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

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

Name		Name	Last commit message	Last commit date
Latest commit History 39 Commits
ABCDE_abg.svg		ABCDE_abg.svg
AB_abg.svg		AB_abg.svg
Coop_abg.svg		Coop_abg.svg
Cooperative.ipynb		Cooperative.ipynb
Cooperative.pdf		Cooperative.pdf
ECR.ipynb		ECR.ipynb
ECR.pdf		ECR.pdf
PD_abg.svg		PD_abg.svg
Phosphorylation.ipynb		Phosphorylation.ipynb
Phosphorylation.pdf		Phosphorylation.pdf
RC_abg.svg		RC_abg.svg
README.md		README.md
RE_abg.svg		RE_abg.svg
environment.yml		environment.yml
modularBondGraph.py		modularBondGraph.py
stoich.ipynb		stoich.ipynb
stoich.pdf		stoich.pdf
stoich.py		stoich.py
stoichBondGraph.py		stoichBondGraph.py
svgBondGraph.ipynb		svgBondGraph.ipynb
svgBondGraph.pdf		svgBondGraph.pdf
svgBondGraph.py		svgBondGraph.py