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 30, 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.
A Python Framework for Modeling and Analysis of Signaling Systems
The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
Ecosystem of Machine-maintained Models with Automated Analysis
LibSBMLSim: A library for simulating SBML models
Patient-Specific Modeling in Python
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
LibSBMLSim: A library for simulating SBML models (Version 2)
A text-based computational framework for patient -specific modeling for classification of cancers. iScience (2022).
DMS1401ZB Mathematical Systems Biology
Matlab code and data for Enzyme Cost Minimisation
A package for researchers working with biological oscillations
Code and models for Flux-balance Enzyme Cost Minimization (fECM)
An efficient Java™ solver implementation for SBML
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal.
Metabolic Network Toolbox for MATLAB
Lecture SS 2022 - Introduction to various topics in Systems Biology
Matlab code for Metabolic Economics calculations
Spatial Model Simulator with SBML Model
Julia interface to BioMASS
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