Systems and Synthetic Biology
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AutoHomology
AutoHomology PublicAutomatically performs rosetta based Homology modeling. For now, semi-automatic.
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KaSim
KaSim PublicForked from Kappa-Dev/KappaTools
Command line stochastic simulator for kappa models. Documentation can be found in the man/ directory
OCaml 1
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metakappa
metakappa PublicForked from kappamodeler/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.
OCaml 1
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kappa
kappa PublicForked from kappamodeler/kappa
A domain-specific language that allows the expression or protein interactions that can be used to build executable models.
OCaml 1
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KaSa
KaSa PublicStatic analyzer for kappa models. Documentation can be found in the man/ directory.
OCaml
Repositories
- iCH360 Public Forked from marco-corrao/iCH360
A compact metabolic model of Escherichia Coli core and biosynthetic metabolism
SysSynBio/iCH360’s past year of commit activity - CNApy Public Forked from cnapy-org/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/CNApy’s past year of commit activity - straindesign Public Forked from klamt-lab/straindesign
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
SysSynBio/straindesign’s past year of commit activity - cobramod Public Forked from Toepfer-Lab/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/cobramod’s past year of commit activity - pymCADRE Public Forked from draeger-lab/pymCADRE
pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
SysSynBio/pymCADRE’s past year of commit activity - CONCERTO Public Forked from PNNL-CompBio/CONCERTO
Continuous integration and validation for genome-scale metabolic model consortia
SysSynBio/CONCERTO’s past year of commit activity - CellBox Public Forked from sanderlab/CellBox
CellBox: Interpretable Machine Learning for Perturbation Biology
SysSynBio/CellBox’s past year of commit activity - reconstructor Public Forked from emmamglass/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/reconstructor’s past year of commit activity - RomicsProcessor Public Forked from PNNL-Comp-Mass-Spec/RomicsProcessor
R package that provides a structured R object to store and analyze omics data
SysSynBio/RomicsProcessor’s past year of commit activity - KineticAssembly_AD Public Forked from mjohn218/KineticAssembly_AD
Python code for numerical simulations of self-assemly with optimization by automatic differentiation
SysSynBio/KineticAssembly_AD’s past year of commit activity
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