Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: systems-biology-simulation
SciML/Catalyst.jl
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Language: Julia - Size: 2.31 GB - Last synced: about 6 hours ago - Pushed: about 13 hours ago - Stars: 423 - Forks: 71
YangLab-um/BiologicalOscillations.jl
A package for researchers working with biological oscillations
Language: Julia - Size: 1.21 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 2
pasmopy/pasmopy
Patient-Specific Modeling in Python
Language: Python - Size: 5.08 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 16 - Forks: 6
draeger-lab/pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
Language: Jupyter Notebook - Size: 37.5 MB - Last synced: 26 days ago - Pushed: about 2 months ago - Stars: 12 - Forks: 5
biomass-dev/biomass
A Python Framework for Modeling and Analysis of Signaling Systems
Language: Python - Size: 25.9 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 24 - Forks: 12
jwdietrich21/cyberunits
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.
Language: Pascal - Size: 826 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 1
creativequotient/mathsysbio
DMS1401ZB Mathematical Systems Biology
Language: Jupyter Notebook - Size: 831 KB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 4
draeger-lab/SBSCL
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.
Language: HTML - Size: 237 MB - Last synced: 4 months ago - Pushed: 10 months ago - Stars: 20 - Forks: 12
libsbmlsim/libsbmlsim
LibSBMLSim: A library for simulating SBML models
Language: C - Size: 33.6 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 13 - Forks: 7
pasmopy/breast_cancer
Imoto et al., A text-based computational framework for patient -specific modeling for classification of cancers. iScience 25, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944
Language: Python - Size: 302 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 5
biomass-dev/BioMASS.jl
Julia interface to BioMASS
Language: Julia - Size: 1.66 MB - Last synced: 8 days ago - Pushed: 12 months ago - Stars: 0 - Forks: 2
gyorilab/emmaa
Ecosystem of Machine-maintained Models with Automated Analysis
Language: Python - Size: 45.5 MB - Last synced: 11 days ago - Pushed: 11 months ago - Stars: 10 - Forks: 10
NeuraXenetica/parinsula
Parinsula is an interactive visual simulator of relatively isolated systems, which are a particular type of complex system.
Language: ASP.NET - Size: 88.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0
liebermeister/metabolic-network-toolbox
Metabolic Network Toolbox for MATLAB
Language: MATLAB - Size: 2.94 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1
Spatial-Systems-Biology-Freiburg/2022-SS-Intro-Sys-Bio
Lecture SS 2022 - Introduction to various topics in Systems Biology
Language: TeX - Size: 31.5 MB - Last synced: 4 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1
draeger-lab/SBMLsimulator
An efficient Java™ solver implementation for SBML
Language: Java - Size: 318 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1
libsbmlsim/sbml-sim
Simulator for SBML Models
Language: Rust - Size: 3.84 MB - Last synced: 24 days ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0
liebermeister/enzyme-cost-minimization
Matlab code and data for Enzyme Cost Minimisation
Language: HTML - Size: 2.72 MB - Last synced: 12 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 3
libsbmlsim/sbml-rs
An SBML parser written in Rust.
Language: Rust - Size: 94.7 KB - Last synced: 28 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
liebermeister/metabolic-economics
Matlab code for Metabolic Economics calculations
Language: MATLAB - Size: 271 KB - Last synced: 12 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1
liebermeister/resource-balance-analysis
Matlab code for resource balance analysis
Language: MATLAB - Size: 63.5 KB - Last synced: 12 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
libsbmlsim/libsbmlsim-v2
LibSBMLSim: A library for simulating SBML models (Version 2)
Language: HTML - Size: 291 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 4 - Forks: 5
rosherbal/thesis
Dynamical analysis of minimnal networks based on approximate majority algorithm (AM)
Language: R - Size: 21.5 KB - Last synced: 12 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0
liebermeister/enzyme-flux-cost-minimization
Code and models for Flux-balance Enzyme Cost Minimization (fECM)
Language: Python - Size: 62.3 MB - Last synced: 12 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 2