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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 39 9

  2. ecmtool ecmtool Public

    Uncover organisms' metabolic blueprints

    Python 12 6

  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

  4. pub-data pub-data Public archive

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

    HTML 2

  5. cbmpy cbmpy Public

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

    Python 17 5

  6. cbmpy-metadraft cbmpy-metadraft Public

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

    HTML 1 2

Repositories

Showing 10 of 18 repositories
  • ecmtool Public

    Uncover organisms' metabolic blueprints

    SystemsBioinformatics/ecmtool’s past year of commit activity
    Python 12 MIT 6 1 1 Updated Jun 18, 2024
  • parcr Public

    Construct parser combinators in R

    SystemsBioinformatics/parcr’s past year of commit activity
    HTML 3 0 1 0 Updated Jun 7, 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 2 0 0 Updated Jun 1, 2024
  • cbmpy Public

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

    SystemsBioinformatics/cbmpy’s past year of commit activity
    Python 17 GPL-3.0 5 13 0 Updated May 12, 2024
  • cbmpy-metadraft Public

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

    SystemsBioinformatics/cbmpy-metadraft’s past year of commit activity
    HTML 1 GPL-3.0 2 5 0 Updated Apr 24, 2024
  • dynamic-community-fba Public

    Dynamic Community FBA repository

    SystemsBioinformatics/dynamic-community-fba’s past year of commit activity
    Python 0 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

    SystemsBioinformatics/stochpy’s past year of commit activity
    Python 39 BSD-3-Clause 9 3 0 Updated Nov 14, 2022
  • analysis-of-EDA-data Public
    SystemsBioinformatics/analysis-of-EDA-data’s past year of commit activity
    HTML 0 0 0 0 Updated Apr 21, 2022
  • anaerobic-benzene-degrading-culture Public

    Code repository for Chrats paper

    SystemsBioinformatics/anaerobic-benzene-degrading-culture’s past year of commit activity
    0 0 0 0 Updated May 8, 2021
  • 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 nutrients and the objective function. As published in Metabolites https://doi.org/10.3390/metabo11050257

    SystemsBioinformatics/elementary-mode-based-FBA-rationale’s past year of commit activity
    Python 1 0 0 0 Updated Apr 15, 2021
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