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Java Adaptive Mathematical Modeling Engine (JAMME)

Java Adaptive Mathematical Modeling Engine (JAMME). Leeland Artra, Cell Systems Initiative (CSI) Zheng Li, Department of Bioengineering University of Washington, Seattle. Introduction of JAMME.

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Java Adaptive Mathematical Modeling Engine (JAMME)

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  1. Java Adaptive Mathematical Modeling Engine(JAMME) Leeland Artra, Cell Systems Initiative (CSI) Zheng Li, Department of Bioengineering University of Washington, Seattle

  2. Introduction of JAMME • Proposed collaborative project between NSR (National Simulation Resource for Circulatory Mass Transport and Exchange NIH/NCRR) and CSI to provide a complete software & database environment for real time biological modeling. • Integration of NSR’s JSIM model simulation environment with CSI’s Moulage System framework, Metagraph data representation model, and a new object database management system. CSI JAMME Proposal for NIGMS Program

  3. Background (available software at NSR and CSI) • JSIM is an integrative model simulation environment being developed at NSR. • Moulage is a real time data sharing & analysis system framework. • Metagraph is a code name for a data and process representation language used to describe structures and methods that capture a computerized abstraction of the scientific process. • The new object database management system being developed at CSI. Its primary goal is to provide a dynamic data engine that can handle complex hyper-graph / XML / Metagraph queries directly. CSI JAMME Proposal for NIGMS Program

  4. JSIM Design Goals • Easy-to-use end-user interface. Low barriers to entry of math modelling for biologically-inclined users. • Facilitate collaborative model development (integration) • Integration at mathematical level. • Integration at component level. (“Plug-and-play”). • Connectivity to heterogeneous data sources. • Facilitate collaborative software development. • Facilitate distributed-computing. • Flexibility and Extensibility at all levels • math model classes and representations • hierarchical component libraries • numeric libraries CSI JAMME Proposal for NIGMS Program

  5. JSIM Architecture CSI JAMME Proposal for NIGMS Program

  6. Items Needed By JSIM • Persistence Engine • Intelligent Distributed Analysis Engine • Visual Programming Ability • Ability to Import Various Modeling Data • Ability to Directly Interface With Experiment Data CSI JAMME Proposal for NIGMS Program

  7. Moulage Design Goals Create a development framework that automatically can provide: • Transparent access • Ability to accept multiple data sources • Easy sharing of data • Data in form usable by object-oriented databases • Multiple tools for analysis • Dynamic version distribution CSI JAMME Proposal for NIGMS Program

  8. Moulage Base Components IOController • Inspector: analysis, application • DataObject: data • IOController: IO operations • DataObjectManager: database • Translator: file to/from object Translator textual data DataObjectManager binary data 0111010101 0101011... DataObject remote data 4 3 2 1 Analysis / Application (Inspector) CSI JAMME Proposal for NIGMS Program

  9. JAMME Approach • 100% Core Java • Any needed classes built directly from on the 1.2 core • Carefully engineered to work within the Java Virtual Machine constraints • Allow operation as • Stand alone application • Command line utility (batch processing) • Applet (Web and Email integration) CSI JAMME Proposal for NIGMS Program

  10. Integration Overview • Start with JSIM JSIM CSI JAMME Proposal for NIGMS Program

  11. Integration Overview - Moulage • Enhance by adapting to Moulage Analysis JSIM MML Data IO CSI JAMME Proposal for NIGMS Program

  12. Integration Overview - Metagraph • Enhance by creating Metagraph Data Structures Analysis JSIM MML Data IO CSI JAMME Proposal for NIGMS Program

  13. Integration Overview - ODB • Enhance by adding new object database Analysis JSIM IO IO CSI JAMME Proposal for NIGMS Program

  14. Integration Overview - ODBMS • Enhance by allowing distributed database processing of analysis Analysis JSIM IO IO ODBMS Analysis Analysis Analysis CSI JAMME Proposal for NIGMS Program

  15. Integration Overview - Result • Resulting in a set of reusable components JAMME Analysis T-Cell Modeling IO IO ODBMS Analysis Analysis Analysis Query Engine ‘X’ CSI JAMME Proposal for NIGMS Program

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