Welcome to the Cellontro Project
Cellontro models and simulates cells, other biological entities, and biochemical networks. Specify the structure and behavior of your models using XML and Java, and optionally using UML 2.0. Cellontro applications are built on top of the Xholon runtime framework, and Cellontro is now entirely contained within the Xholon project. Xholon features include SBML import and simple export to allow exchange of biochemical reaction models with other tools.
Between 1997 and 2000 I developed an early version of Cellontro using C++ and Rational Rose RealTime (originally called Objectime Developer, and now called IBM Rational Rose RealTime or IBM Rational Technical Developer).
In collaboration with Dr. Tony White, I have published a number of papers about this earlier version.
The primary focus in developing the initial releases has been on building a scalable framework that is capable of simulating large models. The simple Cell example (Glycolytic pathway) generates quantitative results that are very similar to those produced by corresponding Gepasi and Copasi models. Cellontro simulations are agent-based, and do not use ordinary differential equations (ODE). Agents execute within time steps, and interact with each other directly or through message passing. The Life example demonstrates that the simple Cell can be reused within a much larger model that includes over 20,000 active objects (agents), passive small molecule types, and containers.
See the download page for instructions on downloading Xholon and Cellontro.
Have a look at the sample applications that are included with Xholon.