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

2. 2 2001.04.15CSI JAMME Proposal for NIGMS Program 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.

3. 3 2001.04.15CSI JAMME Proposal for NIGMS Program 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.

4. 4 2001.04.15CSI JAMME Proposal for NIGMS Program 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

5. 5 2001.04.15CSI JAMME Proposal for NIGMS Program JSIM Architecture

6. 6 2001.04.15CSI JAMME Proposal for NIGMS Program 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

7. 7 2001.04.15CSI JAMME Proposal for NIGMS Program 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

8. 8 2001.04.15CSI JAMME Proposal for NIGMS Program Moulage Base Components Inspector: analysis, application DataObject: data IOController: IO operations DataObjectManager: database Translator: file to/from object textual data binary data remote data 0111010101 0101011... Translator DataObject DataObjectManager IOController 1 2 3 4 Analysis / Application (Inspector)

9. 9 2001.04.15CSI JAMME Proposal for NIGMS Program 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)

10. 10 2001.04.15CSI JAMME Proposal for NIGMS Program Integration Overview Start with JSIM JSIM

11. 11 2001.04.15CSI JAMME Proposal for NIGMS Program Integration Overview - Moulage Enhance by adapting to Moulage JSIM Analysis MML Data IO

12. 12 2001.04.15CSI JAMME Proposal for NIGMS Program Integration Overview - Metagraph Enhance by creating Metagraph Data Structures JSIM Analysis MML Data IO

13. 13 2001.04.15CSI JAMME Proposal for NIGMS Program Integration Overview - ODB Enhance by adding new object database JSIM Analysis IO

14. 14 2001.04.15CSI JAMME Proposal for NIGMS Program Integration Overview - ODBMS Enhance by allowing distributed database processing of analysis JSIM Analysis IO Analysis ODBMS

15. 15 2001.04.15CSI JAMME Proposal for NIGMS Program Integration Overview - Result Resulting in a set of reusable components Analysis IO Analysis ODBMS JAMME T-Cell Modeling Query Engine ‘X’