Tutorial on

Using Fine-grained Agents to Simulate Biological Systems 

Part of the 2006 Spring Simulation Multiconference (SpringSim'06)
Agent-Directed Simulation 2006 (ADS'06)

Sponsored by:
The Society for Modeling and Simulation International (SCS)

Monday April 2, 2006
8:30am - 11:30am

Von Braun Center
Huntsville, AL

presented by
Glen E. Ropella

Tempus Dictum Inc.

Great strides have been made in methods for software and systems engineering for the modeling of man-made artifacts like bridges and missiles. We've reached the point in the discipline of simulation where there is a good spread of practitioners using home-grown systems and a spectrum of Off-The-Shelf tool kits. The discipline is not yet so advanced that a competent simulation cannot be generated from scratch. And it is not so primitive that a motivated researcher from any background cannot find a tool that will facilitate a large share of the work to construct a simulation. However, the modeling and simulation of biological phenomena mostly uses the former, artisan-oriented methods. Progress toward the latter, more formal methods justifiably lags simulation methods for man-made artifacts. The advent of complexity theory has brought focus on systems composed of many relatively simple elements interacting to create a complex whole, so-called Fine-grained Agent Based Systems (FABS). The simulation of such systems has given rise to specialized methods and tool kits. Since much of the motivation for complexity theory and FABS comes from biology, it is natural to apply these methods and tools to the simulation of biological systems. This tutorial will synoptically cover some FABS methods and tools in the context of simulating biology. It is intended to provide a foundation to help modelers decide which tools and methods to use when simulating particular systems. It will include brief descriptions of the Swarm-like tool kits (e.g. Swarm, Repast, Mason, JAS, etc.) and it will place them within the spectrum of more traditional tools and methods.

Biography: Glen Ropella has been working in modeling and simulation for over 13 years in many contexts. He got a B.S. in Applied Math from Texas A&M University and went to work in the Operations Analysis group at Lockheed Martin's Missiles and Fire Control in Texas where he built simulations of missiles, aircraft, and ground equipment. He then took a position at the Santa Fe Institute continuing the development of the Swarm simulation tool kit. After the first production release of Swarm, he co-founded SwarmCorp with Chris Langton and Doug Orr to provide fine-grained agent based simulation services to industry. He continues to provide these services as well as more traditional software and systems engineering through his new company Tempus Dictum. His latest efforts have focused on techniques for building artificial systems that exhibit the fundamental properties of robustness and plasticity seen in biological systems. This work has been done for Dr. C. Anthony Hunt's Biosystems Group at the University of California, San Francisco

Sponsored by The Society for Modeling and Simulation International
P.O. Box 17900
San Diego, California 92177
Phone 858-277-3888
Fax 858-277-3930
E-mail scs@scs.org

Return to SpringSim'06 Home Page

Return to SCS Home Page

Mission Membership Conferences Publications

Copyright 2006, SCS. All Rights Reserved.