Simulation code for GeneNetWeaver ODE model data fitting
Use this module to generate the data fitting results in the paper "From graph topology to ODE models for gene regulatory networks" by Kang et al.
- Install Python packages
pandas,numpy,scipy,lmfit, andmatplotlib. - Use
fit_synthetic(niter=100, tol=0.001)to generate data fitting result in row 1, column 1 of Table 4. - To generate other entries, modify the following options.
- For other columns, use
num_exp=<num_exp>, where<num_exp>is the number of experiments. - For the 2nd row, use
module_type_fit=[2, 4]. - For the 3rd row, use
col1a_activates_e1_fit=False. - For the 4th row, use
ode_func_fit=repressilator_ode. - For the 5th row, use
gen_net='brownian'.
- For other columns, use