Kinetikit
Interface and simulator for biological signaling pathways.
Click to see full-screen dump of kinetikit
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.
Downloading GENESIS and Kinetikit.
Example models using kkit.
Database of signaling pathways.
Stochastic methods in Kinetikit.
Kinetikit manual.
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
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