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Additional Python packages

Python is a language with an extensive ecosystem of additional packages that can be used for various things. Here we list some key packages which can be useful for doing modelling.

Due to the vast amount of packages available, and different packages using different versions, we strongly recommend working in a virtual environment. You can find more on that in the virtual environment page.

Installing additional packages

Additional package are typically installed using uv from astral.sh or pip from the pypi.org repository. Simply run 

uv add packagename
Where packagename is the name of the package you want to install (e.g. numpy).

No pyproject.toml found in current directory or any parent directory

If you get this error, you need to initialize the uv environment before installing packages: 

uv init

or alternatively, create the pyproject.toml file manually.

pip install packagename

Where packagename is the name of the package you want to install (e.g. numpy).

It is also possible to install a group at the same time. One common method of grouping packages for a project is a so-called requirements file (often named requirements.txt). To do this, run 

uv add -r requirements.txt
or if using a uv-based project, with the packages defined in the pyproject.toml file
uv sync


pip install -r requirements.txt
If you want to save the packages you have installed to such a requirements file, you can run 

pip freeze > requirments.txt

NumPy and SciPy

NumPy and SciPy are staples when it comes to scientific computing in Python. You can install them using pip:

uv add numpy scipy

pip install numpy scipy

SUND

The SUND (Simulation Using Nonlinear Dynamic models) package is a package for simulating ODE models inspired by the MATLAB package IQM. It features a simple syntax for writing the model, and is able to combine models in a modular way by exposing inputs/outputs between models. It is also possible to give inputs in the form of predefined activities, which can contain constant outputs as well as more complex piecewise or interpolated outputs.

The easiest way is to install the sund package using pip:

uv add https://isbgroup.eu/sund-toolbox/releases/sund-latest.tar.gz

pip install https://isbgroup.eu/sund-toolbox/releases/sund-latest.tar.gz

It can then be used by importing the package sund:

import sund
If the compiler is not found by setuptools (typically not a problem)

If you get problems that the compiler is not found (even if you have installed the compiler), sometimes it helps to upgrade setuptools and then try to install the package again:

uv add --upgrade setuptools

pip install --upgrade setuptools

AMICI (not currently used for the courses on this page)

AMICI is a package for simulating ODE models specified in the SBML format. It is using C in the background, and is able to both simulate the model and do parameter estimation.

For installing AMICI, we refer to the official install instructions available here.