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BondGraphTools-Biomolecular

This repository contains

  • Extensions to BondGraphTools to support stoichiometric analysis (.py)
  • Tutorials and examples as jupyter notebooks (.ipynb)
  • PDF versions of the notebooks (.pdf). These contain a table of contents as well as citations.
  • Graphical bond graphs in SVG (scaleable vector graphics) format (.svg)

Tutorials

Each of the following links displays the notebook using nbviewer. The notebook may be run using the binder link in the nbviewer menu.

  • stoich: The stoichiometric analysis module
  • svgBondGraph: The module for converting bond graphs in SVG (scaleable vector graphics) format to BondGraphTools format
  • stoichBondGraph: The module for converting a stoichiometric system representation to BondGraphTools format
  • Complexes: Bond Graph Representation of Complexes: Bringing Graph Theory to Bond Graphs
  • Linearisation: Linearisation of Biomolecular Systems

Examples

Each of the following links displays the notebook using nbviewer. The notebook may be run using the binder link in the nbviewer menu.

  • ECR: Enzyme-catalysed Reactions
  • Cooperative: Cooperative Enzyme-catalysed Reactions
  • Phosphorylation: Phosphorylation, Dephosphorylation and the Mitogen-activated Protein Kinase (MAPK) cascade
  • EcoliCoreModel: The Escherichia coli Core Model: Bond Graph Analysis
  • Chloroplast: The Chloroplast Electron Transport Chain
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