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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cameo
cameo PublicForked from biosustain/cameo
cameo - computer aided metabolic engineering & optimization
Python 1
Repositories
- pdbtbx Public Forked from douweschulte/pdbtbx
A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.
SysSynBio/pdbtbx’s past year of commit activity - spateo-release Public Forked from aristoteleo/spateo-release
Spatiotemporal modeling of spatial transcriptomics
SysSynBio/spateo-release’s past year of commit activity - good_lp Public Forked from rust-or/good_lp
Linear Programming for Rust, with a user-friendly API. This crate allows modeling LP problems, and lets you solve them with various solvers.
SysSynBio/good_lp’s past year of commit activity - 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
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