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MyersResearchGroup / iBioSim

iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
http://www.async.ece.utah.edu/ibiosim
Apache License 2.0
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FEATURE: combine ODE and Monte Carlo methods #1

Open buggsley opened 7 years ago

buggsley commented 7 years ago

Monte Carlo methods currently use an Euler style update for continuous dynamics. Should add support for other ODE update methods to create a variety of hybrid simulators.

buggsley commented 7 years ago

This can be done by having the waiting time computed using the following equation:

\int_t^{t+\tau} \alpha_0(t)dt + log(p1) = 0

where p1 is a random number and you solve for \tau.

buggsley commented 7 years ago

When you reach \tau, find reaction as follows:

\Sum_{i=1}^{k-1} \alpha_i(t+\tau) < p2 * \alpha0(t+\tau) <= \sum{i=1}^k \alpha_i(t + \tau)

buggsley commented 7 years ago

This is being done by Leandro's Java simulator.