The MEMOPS Programming Framework Wayne Boucher, Cambridge

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Presentation transcript:

The MEMOPS Programming Framework Wayne Boucher, Cambridge

Introduction CCPN: Collaborative Computing Project for NMR (Nuclear Magnetic Resonance) MEMOPS: MEtaMOdelling Programming System

NMR Software Problem –Heterogeneous collection of developers –Lots of stand-alone programs –Lots of proprietary data formats –Lots of conversion scripts Solution –Standards (production to deposition) –Libraries (open, modular, …)

Data Format vs. Model Data format (how data is stored) –STAR –XML –SQL –Tab-separated ascii –Python pickle file Data model (what data means) –RCSB (PDB) mmCIF –XML DTD or schemas –SQL schema

NMR Community Consensus Data model rather than data format –Format independent –Language independent –Science (descriptive) API to manipulate data model in memory –Creation and manipulation of objects –One for each language –Bookkeeping I/O modules to load/store data from/to disk –One for each (storage format, language) –Bookkeeping

Application View User Application 1 Data Store Application 2 Application 3 In Memory Representation GUI API I/O (Python, Java, C++, C) (XML, SQL)

Model Driven Architecture UML: Unified Modelling Language –Abstract representation of semantics –Pictorial Mapping from UML: to anything –Multi-language –Multi-format –Architecture neutral (e.g. distributed or not) Power: good and bad CCPN uses Object Domain as its UML tool –Python as scripting language

Framework Overview Information is stored in the UML data model from which –XML schema, –SQL schema, –Python and Java application program interfaces (APIs) and –Documentation are generated automatically PHYSICAL world UML data model Auto-generated Java API Python API Doc SQL schema CCPN framework XML schema

UML Example

MEMOPS UML MEMOPS only uses part of UML (logical model) Roughly equivalent to MOF subset of UML Influenced by XML –Parent classes (but not all links are parent-child) Influenced by SQL –Keys Modular (packages) Main focus is NMR but entire architecture is independent of NMR

Methodology Summary MetaModel: classes for defining semantics –E.g. MetaClass, MetaAttribute, MetaRole Model: instantiation of MetaModel classes –E.g. (Meta)Experiment API: classes which define semantics –E.g. Experiment Developer: instantiation of API classes

UML to API Stage 1: UML to MEMOPS Model –Currently script dependent on UML program –Eventually move to XMI Stage 2: MEMOPS Model to MEMOPS API –Script independent of UML program Most CCPN people work independently of UML

MEMOPS MetaModel Method of describing model semantics Implemented as Python classes –Could do same in Java, … –Independent of end language –Independent of actual model Hand coded Currently around 12 classes, 3000 lines –MetaPackage, MetaClass, MetaAttribute, …

MEMOPS Model Instantiation of MetaModel –Creation of MetaClass objects, … Might disappear with introduction of XMI Auto generated from UML Currently over 300 classes (2300 metaobjects) NMR main focus so far –Being worked on: protein production –In future: X-ray, … –Shared packages: Molecule, Coordinates, etc.

MEMOPS API Classes for developers –Mainly getters and setters –More than just code stubs –Constraints (e.g. cardinality) enforced –Links the hard part Mostly (> 99%) auto generated from UML –Some helper functions and constraints hand coded Currently around lines in Python and lines in Java

Developer Benefits Specified data model and API No I/O code Concentrate on science, not bookkeeping Extendible –Application data can be assigned to any object –UML model can be extended (packages) Notifiers –Register interest when specified attribute changes (class, not object, level) Undo/Redo (in future)

Current State API releases –  release of Python API in May 2003 –  release of Java API in December 2003 –C/C++ API next (probably 2005) Storage formats –XML with Python and Java –SQL with Java in April 2004, Python later Applications –Conversion scripts for legacy NMR data –Graphical NMR assignment program

Acknowledgements Department of Biochemistry, University of Cambridge –Rasmus Fogh –Tim Stevens European Bioinformatics Institute (EBI) –John Ionides –Anne Pajon –Wim Vranken Funding: BBSRC and EU (NMRQUAL and TEMBLOR) Website: