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@SystemsBioinformatics

Systems Biology Lab, Vrije Universiteit Amsterdam

This is the code repository of the Systems Biology Lab. Our lab studies the molecular networks inside cells that give rise to cell behaviour and fitness.

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  1. stochpy stochpy Public

    StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

    Python 43 11

  2. ecmtool ecmtool Public

    Uncover organisms' metabolic blueprints

    Python 13 5

  3. elementary-mode-based-FBA-rationale elementary-mode-based-FBA-rationale Public

    Code that uses Elementary Conversion Mode computation to obtain all relevant conversions for a constraint-based optimization problem, i.e., all possible optimal yields between the constrained nutri…

    Python 1

Repositories

Showing 10 of 22 repositories
  • excelDataGuide Public

    Simplify reading data from Excel templates (R-package)

    SystemsBioinformatics/excelDataGuide’s past year of commit activity
    R 0 0 2 0 Updated Mar 4, 2026
  • dataSheetParcr Public
    SystemsBioinformatics/dataSheetParcr’s past year of commit activity
    R 0 0 0 0 Updated Feb 17, 2026
  • parcr Public

    Construct parser combinators in R

    SystemsBioinformatics/parcr’s past year of commit activity
    HTML 6 0 0 0 Updated Feb 17, 2026
  • dynamic-community-fba Public

    Dynamic Community FBA repository

    SystemsBioinformatics/dynamic-community-fba’s past year of commit activity
    Python 4 MIT 0 2 0 Updated Oct 28, 2025
  • DisentangleMetabolism Public
    SystemsBioinformatics/DisentangleMetabolism’s past year of commit activity
    Python 0 0 0 0 Updated Sep 16, 2025
  • stochpy Public

    StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

    SystemsBioinformatics/stochpy’s past year of commit activity
    Python 43 BSD-3-Clause 11 2 0 Updated Jun 20, 2025
  • cbmpy-metadraft Public

    CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool

    SystemsBioinformatics/cbmpy-metadraft’s past year of commit activity
    Python 2 GPL-3.0 1 5 0 Updated Mar 19, 2025
  • GECKO Public Forked from SysBioChalmers/GECKO

    Toolbox for including enzyme constraints on a genome-scale model.

    SystemsBioinformatics/GECKO’s past year of commit activity
    MATLAB 0 MIT 51 0 0 Updated Jul 18, 2024
  • ecmtool Public

    Uncover organisms' metabolic blueprints

    SystemsBioinformatics/ecmtool’s past year of commit activity
    Python 13 MIT 5 0 1 Updated Jun 18, 2024
  • pub-data Public archive

    Repository for published, public supplementary material (archived, for new data please use a data repository)

    SystemsBioinformatics/pub-data’s past year of commit activity
    HTML 0 3 0 0 Updated Jun 1, 2024
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