ODE-Modelling

Introduction

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Slides: Download Lecture Slides

Lesson 1: Reactions, populations and analytical solutions to simple ODEs

Work through the following section on Reactions.

Reactions

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Notes: Download Notes

Please download

The JupyterLab notebook for this Lesson.

A PDF of the JupyterLab notebook for reference and offline reading

Lesson Assignment

Assignment can be accessed at GitHub classroom.

Lesson 2: Dynamics, deriving differential equations and using Python to simulate them

Work through the following section on Dynamics.

Dynamics

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Slides: Download Lecture Slides

Notes: Download Notes

Please download

The JupyterLab notebook for this Lesson.

A PDF of the JupyterLab notebook for reference and offline reading

Lesson Assignment

Assignment can be accessed at GitHub classroom.

Lesson 3: Interconnected Systems

Work through the following section.

Interconnected Systems

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Slides: Download Lecture Slides

Notes: Download Notes

Please download

The JupyterLab notebook for this Lesson.

A PDF of the JupyterLab notebook for reference and offline reading

Lesson Assignment

Assignment can be accessed at GitHub classroom.

Optional material: Modelling gene regulatory networks

Work through the following sections on gene regulatory networks.

Gene regulation

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Gene regulatory networks: the toggle switch and the repressilator

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Lesson 4: Mini projects

This week you get to choose one of five mini projects to tackle on your own. You will need to use what you have learned over the past three sessions to simulate and explore some classic dynamic biological systems.

Assignment can be accessed at GitHub classroom.