graph-ode

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.

1. Install Python packages pandas, numpy, scipy, lmfit, and matplotlib.
2. Use fit_synthetic(niter=100, tol=0.001) to generate data fitting result in row 1, column 1 of Table 4.
3. 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'.