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
• modulatedCooperative: Modulated Cooperative Enzyme-catalysed Reactions
• Phosphorylation: Phosphorylation, Dephosphorylation and the Mitogen-activated Protein Kinase (MAPK) cascade
• EcoliCoreModel: The Escherichia coli Core Model: Modular Bond Graph Analysis
• EcoliCoreModelEnergy: The Escherichia coli Core Model: Modular Energetic Bond Graph Analysis of Glycolysis and Pentose Phosphate Pathways
• Chloroplast: The Chloroplast Electron Transport Chain
• Retroactivity: Modules, Linearisation and Retroactivity
• ElectroChemical: Electrochemical Modelling and Ion Channels
• Redox: Redox reactions and Proton Pumps
• SGLT: Sodium Glucose Symporter
• MWC: Monod-Wyman-Changeux Model

In progress

• fECR: Enzyme-catalysed reaction: analysis as a feedback control actuator.
• Allosteric: Allosteric inhibition as a control actuator: loop-gain analysis.
• modularAllosteric: Allosteric inhibition as a control actuator - modular approach: passive and active feedback.
• Cyclic Flow Modulation (CFM): control of metabolism based on biomolecular cycles.