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@SysSynBio

Systems and Synthetic Biology

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  1. AutoBlast AutoBlast Public

    Automatically performs rosetta homology modeling

    Python 2 2

  2. AutoHomology AutoHomology Public

    Automatically performs rosetta based Homology modeling. For now, semi-automatic.

    Python 2 2

  3. KaSim KaSim Public

    Forked from Kappa-Dev/KappaTools

    Command line stochastic simulator for kappa models. Documentation can be found in the man/ directory

    OCaml 1

  4. metakappa metakappa Public

    Forked 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

  5. kappa kappa Public

    Forked from kappamodeler/kappa

    A domain-specific language that allows the expression or protein interactions that can be used to build executable models.

    OCaml 1

  6. cobramod 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-c…

    Python 1

Repositories

Showing 10 of 314 repositories
  • modern_egfrd Public Forked from gfrd/modern_egfrd

    modern C++ implementation of eGfrd

    SysSynBio/modern_egfrd’s past year of commit activity
    C++ 0 GPL-2.0 9 0 0 Updated Dec 11, 2024
  • spateo-release Public Forked from aristoteleo/spateo-release

    Spatiotemporal modeling of spatial transcriptomics

    SysSynBio/spateo-release’s past year of commit activity
    Python 0 BSD-2-Clause 31 0 0 Updated Nov 12, 2024
  • 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
    Rust 0 MIT 17 0 0 Updated Nov 9, 2024
  • 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
    Rust 0 MIT 39 0 0 Updated Aug 29, 2024
  • 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
    Python 0 MIT 1 0 0 Updated Jul 2, 2024
  • PheArrMe Public Forked from jrcasey/PheArrMe

    Phenotype array guided GEM gap-filling

    SysSynBio/PheArrMe’s past year of commit activity
    Python 0 MIT 1 0 0 Updated May 2, 2024
  • 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
    Python 0 Apache-2.0 7 0 0 Updated Jan 27, 2024
  • 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
    Python 0 Apache-2.0 7 0 0 Updated Jan 10, 2024
  • 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
    Python 1 GPL-3.0 1 0 0 Updated Dec 30, 2023
  • 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
    Jupyter Notebook 0 GPL-3.0 5 0 0 Updated Dec 27, 2023
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