I ISPyB

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Information System for Protein crystallography
Beamlines
I ISPyB II Pipeline scenario III Receive,
store, retrieve, export Information IV Interaction
s V Results and future plans
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Information System for Protein crystallography
Beamlines
Collaboration Joint development
DevelopersSolange DelageniereRicardo
LealDarren SpruceScientific InputS. Monaco
coordinates input from JSBG scientists
DevelopersLudovic LaunerE-HTPX
developershttp//www.e-htpx.ac.uk Scientific
adviceM. WalshM. NanaoJ.B ReiserH. Belrhali
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Information System for Protein crystallography
Beamlines
ISPyB (Information System for Protein
crYstallography Beamlines) is an information
management system which goal is to receive,
store, track and retrieve experiment related
information. Its scope of action ranges from
receiving sample and crystal related information
from home laboratories to exporting data
collection experiments back to the users. In a
typical scenario a user having crystals ready to
be shipped to a synchrotron has to prepare the
samples and keep track of the experiment related
information. To facilitate this step, a Personal
Digital Assistant (PDA) based software was
developed.
ISPyB is made of several modules each of them
performing a dedicated task. It gathers the
information from various sources and aggregates
it. It is beamline and user centric and is aiming
at improving the experimentalist work
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ISPyB

• Management of experimental data produced in
  protein crystallography
• Management of experiment related information
• (shipping of samples, beam time allocation,
  safety information)
• Tracking your progress through the experimental
  process
• Retrieves information from DataCollection
  automatically
• Stores both Beamline and Experimental information
• Allows disparate groups to monitor projects
• Communicates with other systems (Sample Changer,
  DNA, )
• Portable Interface (using PDA wireless
  DataMatrix reader) to track Samples
• User friendly web interface
• Custom interface and access restricted based on
  privileges
• Generates report

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Pipeline scenario
Protein and Crystalinformation
Sample and Shipmentinformation
ISPyB
Diffraction Plan
Screening, Indexing
Collect Diffraction Data
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ISPyB Submission of information
Automatic submission or User Interface

• 2 ways to submit information
• Webservice interaction with other systems
  (crystallography IS, PIMS, eHTPX Hub, )

lt?xml version"1.0" encoding"UTF-8"?gt ltSampleShee
t xmlnsxsi"http//www.w3.org/2001/XMLSchema-inst
ance" xsinoNamespaceSchemaLocation"./SafetySheet
.xsd"gt ltProposalgt ltRefNumbergt345lt/RefNumbergt
ltFinalNumbergtU345lt/FinalNumbergt lt/Proposalgt
ltSampleDescriptiongt
ltProteinNamegtSFGlt/ProteinNamegt
ltProteinAcronymgtSFG23blt/ProteinAcronymgt lt/SampleDe
scriptiongt .. lt/SampleSheetgt
http
http

• Web based user interface

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ISPyB Crystal and protein details
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ISPyB Shipment
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ISPyB Webservice or web based user interface

• Webservices available for
• Crystal details
• Shipment
• Diffraction and Screening plan
• Diffraction results

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Interactions with other projects
Experiment information Data Collection information
BCM (e.g. ProDC) drives SampleChanger Normal
operationAdvanced Strategy
Experiment Sample information
Protein Information Management System
http//www.pims-lims.org
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ISPyB Pipeline experiments, results and future
plans

• Alpha test users of e-htpx at BM14
• York, Oxford and Glasgow 26-9-05 to 30-9-05
• Pipeline tests on ESRF MX beamlines
• Pipeline tests on BM14 from 28-11-05 to 4-12-05

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Test results

• Sample data with barcodes entered using hub
• Data sent to ISPyB
• Samples brought in dewar on train/plane
• Samples loaded in sample changer
• Screening using DNA/ISPyB
• Autocentering
• Results in ISPyB

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Details of Pipeline success

• York 27 samples
• Oxford 16 samples
• Glasgow 17 samples
• In total 280 samples loaded by SC by the 3 groups
  during the tests no critical SC problem which
  would of caused sample loss occurred
• Real experiments performed by Glasgow and Oxford
  groups
• Glasgow screened 20 crystals of a single protein
  which allowed them to discover a crystal giving
  diffraction gt 0.95A (previous best was 1.4A which
  they collected at BM14 the previous evening
  before the SC was ready for testing they did not
  imagine to find a crystal going to 0.95A as they
  had characterized these crystals at home to
  diffract to 2 -2.5A)
• Oxford used the SC to screen for crystals of a
  protein-protein complex by using the SC they
  were able to screen through 30 samples in rapid
  fashion and found this a major advantage for the
  project
• All user groups very positive about the SC even
  if we did have small software/hardware hiccups!

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Detailed remarks from groups

• Submitting sample information needs to be more
  flexible (difficult?)
• Sample changer very good
• DNA auto-indexing weak point (central beam
  position?)
• Autocentering
• More crystals per project screened (unexpected
  success for Glasgow)
• ISPyB hampered by firewall, results visible
  locally and useful
• Much more testing needed with external user
  groups. This will provide essential feedback
• This can provide what we need desperately to
  provide us with the means to use beamtime more
  efficiently and also provide us with a platform
  for finding the best sample for a particular
  project

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Future project deadlines

• Beta testing of automation pipeline to continue
  with external UK based groups till end 2005
• External user groups scheduled for 28-11-05
  -1/12/05
• Internal testing of software and hardware (7 days
  without beam, 4 days with beam)
• ISPyB to become the default LIMS for MX beamlines
  at ESRF on 24th October 2005
• Complete automated pipeline predicted for first
  release in early 2006

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ISPyB associated
Collaboration to develop joint system
Solange DelageniereRicardo Leal Darren
SpruceDominique Porte MIS GroupLilian
CardonneMatias GuijarroOlof SvenssonJose
Gabadinho
Ludovic LaunerMartin WalshHugo CaserottoMax
NanaoJean_Baptiste ReiserHassan
Belrhali Laurent Geoffroy (Maatel)
Florent CiprianiFranck FelisazJean-Sebastien
Aksoy Bernard LavaultArnaud ClereJulien
HuetS. Cusack
eHTPX
eHTPX members and associated collaborations
David Stuart, Robert Esnouf Oxford, Colin Nave,
Rob Allan, Martyn Winn, Daresbury, Kim Henrick
EBI, Kevin Cowtan York, Martin Walsh
Grenoble DEVELOPERS Chris Mayo, Ian Berry
(Oxford) Graeme Winter, Ronan Keegan, David
Meredith (Daresbury) Joel Fillon (EBI), Paul
Young (York), Ludovic Launer (Grenoble)
BM14