We will use conda to setup a new virtual environment using the provided `brianenv2.yml` file.

To setup your environment, follow these steps:

1. Make sure you have Anaconda (or miniconda) installed. The software has been tested on Ubuntu 21.10 using miniconda version 4.10.3

2. Create a conda environment using the provided .yml file as follows (without the quotes): "conda env create --file=brianenv2.yml"

3. Activate the environment in conda: "conda activate brianenv2"

4. You will also need to install `matplotlib-3d` (https://github.com/rougier/matplotlib-3d) as follows:
    4a. Make sure you have installed git. Follow the instructions here (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) depending on your system
    4b. Type the following command in your terminal, after making sure the conda environment is activated (step 3): "pip install git+https://github.com/rougier/matplotlib-3d"

5. You can run simulations using the following command, using the appropriate arguments: "python3 run_simulation.py -p [parameter_file.json] -sd [output folder]""

Note: for a full list of arguments, run: 'python3 run_simulation.py [-h|--help]