We will use Programming For Computations (2nd edition, 2020) by S Linge and HP Langtangen, which is available in PDF format, although you will need your EASE password. We will mostly use chapters 1-4.

For the first few weeks, we will focus on learning Python, and you should read the recommended sections of Linge and Langtangen — trying things out in Python as you read — and solve the suggested exercises.

There are recordings to help with learning both the core material and Python.

Week 1 (14 January)

Before class

Watch the introductory lecture (slides are available too).

After class

Install Python and the associated modules for scientific work on your laptop.

Try out a Jupyter notebook. Watch a brief introduction.

Read the following sections of Linge and Langtangen:

• 1.1 What is Python?
• 1.2 - 1.2.4 A Python program with variables
• 1.5 A Python program with vectorization and plotting
• 1.6.1 Plotting with Matplotlib
• 1.7 Error messages and warnings
• 2.1 Using Python interactively

Try Linge and Langtangen's exercise 1.3.

There are also two Jupyter notebooks: one with examples of implementing formulae including exercises with solutions and a second with examples of plotting also including exercises with solutions.

Week 2

Before class

Read the following sections of the lecture notes, and here are the slides:

• 2.1 Chemical rate equations
• 2.2 Equilibrium and detailed balance
• 2.3 The law of mass action
• 2.4 Modelling signal transduction I

Try the test-your-understanding exercises.

After class

Read the following sections of Linge and Langtangen:

• 2.3 - 2.3.5 Numerical Python arrays
• 3.1 The for loop
• 3.3 Branching

Try Linge and Langtangen's exercise 3.11.

There is also a Jupyter notebook with examples of loops and exercises with solutions.

Week 3 (28 January)

Before class

Read the following sections of the lecture notes, and here are the slides:

• 2.5 Thermodynamic cycles
• 2.6 Ultrasensitivity and the Hill number
• 2.7 Describing response curves
• 2.8 Modelling signal transduction II

Try the test-your-understanding exercises.

After class

Read the following sections of Linge and Langtangen:

• 4.1 - 4.1.7 Functions
• 5.1 Lists and tuples
• 2.3.6 Two-dimensional arrays and matrix computations

Try Linge and Langtangen's exercises 4.4, 4.5, and 4.6.

There is also a Jupyter notebook with examples of functions and exercises with solutions and another notebook covering all the Python needed for the first assignment.

Week 4

Before class

Read the following sections of the lecture notes, and here are the slides:

• 2.9 Allostery
• 2.10 Modelling signal transduction III

Try the test-your-understanding exercise.

After class

Do Assignment 1.

Week 5 (11 February)

Before class

Read the following sections of the lecture notes, and here are the slides:

• 2.11 Enzyme kinetics
• 2.12 Modelling signal transduction IV
• 2.13 Enzymatic cascades

Try the test-your-understanding exercise.

Week 6 (25 February)

Before class

Read the following sections of the lecture notes, and here are the slides:

• 3.1 Modelling constitutive gene expression
• 3.2 Repression by a single repressor
• 3.3 Activation by a single activator
• 3.4 Activation by two activators
• 3.5 General regulation

Try the test-your-understanding exercise.

After class

Watch the recording on simulating biochemical systems.
There is an illustrative Jupyter notebook and an online example of simulating bistability.

Week 7

Before class

Read the following sections of the lecture notes, and here are the slides:

• 3.6 Modelling signal transduction V
• 4.1 MAP kinase cascades
• 4.2 Bifurcation diagrams and hysteresis

Try the test-your-understanding exercise.

After class

Do Assignment 2.

Week 8 (11 March)

Before class

Read the following sections of the lecture notes, and here are the slides:

• 4.3 A genetic switch
• 5.1 Degradation stabilises molecular numbers
• 5.2 Negative feedback is stabilising
• 5.3 Delayed negative feedback can cause oscillations

There is an an example of creating a phase plot using Python.

Week 9

Make sure you have a topic for your research project.

Before class

Read the following sections of the lecture notes, and here are the slides:

• 5.4 Circadian rhythms
• 5.5 Relaxation oscillations

Week 10

Before class

Read the following sections of the lecture notes, and here are the slides:

• 5.6 Oscillations through positive and negative feedback
• Appendix A Simulating stochastic biochemical reactions

Watch the recording showing how to run stochastic simulations.

You will need to install StochPy; there are instructions online. If you have pip working — it comes with Anacaonda, then the easiest way to install is to type

  pip install stochpy

in a terminal.

You may need to downgrade Numpy to allow StochPy to work:

  conda install -c conda-forge numpy=1.23.0

Alternatively you can use conda to create a dedicated virtual environment. From either the Anaconda prompt on Windows or the terminal on OS X or Linux, first try

  conda create -n stochpyenv python=3.9
  conda activate stochpy

Then

  pip install setuptools==59.8.0
  pip install "numpy==1.23.0" scipy matplotlib jupyter
  pip install stochpy

After class

There is an example Jupyter notebook and some exercises and solutions and a test-your-understanding exercise.

Week 11 (1 April)

Before class

Read the following sections of the lecture notes

• Appendix B Fitting data

and there is a notebook to use in class.

After class

Here is the entire notebook. Work on the research project.