Software

Codes for software programs and mathematical models developed by our research.

Mathematical models for biological oscillators

  • Phosphoswitch_Clock
    Mathematical models for mammalian circadian clock with the phosphoswitch (Mathematica). See Zhou, Kim et al, Mol Cell (2015) and Narasimamurthy R et al, PNAS (2018) for details.

Bayesian inference algorithms

Stochastic analysis

  • Feedme
    Matlab code for the calculation of exact moments of biochemical reaction networks with feed-forward structures. See Kim and Sontag, Reduction of Multiscale Stochastic Biochemical Reaction Networks using Exact Moment Derivation, PLoS Com Biol (2017) for details.
  • ASSISTER
    Matlab code for efficient and accurate simulations of stochastic biochemical systems containing rapid reversible binding reactions. See Song et al., Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities, PLoS Com Biol (2021) for details.
  • CASTANET
    Matlab code to analytically derive stationary distributions for a given stochastic biochemical reaction networks using network translation and propensity factorization based on chemical reaction network theory. See Hong et al., Derivation of stationary distributions of biochemical reaction networks via structure transformation, Commun Biol (2021) for details.

Causality Inference

Diagnosis for sleep disorders