| M&S tool |
Modeling Technique |
Spatial
Representation |
Temporal Evolution |
Reaction Model |
Comments & Availabilityq |
| Promot/DIVA |
00 paradigm |
Not explicity
defined |
Continuous time |
CCK |
http://megdeburg.mpg.de/de/
research/projects/1002/comp_
bio/promot |
| JARNAC |
ODE based |
Not explicity
defined |
Continuous time |
CCK |
http://www.sys-bio.org |
| V-Cell |
Continuous domain |
Compartments,
sub volumes |
Continuous time |
CCK, Mass action |
http://www.vcell.org |
| M-Cell |
Monte Carlo simulator of cellular micro physiology |
Off lattice |
Time-step driven |
At surfaces, CME |
http://www.mcell.pse.edu |
| E-Cell |
Object-oriented software suite for modeling,
simulation, and analysis of complex systems |
Compartmental |
Supports CCK/SSA |
CCK, CME |
http://www.e-cell.org |
| SimBiology |
Primarily ODE based simulation package |
Not explicity
defined |
Supports CCK/SSA |
CCK, CME |
The Math Works Inc. |
| Dizzy |
Stochastic simulation package |
Compartmental |
Supports CCK/SSA |
CCK, CME |
ISB, Sealtle, WA |
| Cellerator |
Mathematical package for automatic equation
generation and simulation for network of cells |
Not explicity
defined |
Continuous time |
CCK |
http://www.cellerator.info |
| Agent Cell |
Agent based simulation of biological systems |
Not explicity
defined |
Time-step driven |
Agents model
molecular behavior |
http://www.agentcell.org |
| FURM |
Functional unit representation of biological
processes |
Not explicity
defined |
Continuous time |
Functional modeling |
http://biosystems.ucesf.edu/
Research/furm/index.html |
Stochastic II
calculus |
Abstract model of system based on DEVs |
Cellular
compartments |
Continuous/discrete
time steps |
Processes model
molecules/domain,
communications
model reactions |
[30,31] |
Stochastic
Petrinets |
Stochastic model of molecular interactive networks |
Compartments |
Continuous/discrete
time steps |
Graphical model |
[26-28] |
Statecharts &
DEVS |
Discrete event system specification |
Distinction
between system
and environment |
Continuous/discrete
time steps |
Atomic models and
coupled models |
[32,33] |
| Smoldyn |
Atomistic modeling of biological processes with
dynamic membrane geometry |
Off lattice |
Inter-particle
collisions |
MD based |
http://genomics.lbl.gov/Sandrews/
software.html |
| CyberCell |
Atomistic modeling of biological processes with
dynamic membrane geometry |
Off lattice |
Inter-particle
collisions |
MD based |
http://projectcybercell.ca |
| MesoRD |
Stochastic domain |
Compartments,
sub volumes |
Event-driven |
CME |
http://mesord.sourgeforge.net |
| Our Simulator |
Stochastic modeling of discrete events |
Compartmental |
Event driven discrete
time steps |
Based on CME,
explicit models |
Event-time distributions drive the
simulation |
