Installation

The following instructions are for both MacOS and Linux systems. Windows users are encouraged to install the Windows Subsystem for Linux (WSL) and then install the software inside Ubuntu Linux.

1. Make a directory protocell/ somewhere on your computer, and change to it:

   mkdir protocell
   cd protocell
   

2. Get the latest source code for Araudia:

   git clone https://bitbucket.org/ben_s_e/araudia.git
   

3. Make a Python3 virtual environment in the protocell/ directory, activate it, and install the required libraries:

   python3 -m venv venv
   source venv/bin/activate
   pip install --upgrade pip
   pip install numpy
   pip install numba==0.60.0
   pip install matplotlib
   pip install networkx
   pip install scipy
   pip install pulp
   pip install colorama
   

Note

Ensure that numba version 0.60.0 (at least) is installed. This requires at least Python version 3.10.

4. The protocell/ directory should now contain two sub-folders:

• araudia/

• venv/

Installation is complete.

HPC Cluster Installation

The software can also be installed and used on an HPC computing cluster, following the same installation instructions above when logged in. The command module load Python may be necessary beforehand. It is advisable to install the same version of numpy on your local machine and on the HPC system (e.g. pip install numpy==2.0.2), such that data files made on the HPC cluster (that contain pickled numpy objects) can later be opened on your local machine.

Simulations in Our Paper were run on a SLURM-based cluster, using the logic in the rstb/hpc.py script.