1. Solange Delageniere ESRF/TID/MIS
Bio Struct BioSAXS meeting
May 22,
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 What is ISPyB? Tracking, experiments, samples, data flows…
Features : how can it be adapted to BioSaxs ?
Architecture
How does it help?
Ongoing Evolutions
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

3. What is ISPyB?
ISPyB: Information System for Protein CrystallographY Beamlines
Laboratory Information Management System (LIMS) for protein crystallography experiments on synchrotron beamlines
Web based interface
Access
To log-in: ESRF experiment number and password
Where is it used at the ESRF?
ID14-1, ID14-4
BM29 very soon ! (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 2005-2011: ISPyB Python/Zope, MySql
JSBG Project (ESRF/EMBL)
Experiment logging for MXPress users (FX users)
: ISPyB
Java/Struts/Jboss, Mysql
ESRF/Spine/Bioxhit and BM14/MRC/eHTPX collaboration
Pxweb features + new features + Dewar Tracking
2009: Collaboration with Diamond (code sharing)
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

6. ISPyB in 2012 Important upgrade Very near future Project management
ISPyB data model extensions (Autoprocessing, EDNA)
Jboss server 6.0, EJBs3
Web services to communicate with BLC (MXCube)
Very near future
ISPyB for MASSIF :
ISPyB for BioSaxs
Project management
Scientist project leader : Elspeth Gordon
Software project leader : Solange Delageniere
Meeting and video conference with Diamond Light Source
Development forge
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

7. ISPyB Features & Modules
Experiment Management
Sample Management
Experiment Recording
Search and Reporting
Ready for BioSaxs ?
To be customized for BioSaxs ?
To be developed for BioSaxs
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

8. Experiment Management
Ready
Experiment Management
Items:
Proposals
Sessions (date, beamline, local contact)
Lab Contacts ( , address,..)
Proteins (approved sample sheets)
Features:
Data retrieved from 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. Sample Management To be customized Items: Features:
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
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

11. Creating Shipments Ready Shipment Creation
Shipment Description (Excel)
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: To be customized To be developed
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
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

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

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

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

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

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

19. ISPyB Data Model To be customized
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 Communication between Users and ESRF Staff
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 Safety
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 MASSIF project ISPyB for BioSaxs
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: Developments:
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 BioSAXS
Other modules: as it is in ISPyB or with small customisations
Link with MX experiments and SANS experiments…
ISPyB - Bio Struct BioSAXS meeting 22 May 2012

27. Thanks to… Questions… Elspeth Gordon ESRF Stéphanie Monaco
Sean McSweeney
Gordon Leonard
Gianluca Cioci
Pernot Petra
Adam Round
EMBL
Matthew Bowler
Max Nanao
Martine Moroni
Serges Ronseaux
Thierry Caruana
Eric Fertin
Markus Oscarsson
Olof Svensson
Darren Spruce
Matias Guijarro
Bernard Lavault
Alun Ashton
DLS
Martin Walsh
DLS/BM14
Karl Levik
Graeme Winter
Patrice Brenchereau
ESRF
Marjolaine Bodin
Alejandro De Maria Antolinos
ESRF - BIOStruct
Ludovic Launer
MRC/BM14
Emmanuel Eyer
Christian Rolland
Samuel Jones
Luke Kirkpatrick
… people I forgot to mention (sorry)
… TID/MIS group for their technical support and kindness
… and all users for their constructive feedbacks
Questions…
ISPyB - Bio Struct BioSAXS meeting 22 May 2012