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 9, 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.
Patient-Specific Modeling in Python
LibSBMLSim: A library for simulating SBML models
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
Ecosystem of Machine-maintained Models with Automated Analysis
Spatial Model Simulator with SBML Model
A text-based computational framework for patient -specific modeling for classification of cancers. iScience (2022).
LibSBMLSim: A library for simulating SBML models (Version 2)
Metabolic Network Toolbox for MATLAB
DMS1401ZB Mathematical Systems Biology
An efficient Java™ solver implementation for SBML
Matlab code and data for Enzyme Cost Minimisation
Parinsula is an interactive visual simulator of relatively isolated systems, which are a particular type of complex system.
Simulator for SBML Models
A package for researchers working with biological oscillations
Matlab code for Metabolic Economics calculations
Code and models for Flux-balance Enzyme Cost Minimization (fECM)
An SBML parser written in Rust.
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