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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 Public

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

    Python 40 12

  2. ecmtool Public

    Uncover organisms' metabolic blueprints

    Python 12 6

  3. 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

  4. pub-data Public archive

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

    HTML 3

  5. cbmpy Public

    CBMPy is a Python based platform for constraint based modelling and analysis.

    Python 19 6

  6. cbmpy-metadraft Public

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

    Python 2 2

Repositories

Showing 10 of 20 repositories
  • excelDataGuide Public

    Simplify reading data from filled excel templates (R-package)

    R 0 0 2 0 Updated Mar 20, 2025
  • cbmpy-metadraft Public

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

    Python 2 GPL-3.0 2 5 0 Updated Mar 19, 2025
  • GECKO Public Forked from SysBioChalmers/GECKO

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

    MATLAB 0 MIT 51 0 0 Updated Jul 18, 2024
  • ecmtool Public

    Uncover organisms' metabolic blueprints

    Python 12 MIT 6 1 1 Updated Jun 18, 2024
  • parcr Public

    Construct parser combinators in R

    HTML 4 0 0 0 Updated Jun 7, 2024
  • pub-data Public archive

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

    HTML 0 3 0 0 Updated Jun 1, 2024
  • cbmpy Public

    CBMPy is a Python based platform for constraint based modelling and analysis.

    Python 19 GPL-3.0 6 14 0 Updated May 12, 2024
  • dynamic-community-fba Public

    Dynamic Community FBA repository

    Python 4 MIT 0 1 0 Updated Jan 10, 2024
  • stochpy Public

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

    Python 40 BSD-3-Clause 12 3 1 Updated Nov 14, 2022
  • analysis-of-EDA-data Public
    HTML 0 0 0 0 Updated Apr 21, 2022
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