TID Day June 8 th 2012 ISPy B

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

Contents • What is ISPy. B? • Tracking, experiments, samples, data flows… • Features Contents • What is ISPy. B? • Tracking, experiments, samples, data flows… • Features • How does it help? • Ongoing evolutions linked to the beamlines upgrade • UPBL 10 - MASSIF (Massively Automated Sample Selection Integrated Facility) • BM 29 Bio. Saxs ISPy. B – TID Day – 8 June 2012 2

What is ISPy. B? • ISPy. B: Information System for Protein Crystallograph. Y Beamlines What is ISPy. B? • ISPy. B: Information System for Protein Crystallograph. Y Beamlines • Laboratory Information Management System (LIMS) for protein crystallography experiments on synchrotron beamlines • Web based interface I spy on Beamlines • 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) ISPy. B – TID Day – 8 June 2012 3

Where is ISPy. B? • Access • http: //ispyb. esrf. fr • To log-in: Where is ISPy. B? • Access • http: //ispyb. esrf. fr • To log-in: ESRF experiment number and password • Where is it used at the ESRF? • • ID 14 -1, ID 14 -4 BM 29 very soon ! (Bio. SAXS) ID 23 -1, ID 23 -2, ID 29 BM 14 ISPy. B – TID Day – 8 June 2012 4

History • 2001 -2005: Pxweb • Python/Zope, My. Sql • JSBG Project (ESRF/EMBL) • History • 2001 -2005: Pxweb • Python/Zope, My. Sql • JSBG Project (ESRF/EMBL) • Experiment logging for MXPress users (FX users) • 2005 -2011: ISPy. B • • Java/Struts/Jboss, Mysql ESRF/Spine/Bioxhit and BM 14/MRC/e. HTPX collaboration Pxweb features + new features + Dewar Tracking 2009: Collaboration with Diamond (code sharing) ISPy. B – TID Day – 8 June 2012 5

ISPy. B in 2012 • Important upgrade • ISPy. B data model extensions (Autoprocessing, ISPy. B in 2012 • Important upgrade • ISPy. B data model extensions (Autoprocessing, EDNA) • Jboss server 6. 0, EJBs 3 • Web services to communicate with BLC (MXCube) • Very near future • ISPy. B for MASSIF : • ISPy. B for Bio. Saxs • Development forge • http: //forge. epn-campus. eu/projects/ispyb ISPy. B – TID Day – 8 June 2012 6

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

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

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

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

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

How does it help? • Users • • Prepare Experiment at home (and not How does it help? • Users • • Prepare Experiment at home (and not waste time at the beamline) Remote tracking by colleagues at home Process experiment results back into the Home LIMS Long term tracking of experiments (stored in the database) • Communication between Users and ESRF Staff Nice crystal • 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 Low resolution ISPy. B – TID Day – 8 June 2012 12

How does it help? • Management and Operations • Dashboards for monitoring operations • 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 ISPy. B – TID Day – 8 June 2012 13

Ongoing Evolutions • Playback Centring and Grid Scanning integration • Data presentation (by project 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) • ISPy. B for Bio. Saxs ISPy. B – TID Day – 8 June 2012 14

UPBL 10 / MASSIF and ISPy. B • Current Workflow: Sequential Data Collection Pipeline UPBL 10 / MASSIF and ISPy. B • Current Workflow: Sequential Data Collection Pipeline • Receiving dewars • [ [ Screening / Online Data Analysis ]* / Ranking / Data Collection ]* • Returning dewars ISPy. B - Bio Struct Bio. SAXS meeting 22 May 2012 15

UPBL 10 / MASSIF and ISPy. B • Sample Sorting (*1) • Depends on UPBL 10 / MASSIF and ISPy. B • Sample Sorting (*1) • Depends on sample description (size, mounting, …) • Depends on beamline workload • 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) ISPy. B – TID Day – 8 June 2012 16

