Supplemental data for paper: "Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability"
Youfang Cao and Jie Liang
BMC Systems Biology 2008, 2:30
Please click below links to download
programs codes of programs
0. README
1. Generate state space: buildStateSpace, buildStateSpace2
2. Generate transition matrix: net2matrix
3. Compute steady state distribution: steadystate
4. Parse results of steadstate computation: parseResult-sstoggle (for toggle), parseResult-ssMAPK (for MAPK)
5. Others: ARPACK, Arpack++, SuperLU
Data of toggle switch
1. The model of toggle switch in SBML format [download mToggle.xml]
2. The initial conditions and enumerated state spaces for the statistics of the sizes of state space [download toggle-sssize.tar.gz]
3. The initial condition, enumerated state space, and computed transition matrix, and the result data file for the computation of steady state probability distribution of toggle switch under the given parameter set. [download toggle-ss.tar.gz]
Data of MAPK
1. The model of MAPK in SBML format. [download BIOMD28.xml]
2. The initial conditions and enumerated state spaces for the statistics of the sizes of state space. [download mapk-sssize.tar.gz]
3. The initial condition, enumerated state space, computed transition matrix, and the result data file for the computation of steady state probability distribution of the MAPK network under the given parameter set. [download mapk-ss.tar.gz]
Apr. 9, 2008