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MEANS Tutorial

This tutorial is designed to provide a quick introduction to the MEANS package.

We split the tutorial into four parts:

  1. [Modelling Using MEANS](1. Modelling Using MEANS.ipynb) -- a general introduction to MEANS -- along with [an example how to parse SBML files](1a. SBML Parsing Example.ipynb)
  2. [Simulation.ipynb](2. Simulation.ipynb) -- introduction on simulation of biological systems using MEANS
  3. [Parameter Inference](3. Parameter Inference.ipynb) -- tutorial on parameter inference in MEANS
  4. [Input & Output](4. Input & Output.ipynb) -- a set of examples of how data can be imported to or exported from MEANS models.

Whilst all examples are available online, we invite the user to interact with them using Jupyter. Jupyter is an interactive interface to python that is easy to install using pip:

pip install jupyter

Alternatively, follow the instructions on Jupyter homepage.

Once Jupyter is installed feel download the source code of MEANS, either by clicking Download ZIP here or cloning the repository, and start the Jupyter notebook in the tutorials directory:

cd tutorials
jupyter notebook

A new browser window will open with the list of tutorials that you can then follow interactively. Consult the package readme file for troubleshooting any issues that may occur.