ISPy. B For Bio. SAXS • Features: • Sample tracking, experiment management and recording, ISPy. B For Bio. SAXS • Features: • Sample tracking, experiment management and recording, search and reporting and web interface as for MX beamlines • Developments: • Experiment recording: data model and GUI extensions for Bio. SAXS • Other modules: as it is in ISPy. B or with small customisations • Link with MX experiments and SANS experiments… ISPy. B – TID Day – 8 June 2012 17

Thanks to… Elspeth Gordon Stéphanie Monaco Sean Mc. Sweeney Gordon Leonard Gianluca Cioci Pernot Thanks to… Elspeth Gordon Stéphanie Monaco Sean Mc. Sweeney Gordon Leonard Gianluca Cioci Pernot Petra Adam Round Matthew Bowler Max Nanao ESRF ESRF EMBL Eric Fertin Thierry Caruana ESRF Markus Oscarsson Olof Svensson Darren Spruce Matias Guijarro Bernard Lavault ESRF EMBL Alun Ashton Martin Walsh Karl Levik Graeme Winter DLS/BM 14 DLS Patrice Brenchereau Marjolaine Bodin Alejandro De Maria Antolinos Ludovic Launer Emmanuel Eyer Christian Rolland Samuel Jones Luke Kirkpatrick Stephanie Veyrier ESRF - BIOStruct MRC/BM 14 ESRF Bio. Xhit … people I forgot to mention (sorry) … TID/MIS group for their technical support and kindness … and all users for their constructive feedbacks Questions… ISPy. B – TID Day – 8 June 2012 18

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

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

Experiment Recording • Items: • Session info (date, beamline name, operator, …) • Experiment Experiment Recording • Items: • Session info (date, beamline name, operator, …) • Experiment parameters (wavelength, energy, detector distance, …) • Beamline parameters (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 ISPy. B – TID Day – 8 June 2012 21

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

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

ISPy. B Technology • • • Pure Web Interface Java Jboss Application Server (Ejb) ISPy. B Technology • • • Pure Web Interface Java Jboss Application Server (Ejb) Struts (MVC Web Application Framework) My. Sql / Oracle Database Communication with User Portal (SMIS) via Web Services • Communication with BCM and EDNA • Through web Services ISPy. B – TID Day – 8 June 2012 24

Dewar Tracking ISPy. B – TID Day – 8 June 2012 25 Dewar Tracking ISPy. B – TID Day – 8 June 2012 25

ISPy. B Features & Modules • Experiment Management • Sample Management • Experiment Recording ISPy. B Features & Modules • Experiment Management • Sample Management • Experiment Recording • Search and Reporting ISPy. B – TID Day – 8 June 2012 26

Experiment Management • Items: • • Proposals Sessions (date, beamline, local contact) Lab Contacts Experiment Management • Items: • • Proposals Sessions (date, beamline, local contact) Lab Contacts (email, address, . . ) Proteins (approved sample sheets) • Features: • Data retrieved from the User Portal (SMIS) • Edit Lab Contact Card ISPy. B – TID Day – 8 June 2012 27

Sample Management • Items: • • Shipments (set of dewars) Dewars (barcode, courier tracking Sample Management • Items: • • Shipments (set of dewars) Dewars (barcode, courier tracking number) Containers (barcode) Samples (barcode, protein acronym, crystal form, …) • Features: • Online shipment description • Shipment description upload (Excel file) • Dewar Tracking ISPy. B – TID Day – 8 June 2012 28

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

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

Reporting for Managers Dashboard ISPy. B – TID Day – 8 June 2012 31 Reporting for Managers Dashboard ISPy. B – TID Day – 8 June 2012 31

Sample tracking and Data Flow Synchrotron Experiment Request Sample Information Home database (1) (2) Sample tracking and Data Flow Synchrotron Experiment Request Sample Information Home database (1) (2) Experiment Reports (5) User Portal SMIS database ISPy. B (5) (4) NICE disk storage Home disk storage User Information System BCM EDNA Control Softwares User Home laboratory Beamline Detector Sample Changer Experiment (5) Files(images , …) (3) Samples ISPy. B – TID Day – 8 June 2012 32

The data flow and application environment of ISPy. B The data flow and application environment of ISPy. B




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