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Presentation on theme: "Click to see attributes."— Presentation transcript:


2 Click to see attributes

3 MSD deposition database MSD search database MSD production database UniProt database Taxonomy database Residue mapping Weekly Update By MSD Incremental Update PDB weekly Update Biweekly Oracle Update load Mapping update views Direct bi-directional exchange via Oracle MSD-UniProt Sequence mapping DBREF analysis



6 Protein Production Crystallisation Data Collection Phasing Protein Structure Deposition Structure analysis Target Selection Overview of Protein Crystallography


8 Dependencies & Standards are between independent packages Olof Svensson

9 Towards automation with CCP4

10 An e-science resource for high throughput protein crystallography e-HTPX

11 Java API to read/write/validate XML Documentation available at: –

12 Web-based user interface Linux/Apache/PHP/PostgreSQL View your plates/crystals View individual wells Slide-show, Zoom/Measure modes Time courses Optional notification of imaging OPPF & Crystallogenesis

13 UML Technology: Models, Views, and Diagrams Use Case Diagrams Use Case Diagrams Use Case Diagrams Scenario Diagrams Scenario Diagrams Collaboration Diagrams State Diagrams State Diagrams Component Diagrams Component Diagrams Component Diagrams Deployment Diagrams State Diagrams State Diagrams Object Diagrams Scenario Diagrams Scenario Diagrams Statechart Diagrams Use Case Diagrams Use Case Diagrams Sequence Diagrams State Diagrams State Diagrams Class Diagrams Activity Diagrams Models

14 Sequence Diagram of the events Scenario Diagrams Scenario Diagrams Statechart Diagrams

15 causal graph Activity Diagrams

16 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

17 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

18 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

19 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

20 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

21 Commercial Individual Step Packages


23 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

24 How far do you go………and when do you stop! Symptom A: Excessive data modeling A: People dont return your phone calls A: New requests and innovations are sending you back to the drawing board Diagnosis: Advanced analysis paralysis

25 The Cure for Advanced analysis paralysis Remember why were doing this? To have a picture of where we are going To be able to scope out the next project To understand the costs in enough detail to get to the next stage To be able to communicate internally and externally When youre there, STOP Get STARTED

26 Further Standardisation Efforts REFERENCE DATA Examples: solutions.xml inclusion.xml detergents.xml buffers.xml screen.xml well.xml

27 Analytical Data: A Tower of Babel MS NMR IR LC

28 ANIML consortia of Waters, NIST, Shimadzu, GSK. Currently covers chromatography, MS, UV/VIS, IR and NMR. 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, 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

29 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



32 ISPyB Ludovic Launer DBDesigner 4

33 Enterprise Architect affordable object oriented CASE tool for the full development life-cycle.


35 Familiar Outline? Mortgage Industry

36 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

37 Mobile Data Collection Data Collection through the use of handheld devices

38 What do molecular biologists really really want? Expectations are High!

39 People with LCDs sewn into their bodies and computers that harness the brains natural computing power The BORG Solution for a research LIMS

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