Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
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Updated
May 31, 2024 - Julia
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Finite State Projection algorithms for chemical reaction networks
CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
A package for researchers working with biological oscillations
LikelihoodProfiler is a Julia package for practical identifiability analysis and confidence intervals evaluation.
Package for modeling glycolysis activity
DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
Julia interface to the Systems Biology Markup Language (SBML) library
Julia interface to BioMASS
Parameter Estimation of ODE/DDE Models in Julia
General tools for gene regulatory circuits modeling.
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.
Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024 (2016).
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).
Reconstruct a Transcriptional Regulatory Network using the principle of Maximum Entropy.
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