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CCPN project modeling framework University of Cambridge European Bioinformatics Institute MSD group.

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Presentation on theme: "CCPN project modeling framework University of Cambridge European Bioinformatics Institute MSD group."— Presentation transcript:

1 CCPN project modeling framework University of Cambridge European Bioinformatics Institute MSD group

2 Contents CCPN goals Data Modeling machinery Data standards for Structural Biology

3 CCPN Goals Make data exchange standard (for macromolecular NMR) Promote software integration in the image of CCP4

4 Context Exchange standard (ontology), –Not freely modifiable –Wide adoption across independent projects Data, not documents –Work-in-progress data for applications

5 Requirements Lossless data exchange between programs Data harvesting (including intermediate data) Precise, verifiable format specification Long-term maintainability Attractive to adopt

6 Strategy Abstract data model for contents (UML) The standard is the API (TN Bhat) –Model can be modified without breaking code Model is normalised Multiple storage formats (XML, databases) Multiple programming languages Maximum functionality Automatic code generation

7 User Documentation Application Deposition APIs Python Java C Perl Storage SQL XML Handcoded(1%) UML Model Package 1 Package 2 Package 3 autogeneration Domain Experts MEMOPS framework Program Developers

8 Contents CCPN goals Data Modeling machinery Data standards for Structural Biology

9 Generating Machinery UML ObjectDomain Rational Rose … Model.py MetaModel.py Api.py XmlIO.py Documentation.html Xml Schema DatabaseIO.java Database Schema Python Objects

10 Generation Machinery Content independent Fully automatic All information taken from UML

11 API Implementation Objects with links Functions: set, get, add, remove, new, delete –Custom functions can be added in model Full validity checking –Arbitrary complex constraints –You cannot add invalid data Transparent storage handling Extension for program-specific data Support for GUI (notifiers)

12 Status Python/XML API 1.0 –350 Classes – lines Python, lines html –In use for large, released applications Java/SQL, Java/XML 0.x –Functional, development use in HALX/PIMS Future –C/C++, PERL?, FORTRAN? –Client/Server, Access Control, Transaction/rollback

13 Contents CCPN goals Data Modeling machinery Data standards for Structural Biology

14 Molecule Sequence NMR Citations Nuclei and Isotopes Experimental Protocols Organisms, Taxonomy CcpNmr Programs Compound Source Structure Targets Compound Preparation Project Tracking Crystallization -Xray Crystallography Structure and Coordinates Residue Template Molecular System Reference Molecule PIMS Samples Data Model Contents

15 Collaborative model Interlocking packages shared between fields Different groups model different fields Copyright follows content

16 Availability CCPN project is on SourceForge Licenses: Generation framework (Memops): GPL Model and libraries (CCPN, PIMS) : LGPL

17 Contributors Core - University of Cambridge Rasmus Fogh, Wayne Boucher, Tim Stevens, Ernest Laue Core - MSD group (EMBL-EBI) John Ionides, Anne Pajon, Wim Vranken, Kim Henrick

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