Systems and Synthetic Biology's repositories
iCH360
A compact metabolic model of Escherichia Coli core and biosynthetic metabolism
PheArrMe
Phenotype array guided GEM gap-filling
CNApy
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
straindesign
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
cobramod
CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway information from various metabolic pathways databases or user-curated data sets.
pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
CONCERTO
Continuous integration and validation for genome-scale metabolic model consortia
shu_case_studies
Shu case study figures.
CellBox
CellBox: Interpretable Machine Learning for Perturbation Biology
reconstructor
This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and benchmarking scores for reconstructor models. Reconstructor is a COBRApy compatible, automated GENRE building tool from gene fastas based on KEGG annotations.
RomicsProcessor
R package that provides a structured R object to store and analyze omics data
KineticAssembly_AD
Python code for numerical simulations of self-assemly with optimization by automatic differentiation
CellModeller
GPU-accelerated multicellular modelling framework
PyFBA
A python implementation of flux balance analysis to model microbial metabolism
evoMEG
evoMEG: evolutionary algorithm-based Model Ensemble Generation
moleculekit
MoleculeKit: Your favorite molecule manipulation kit
NERDSS
NonEquilibrium Reaction-Diffusion Self-assembly Simulator
vivarium-ecoli
Whole cell model of E. coli implemented with Vivarium
comets
Computation of Microbial Ecosystems in Time and Space
wcEcoli
Whole Cell Model of E. coli
tissue-forge
Interactive, particle-based physics, chemistry and biology modeling and simulation environment
i-At-LSPHERE
Collection of genome-scale metabolic models, genomes, and scripts for At-LSPHERE bacterial culture collection
KaiSystem2017
The code come along with a PLoS Comp Biol paper of Kai system model
pyPESTO
python Parameter EStimation TOolbox