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@SysSynBio Systems and Synthetic Biology

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    315 repositories

    • PyBNF

      Public
      An application for fitting systems biology models using metaheuristic algorithms
      Python
      •
      Other
      •20•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • pdbtbx

      Public
      A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.
      Rust
      •
      MIT License
      •21•0•0•0•Updated May 17, 2025May 17, 2025

    • CAII-Orb-d3-v2

      Public
      Supporting data for publication "Carbonic Anhydrase II simulated with a universal neural network potential"
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Mar 17, 2025Mar 17, 2025

    • KcsA-SF_Orb-d3-v2

      Public
      Input files and scripts to simulate the selectivity filter of the KcsA potassium ion channel with the Orb-d3-v2 universal neural network potential.
      Python
      •
      Apache License 2.0
      •2•0•0•0•Updated Feb 13, 2025Feb 13, 2025

    • modern_egfrd

      Public
      modern C++ implementation of eGfrd
      C++
      •
      GNU General Public License v2.0
      •8•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • spateo-release

      Public
      Spatiotemporal modeling of spatial transcriptomics
      Python
      •
      BSD 2-Clause "Simplified" License
      •43•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • good_lp

      Public
      Linear Programming for Rust, with a user-friendly API. This crate allows modeling LP problems, and lets you solve them with various solvers.
      Rust
      •
      MIT License
      •58•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • iCH360

      Public
      A compact metabolic model of Escherichia Coli core and biosynthetic metabolism
      Python
      •
      MIT License
      •3•0•0•0•Updated Jul 2, 2024Jul 2, 2024

    • PheArrMe

      Public
      Phenotype array guided GEM gap-filling
      Python
      •
      MIT License
      •1•0•0•0•Updated May 2, 2024May 2, 2024

    • CNApy

      Public
      An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodyna…
      Python
      •
      Apache License 2.0
      •18•0•0•0•Updated Jan 27, 2024Jan 27, 2024

    • straindesign

      Public
      StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
      Python
      •
      Apache License 2.0
      •7•0•0•0•Updated Jan 10, 2024Jan 10, 2024

    • cobramod

      Public
      CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway information from various m…
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Dec 30, 2023Dec 30, 2023

    • pymCADRE

      Public
      pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • CONCERTO

      Public
      Continuous integration and validation for genome-scale metabolic model consortia
      HTML
      •
      Apache License 2.0
      •3•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • shu_case_studies

      Public
      Shu case study figures.
      Jupyter Notebook
      •1•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • CellBox

      Public
      CellBox: Interpretable Machine Learning for Perturbation Biology
      Jupyter Notebook
      •
      MIT License
      •28•0•0•0•Updated Oct 30, 2023Oct 30, 2023

    • reconstructor

      Public
      This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and benchmarking scores fo…
      HTML
      •
      MIT License
      •3•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • RomicsProcessor

      Public
      R package that provides a structured R object to store and analyze omics data
      HTML
      •
      BSD 2-Clause "Simplified" License
      •2•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • KineticAssembly_AD

      Public
      Python code for numerical simulations of self-assemly with optimization by automatic differentiation
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • KaSim

      Public
      Command line stochastic simulator for kappa models. Documentation can be found in the man/ directory
      OCaml
      •
      GNU Lesser General Public License v3.0
      •41•1•0•0•Updated Sep 28, 2023Sep 28, 2023

    • CellModeller

      Public
      GPU-accelerated multicellular modelling framework
      Python
      •
      Other
      •54•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • PyFBA

      Public
      A python implementation of flux balance analysis to model microbial metabolism
      Python
      •
      MIT License
      •14•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • evoMEG

      Public
      evoMEG: evolutionary algorithm-based Model Ensemble Generation
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • moleculekit

      Public
      MoleculeKit: Your favorite molecule manipulation kit
      Python
      •
      Other
      •38•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • NERDSS

      Public
      NonEquilibrium Reaction-Diffusion Self-assembly Simulator
      C++
      •
      GNU General Public License v3.0
      •13•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • vivarium-ecoli

      Public
      Whole cell model of E. coli implemented with Vivarium
      Jupyter Notebook
      •
      MIT License
      •15•0•0•0•Updated Sep 16, 2023Sep 16, 2023

    • comets

      Public
      Computation of Microbial Ecosystems in Time and Space
      Java
      •
      GNU General Public License v3.0
      •13•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • grn-gpu-performance

      Public
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 14, 2023Aug 14, 2023

    • wcEcoli

      Public
      Whole Cell Model of E. coli
      Python
      •
      Other
      •12•0•0•0•Updated Aug 9, 2023Aug 9, 2023

    • tissue-forge

      Public
      Interactive, particle-based physics, chemistry and biology modeling and simulation environment
      C++
      •
      Other
      •12•0•0•0•Updated Jul 27, 2023Jul 27, 2023
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