Pinned Repositories
AutoBlast
Automatically performs rosetta homology modeling
AutoHomology
Automatically performs rosetta based Homology modeling. For now, semi-automatic.
BLAST-tutorial
evolve-bifurcation
Fungal_Networks
kappa
A domain-specific language that allows the expression or protein interactions that can be used to build executable models.
KaSim
Command line stochastic simulator for kappa models. Documentation can be found in the man/ directory
MEP-SidersPond
Fortran code used for MEP model to describe microbial biogeochemistry in Siders Pond, MA
metakappa
A meta-language for Kappa generation that allows the creation of protein hierarchies and the concise representation of protein-interaction rules. These structures can then be expanded into Kappa.
netevo
NetEvo – Complex Dynamical Network Evolution
Systems and Synthetic Biology's Repositories
SysSynBio/KaSim
Command line stochastic simulator for kappa models. Documentation can be found in the man/ directory
SysSynBio/AIOrganoids
SysSynBio/antimony
SysSynBio/CellBox
CellBox: Interpretable Machine Learning for Perturbation Biology
SysSynBio/CellModeller
GPU-accelerated multicellular modelling framework
SysSynBio/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!
SysSynBio/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.
SysSynBio/comets
Computation of Microbial Ecosystems in Time and Space
SysSynBio/CONCERTO
Continuous integration and validation for genome-scale metabolic model consortia
SysSynBio/evoMEG
evoMEG: evolutionary algorithm-based Model Ensemble Generation
SysSynBio/grn-gpu-performance
SysSynBio/i-At-LSPHERE
Collection of genome-scale metabolic models, genomes, and scripts for At-LSPHERE bacterial culture collection
SysSynBio/iCH360
A compact metabolic model of Escherichia Coli core and biosynthetic metabolism
SysSynBio/KaiSystem2017
The code come along with a PLoS Comp Biol paper of Kai system model
SysSynBio/KineticAssembly_AD
Python code for numerical simulations of self-assemly with optimization by automatic differentiation
SysSynBio/LGL-VAE
SysSynBio/moleculekit
MoleculeKit: Your favorite molecule manipulation kit
SysSynBio/NERDSS
NonEquilibrium Reaction-Diffusion Self-assembly Simulator
SysSynBio/PheArrMe
Phenotype array guided GEM gap-filling
SysSynBio/PTMPSI
SysSynBio/PyFBA
A python implementation of flux balance analysis to model microbial metabolism
SysSynBio/pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
SysSynBio/pyPESTO
python Parameter EStimation TOolbox
SysSynBio/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.
SysSynBio/RomicsProcessor
R package that provides a structured R object to store and analyze omics data
SysSynBio/shu_case_studies
Shu case study figures.
SysSynBio/straindesign
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
SysSynBio/tissue-forge
Interactive, particle-based physics, chemistry and biology modeling and simulation environment
SysSynBio/vivarium-ecoli
Whole cell model of E. coli implemented with Vivarium
SysSynBio/wcEcoli
Whole Cell Model of E. coli