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