Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

We describe a multiset of agents based modeling and simulation paradigm for synthetic biology. The multiset of agents -based programming paradigm, can be interpreted as the outcome arising out of deterministic, nondeterministic or stochastic interaction among elements in a multiset object space, that includes the environment. These interactions are like chemical reactions and the evolution of the multiset can emulate the system biological functions. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward equilibrium or emergent state. Practical realization of this paradigm for system biological simulation is achieved through the concept of transactional style programming with agents, as well as soft computing (neural- network) principles. Also we briefly describe currently available tools for agent-based-modeling, simulation and animation.