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TRANSCRIPT
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http://www.ebi.ac.uk/msd
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Click to see attributes
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MSD deposition database
MSD search database
MSD production database
UniProt database
Taxonomy database
Residue mappingWeekly
Update By MSD
IncrementalUpdate
PDB weeklyUpdate
BiweeklyOracle Update
load
load
Mapping update
views
Direct bi-directional exchange via Oracle
MSD-UniProtSequence mapping
DBREF analysis
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Protein Production
CrystallisationData Collection Phasing
Protein Structure
DepositionStructure analysis
TargetSelection
Overview of Protein Crystallography
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The PLAYERS
SPINE
THE BIG PLAYERS – THE SYNCHROTRON STAFF
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Dependencies & Standards are between independent packages
Olof Svensson
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Towards automation with CCP4
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An e-science resource for high throughput protein crystallography
www.e-htpx.ac.uk
e-HTPX
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Java API to read/write/validate XML
Documentation available at:
– http://www.ebi.ac.uk/msd-srv/docs/ehtpx/fillon/api/
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Web-based user interface Linux/Apache/PHP/PostgreSQL View your plates/crystals View individual wells
Slide-show, Zoom/Measure modes Time courses Optional email notification of imaging
OPPF & Crystallogenesis
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UML Technology:Models, Views, and Diagrams
Use CaseDiagramsUse Case
DiagramsUse CaseDiagrams
ScenarioDiagramsScenario
DiagramsCollaborationDiagrams
StateDiagramsState
DiagramsComponentDiagrams
ComponentDiagramsComponent
DiagramsDeploymentDiagrams
StateDiagramsState
DiagramsObjectDiagrams
ScenarioDiagramsScenario
DiagramsStatechartDiagrams
Use CaseDiagramsUse Case
DiagramsSequenceDiagrams
StateDiagramsState
DiagramsClassDiagrams
ActivityDiagrams
Models
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Sequence Diagram of the events
ScenarioDiagramsScenario
DiagramsStatechartDiagrams
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causal graph
ActivityDiagrams
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•At SOLEIL – Andy Thompson, D. Dalle, M. Ounsy, E. Girard, P, Legrand, L. Roussier, P. Gourhant, R. Fourme, M. Idir, T. Moreno, O. Chubar.
•At ESRF – O. Svensson, O. Hignette, M. Walsh, W. Shepard.
•At IRISA, Rennes – S. Robin, R. Quiniou, M-O. Cordier.
•At INRA, Narbonne – J-P. Steyer.
Beamline model
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PXWEB Protein sample information is stored in MySQL
database allows users to link this information via BCM ProDC
Users van view/edit reports generated from data collections
Search data base for previous experiments Further development
transferred to ISPyB as a joint e-HTPX/ESRF project
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Info. On current Basket + Sample
Sample Changer Graphical User Interface
Graphical representation
of Basket + Basket Selector
position
Log of events
Hardware status Change current position
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ISPyB Progress to date
Data model developed Implementation of sample tracking to/from beamline Linking of crystallization database information to ISPyB
through mobile PDA
Information System for Protein crystallography Beamlines
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PIMS
BBSRC Partners
Kim Henrick European Bioinformatics Institute
Colin Nave CCLRC Daresbury Laboratory
Keith Wilson The University of York
Dave Stuart Oxford Protein Production Facility
Martyn Winn CCP4
Alun Ashton Diamond Light Source Ltd
EU/HALX Partners
Anne Poupon CNRS – Université Paris-Sud
SPORT Consortia
Jim Naismith The University of St. Andrews
Neil Isaacs The University of Glasgow
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Commercial Individual Step Packages
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Project Management
All Projects have competing constraints
Time, Costs and Functionality
Constraints management – key to success
Must Have
Should Have MoSCow
Could Have
Some requirements may slip to meet constraints
Pareto Principle
80% benefit achieved with 20% of effort
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How far do you go………and when do you stop!
SymptomA: Excessive data modeling A: People don’t return your phone callsA: New requests and innovations are sending you
back to the drawing board Diagnosis:
Advanced analysis paralysis
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The Cure for Advanced analysis paralysis
Remember why we’re doing this? To have a picture of where we are goingTo be able to scope out the next projectTo understand the costs in enough detail to get to the
next stageTo be able to communicate internally and externally
When you’re there, STOP Get STARTED
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Further Standardisation Efforts
REFERENCE DATAExamples: solutions.xml inclusion.xml detergents.xml buffers.xml screen.xml well.xml
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Analytical Data: A Tower of Babel
0 20 40 60 80 100 120 140 160 180 200 Mass (m/z)
MSMS
12 11 10 9 8 7 6 5 4 3 2 1 0 Parts Per Million
NMRNMR 4000 3500 3000 2500 2000 1500 1000 Wavenumber (cm-1)
IRIR
.389
.863
1.24
4
1.92
7
2.83
4
.5 1 1.5 2 2.5 3 3.5 Minutes
LCLC
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ANIML consortia of Waters, NIST, Shimadzu, GSK. Currently covers chromatography, MS, UV/VIS, IR and NMR. http://animl.sourceforge.net/
Defines the exchange of data defining, the sample-set, measurment data and audit trail. Evolved from Generalized Analytical Markup Language Hierarchy (GAML) for Analytical Instruments
There are specific technique definitions that include Nuclear Magnetic Resonance spectroscopy and Mass Spectroscpy. In addition the HUPO Proteomics Standards Initiative (PSI, http://psidev.sourceforge.net/) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification. PSI currenty develops standards for two key areas of proteomics, mass spectrometry and protein-protein interaction data, as well as a standardised general proteomics format.
An XML Data Model for Analytical Instruments
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2 parts : Selection of the window type with a left button bar
Targets Blueprints Workflow Protocols
Associated window
Eric Oeuillet & Anne Pajon
HALX/EBI
Protocols Editer
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Workflow
KEPLER
PTOLEMY II
TAVERNA
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ISPyB Ludovic Launer DBDesigner 4
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Enterprise Architect affordable object oriented CASE tool for the full development life-cycle.
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www.ebi.ac.uk/msd-srv/docs/workflow/
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Familiar Outline? Mortgage Industry
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ChemCore registration Registration Capture and Share
Chemical Data Flexible to support
additional data types and business rules
Extensive ability to search and view information captured by the system
Maintain Data Integrity Enforce Data Security
Flexible business rules can restrict access to data as necessary
Logging full history of changes to information
Based on well-established UNITY™ database system and Oracle
EMBL Chemical Genomics Core Facility
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Mobile Data Collection
Data Collection through the use of handheld devices
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What do molecular biologists
really really want?
Expectations are High!
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People with LCD’s sewn into their bodies and computers that harness the brains natural computing power
The BORG Solution for a research LIMS