R and Python packages for ODE models of biochemical reaction networks: simulation with sensitivities, parameter estimation and structural identifiability analysis.
| Package | What it does |
|---|---|
| dMod2 R |
Models, objectives, optimisers and profile likelihoods for ODE models; PEtab import and export. Successor to dMod. |
| cppDE R, C++ |
Generated C++ for ODE integration with forward and reverse sensitivities to second order, events and switches; the backend of dMod2. |
| symident Python, C++ |
Structural identifiability by Lie symmetries over finite fields, with reduction to identifiable parameters. Documentation |
# install.packages("remotes")
remotes::install_github("dModverse/cppDE")
remotes::install_github("dModverse/dMod2")pip install symidentMaintainer: Simon Beyer, University of Freiburg, simon.beyer@fdm.uni-freiburg.de.
Please report bugs and requests for further functions as issues in the repository concerned, or by e-mail.
dMod was created by Daniel Kaschek; dMod2 builds on its design.
