In this tutorial you will learn in detail about the deterministic formalism for the temporal modelling of simple\* chemical systems, and you will learn to write a simulation program, from scratch, using Python 2.7.
- Python 2.7 (we recommend the Anaconda distribution, which includes most of the required modules)
- Modules: NumPy, SciPy, Matplotlib
- Files you should have: ipython notebook titled modelling_signalling_transduction_exercises.ipnb
- To start the ipython notebooks, start a new terminal window and type “jupyter notebook”, then press enter. When a new browser window opens, navigate to the folder where you have saved the tutorials. Click on the tutorial that you want to follow.
- Using Jupyter notebook: When you want to type code into a cell, simply click on it to activate it. When you want to run the code, press shift+enter. You can learn how to use Jupyter notebooks from, e.g., https://jupyter-notebook-beginner-guide.readthedocs.io/en/latest/
- The tutorial is self explanatory, indicating the steps to be taken next, what you should aim at achieving after carrying out those steps and the commands that could be used (there is not a one correct answer; these are suggestions).
- With this exercise we want to encourage you to become a more independent programmer, so if there is a command you don't quite know how to use, make sure you read the documentation. To do so, most of the time is enough to google the words 'documentation, python' and the name of the module or function you want to use.
- If you are following this tutorial in class, if you have any questions, raise your hand and someone will come to help you.
- We provide you with relevant papers.
We welcome any feedback on this course!
Feel free to contact us at [email protected]