Supplementary code for "Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data."

Notebooks

The nbviewer links will display the notebooks containing the code for each of the examples. These notebooks can be interactively run online using the Binder links.

Notebook	nbviewer	Binder	PDF
3.1. Glycolysis & Pentose Phosphate pathway			PDF
3.2. Respiration			PDF
4. Dynamic Modelling and Parameter Estimation			PDF

Name		Name	Last commit message	Last commit date
Latest commit History 21 Commits
CobraExtract.py		CobraExtract.py
EcoliPPPnoPhi.ipynb		EcoliPPPnoPhi.ipynb
EcoliPPPnoPhi.pdf		EcoliPPPnoPhi.pdf
LICENSE		LICENSE
ModularEcoli.ipynb		ModularEcoli.ipynb
ModularEcoli.pdf		ModularEcoli.pdf
Parameter.ipynb		Parameter.ipynb
Parameter.pdf		Parameter.pdf
RE.py		RE.py
README.md		README.md
RE_abg.py		RE_abg.py
RE_abg.svg		RE_abg.svg
environment.yml		environment.yml
identBondGraph.py		identBondGraph.py
modularBondGraph.py		modularBondGraph.py
phiData.py		phiData.py
postBuild		postBuild
stoich.py		stoich.py
stoichBondGraph.py		stoichBondGraph.py
svgBondGraph.py		svgBondGraph.py

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mic-pan/GawPanCra21

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Supplementary code for "Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data."

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