Proposals • Sessions (date, beamline, local contact) • Lab Contacts (email, address,..) • Proteins (approvedsamplesheets) ISPyB Features & Modules Experiments management Samples management Experiments logging Search and reporting ISPyB – TID Day – 8 June 2012

  10. ISPyB Features & Modules Experiments logging Experiments management Image thumbnails Parameters & Results Crystal Snapshots Samples management Experiments logging Search and reporting XRF Spectrum Crystal ranking ISPyB – TID Day – 8 June 2012

  11. ISPyB Features & Modules Reporting Experiments management Samples management Experiments logging Search and reporting ISPyB – TID Day – 8 June 2012

  12. How does it help? • Users • PrepareExperimentat home (and not waste time at the beamline) • Remote tracking by colleagues at home • Processexperimentresults back into the Home LIMS • Long term tracking of experiments (stored in the database) • CommunicationbetweenUsers 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) • Operatorcomments on data collections Nice crystal Low resolution ISPyB – TID Day – 8 June 2012

  13. 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/redsamplesdepending on the level of risk • Sample location thanks to the Dewar Tracking ISPyB – TID Day – 8 June 2012

  14. Ongoing Evolutions • Playback Centring and Grid Scanning integration • Data presentation (by project or acronym instead of sessions) • MASSIF project (Massively Automated Sample Selection Integrated Facility) • ISPyB for BioSaxs ISPyB – TID Day – 8 June 2012

  15. UPBL10 / MASSIF and ISPyB • CurrentWorkflow: Sequential Data Collection Pipeline • Receivingdewars • [ [ Screening / Online Data Analysis ]* / Ranking / Data Collection ]* • Returningdewars ISPyB - Bio Struct BioSAXS meeting 22 May 2012

  16. UPBL10 / MASSIF and ISPyB • SampleSorting(*1) • Depends on sample description (size, mounting,…) • Depends on beamlineworkload • Concurrent 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 – TID Day – 8 June 2012

  17. 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 – TID Day – 8 June 2012

  18. Thanks to… Questions… ISPyB – TID Day – 8 June 2012

  19. Creating Shipments Shipment Description (Excel) Shipment Creation Dewar Labels (sending, return) ISPyB – TID Day – 8 June 2012

  20. To be customized ISPyB Data Model ISPyB – TID Day – 8 June 2012

  21. 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 – TID Day – 8 June 2012

  22. Data Collections Data Collections of a Session ISPyB – TID Day – 8 June 2012

  23. To be developed Search and Reporting • Search • Data Collection (protein, sample, experiment date,…) • Proteins • Samples • Reports • Pdf, Word, Csv ISPyB – TID Day – 8 June 2012

  24. 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 – TID Day – 8 June 2012

  25. Dewar Tracking ISPyB – TID Day – 8 June 2012

  26. ISPyB Features & Modules • Experiment Management • Sample Management • ExperimentRecording • Search and Reporting ISPyB – TID Day – 8 June 2012

  27. Experiment Management • 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 – TID Day – 8 June 2012

  28. 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 – TID Day – 8 June 2012

  29. Data Collections Parameters & Results Image thumbnails (image wall) Crystal Snapshots Data Analysis reports XRF Spectrum Edge Scan ISPyB – TID Day – 8 June 2012

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

  31. Reporting for ManagersDashboard ISPyB – TID Day – 8 June 2012

  32. User Home laboratory Synchrotron User Portal SMIS Experiment ( 1 ) SMIS Request database Sample ( 2 ) ISPyB s e Information Beamline r database a w t f o Home ISPyB S BCM Detector ( 5 ) ( 4 ) l database o ( 5 ) r Experiment t n Reports o Sample C EDNA NICE Changer disk storage ( 5 ) Experiment Home Files ( images , … ) disk storage User Information System ( 3 ) Samples Sample tracking and Data Flow ISPyB – TID Day – 8 June 2012

  33. The data flow and application environment of ISPyB

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