Interface and simulator for biological signaling pathways

Description

Kinetikit is an interface and utility for developing simulations of chemical kinetics. It is designed to be 'click and drag' and friendly to use.
Kinetikit currently simulates 'well stirred', that is, non-diffusive chemical reactions. It can simulate continuous (that is mass-action/ deterministic) descriptions of chemical reactions, as well as stochastic calculations. It uses the exponential Euler method for deterministic calculations and provides four different stochastic methods.
The main purpose of kinetikit is to allow users to scale up models to tens of pathways, hundreds of reactions, and thousands of parameters. As an example of such a simulation, see this paper.

The development of Kinetikit and related parts of GENESIS is carried out at the National Centre for Biological Sciences in collaboration with Prof. Ravi Iyengar at the Mount Sinai School of Medicine, New York, New York.

Development team:
Upinder S. Bhalla
Karan Vasudeva
Adithya Vasudevan