This is a tool for the identification of unknown rate parameters of chemical reaction networks.

The approach was presented in the article Adaptive moment closure for parameter inference of biochemical reaction networks in BioSystems, 2016. See below for how to cite this work.

Installation

You need to have Matlab.

We use the following libraries:

• StochDynTools
• SUNDIALS (which provides CVODE, an optional but much faster solver of ordinary differential equations)

We deploy the libraries, but it may be necessary to install them anyway.

Run

Initialization

Open Matlab. Run init at the beginning of each session.

Running a model or benchmarks

There are some model scripts in the folder examples/. Just run them with runX, where X is the model/folder name.

There are also some benchmark scripts in the folder functions/benchmarks/.

Citation

@article{SchillingBHPR16,
  author    = {Christian Schilling and
               Sergiy Bogomolov and
               Thomas A. Henzinger and
               Andreas Podelski and
               Jakob Ruess},
  title     = {Adaptive moment closure for parameter inference of biochemical reaction
               networks},
  journal   = {Biosyst.},
  volume    = {149},
  pages     = {15--25},
  year      = {2016},
  url       = {https://doi.org/10.1016/j.biosystems.2016.07.005},
  doi       = {10.1016/j.biosystems.2016.07.005}
}