BioDEVS: System-Oriented, Multi-Agent, Disttributed/Parallel Framework for Modeling and

Simulation of Biomimetic In Silico Devices

Sunwoo Park1 and C. Anthony Hunt1,2

July 25, 2004

BioSystems Group, Department of Biopharmaceutical Sciences1, and Joint UCSF/UC Berkeley Bioengineering Graduate Program1,2,

University of California, San Francisco, CA

Take-Home Messages

BioDEVS is a computational environment that supports modeling, simulation, and visualization of biological systems

BioDEVS provides very powerful modeling techniques for in silico biological systems construction in terms of structural, temporal, and behavioral aspects

BioDEVS supports distributed/parallel simulation infrastructure that runs in silico models faster and more efficiently

BioDEVS minimizes efforts required to run in silico models in high perforamnce computing environment by achieving fully automated simulation life cycle

In Silico Perfused Rat Liver

For more information :“A Novel Agent-Based Approach to Simulating Leukocyte-Venule Interactions,” Jon Tang, C. Anthony Hunt, Jason Mellein, and Klaus Ley

“Biomimetic In Silico Devices For Linking Genotype to Phenotype,” Li Yan, C. Anthony Hunt, Glen E.P. Ropella, and Michael S. Roberts

Discrete Event System Specification

A mathematical formalism providing a means of specifying a system and a network of systems

Modular and hierarchical model structure

Supports hybrid system construction

Discrete event oriented modeling and simulation (M&S) methodology

DEVS Formalism: Atomic

Describes dynamic and temporal behaviors of a systemConsists of a set of I/O interfaces, states, temporal behaviors, and time management schemes

DEVS Formalism: Coupled

Describes structural relationship and event propagation between components of a system*Consists of a set of I/O interfaces, components, and couplings**

* A component can be an atomic or a coupled system** A coupling specifies one-directional event propagation from an event producer to a set of event consumers

Hybrid Systems Construction

System LevelDifferential Equation System

Discrete Time System

Discrete Event System

Formalism LevelFinite State Automata

Bond Graph

etc.

Trajectory Level

BioDEVS

A computational environment for modeling, simulation, and visualization of biological systems and their behaviors

Supports DEVS-based system-oriented, multi-agent, and hybrid modeling

Fully automated high performance simulation infrastructure

High quality 3D visualization and animation

Self-evolving and configurable model repository system

BioDEVS M&S Framework

* In Silico Device (ISD): an artifact constructed in softwareBiomimetic In Silico Device (BD): an ISD which mimics biology

BioDEVS Modeling

Elucidates the structural, temporal, and behavioral properties of biological systems

System-oriented BD construction

Multi-agent-based BD construction

Hybrid BD construction

Extends DEVS formalism to support Biological behavior formal representation

Biological system evolution and adaptation

BioDEVS Simulation

Provides high-performance distributed/parallel BD execution environment

Supports fully automated simulation life cycle with Cost-based hierarchical partitioning Automatic BD deploymentRemote simulator activationSelf-communication channel setupGeneric M&S naming directory service

Conclusion

BioDEVS is a computational environment that supports modeling, simulation, and visualization of biological systems

BioDEVS provides very powerful modeling techniques for in silico biological systems construction in terms of structural, temporal, and behavioral aspects

BioDEVS supports distributed/parallel simulation infrastructure that runs in silico models faster and more efficiently

BioDEVS minimizes efforts required to run in silico models in high perforamnce computing environment by achieving fully automated simulation life cycle

Q&A