Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

Julia interface to the Systems Biology Markup Language (SBML) library

Finite State Projection algorithms for chemical reaction networks

LikelihoodProfiler is a Julia package for practical identifiability analysis and confidence intervals evaluation.

DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays

Package for modeling glycolysis activity

Interface between the Systems Biology Markup Language and Julia

Network inference for gene expression using gradient matching. Final research project as part of the MSc in Bioinformatics and Theorectical Systems Biology at Imperial College London 2016/2017.

Parameter Estimation of ODE/DDE Models in Julia

Developed a registered Julia package which quantifies the redundancies in genome-scale metabolic networks and provides local sparse certificates which are both efficiently verifiable and interpretable

A package for researchers working with biological oscillations

This package simplifies evolutionary algorithms for applications in systems biology. It can be used to generate oscillating reaction networks, networks that match input timeseries data, or fit parameters (rateconstants).

Imoto, H. & Okada, M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100–108 (2019).

General tools for gene regulatory circuits modeling.

Julia interface to BioMASS

Reconstruct a Transcriptional Regulatory Network using the principle of Maximum Entropy.

Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024 (2016).