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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

Java Adaptive Mathematical Modeling Engine(JAMME)

Leeland Artra, Cell Systems Initiative (CSI)

Zheng Li, Department of Bioengineering

University of Washington, Seattle

introduction of jamme
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

background available software at nsr and csi
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

jsim design goals
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

jsim architecture
JSIM Architecture

CSI JAMME Proposal for NIGMS Program

items needed by jsim
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

moulage design goals
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

moulage base components
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

jamme approach
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

integration overview
Integration Overview
  • Start with JSIM

JSIM

CSI JAMME Proposal for NIGMS Program

integration overview moulage
Integration Overview - Moulage
  • Enhance by adapting to Moulage

Analysis

JSIM

MML Data

IO

CSI JAMME Proposal for NIGMS Program

integration overview metagraph
Integration Overview - Metagraph
  • Enhance by creating Metagraph Data Structures

Analysis

JSIM

MML Data

IO

CSI JAMME Proposal for NIGMS Program

integration overview odb
Integration Overview - ODB
  • Enhance by adding new object database

Analysis

JSIM

IO

IO

CSI JAMME Proposal for NIGMS Program

integration overview odbms
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

integration overview result
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