Sunwoo Park 1 and C. Anthony Hunt 1,2

1. BioDEVS: System-Oriented, Multi-Agent, Disttributed/Parallel Framework for Modeling and Simulation of Biomimetic In Silico Devices July 25, 2004 • Sunwoo Park1 and C. Anthony Hunt1,2 BioSystems Group, Department of Biopharmaceutical Sciences1, and Joint UCSF/UC Berkeley Bioengineering Graduate Program1,2, University of California, San Francisco, CA

2. 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

3. “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 In Silico Perfused Rat Liver For more information :

4. 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

5. DEVS Formalism: Atomic • Describes dynamic and temporal behaviors of a system • Consists of a set of I/O interfaces, states, temporal behaviors, and time management schemes

6. 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

7. Hybrid Systems Construction • System Level • Differential Equation System • Discrete Time System • Discrete Event System • Formalism Level • Finite State Automata • Bond Graph • etc. • Trajectory Level

8. 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

9. BioDEVS M&S Framework * In Silico Device (ISD): an artifact constructed in software Biomimetic In Silico Device (BD): an ISD which mimics biology

10. 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

11. BioDEVS Simulation • Provides high-performance distributed/parallel BD execution environment • Supports fully automated simulation life cycle with • Cost-based hierarchical partitioning • Automatic BD deployment • Remote simulator activation • Self-communication channel setup • Generic M&S naming directory service

12. 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

13. Q&A