nosratullah / NeuralDynamics

This is a repository for Neural Dynamics course. To install the dependencies, follow this instructions: .. _setup:

Installation

To solve the exercises you need to install Python, the Brian2 simulator and the neurodynex3 package. The tutorial below will explain two different ways of installing everything:

• using the :ref:pip <setup-pip> package manager (Linux, macOS)

• using the :ref:conda <setup-conda> package manager, if you have Anaconda installed (Linux, macOS, Windows).

In both cases, we will use the package manager to create a virtual environment called bmnn and install everything there.

.. _setup-pip:

Using pip

1. We will start by creating a virtual environemt that contains a separate Python installation. To do this, we first need the virtualenv package. Install this by running:

   .. code-block:: bash

   pip install virtualenv

2. Now create the virtual environment in a folder called bmnn:

   .. code-block:: bash

   virtualenv bmnn

3. Activate the virtual environment:

   .. code-block:: bash

   source bmnn/bin/activate

4. Now install neurodynex3 and all its requirements:

   .. code-block:: bash

   pip install --upgrade neurodynex3 pip install jupyter

5. You can now use Python in this environment as you normally would. Move to the folder where you want your code to be stored and start a Jupyter notebook by running:

   .. code-block:: bash

   cd your_folder jupyter notebook

6. Finally, when you are done using the virtual environment, you can deactivate it:

   .. code-block:: bash

   deactivate

.. note::

If something goes wrong inside the virtual environment, you can simply delete it by removing its folder (with the regular rm -r command) and start over:

.. code-block:: bash

  >> deactivate
  >> rm -r bmnn

.. _setup-conda:

Using conda

Anaconda <https://www.anaconda.com/distribution/>_ is a Python distribution that can be installed on Linux, macOS, and Windows. It comes together with a package manager called conda. To run conda commands if you are using Windows, first start the Anaconda Prompt.

.. image:: setup_images/anaconda-prompt.png :align: center

If you are using Linux or macOS, you can run conda commands in a regular terminal.

1. We start by creating a virtual environemt that contains a separate Python installation. The virtual environment is called bmnn:

   .. code-block:: bash

   conda create --name bmnn python

2. Activate the virtual environment:

   .. code-block:: bash

   conda activate bmnn

3. Now install required Python packages:

   .. code-block:: bash

   conda install numpy scipy jupyter matplotlib mpmath setuptools setuptools_scm mock nose

4. Install Brian2:

   .. code-block:: bash

   conda install -c conda-forge brian2

5. We will now install neurodynex3. Note: this step is done using pip, not conda. First make sure that you are using pip inside the virtual environment:

   .. code-block:: bash

   pip --version pip 20.0.2 from //anaconda3/envs/bmnn/.../pip (python 3.8)

6. Now run the install command:

   .. code-block:: bash

   pip install neurodynex3

7. You can now use Python in this environment as you normally would. Move to the folder where you want your code to be stored and start a Jupyter notebook by running:

   .. code-block:: bash

   cd your_folder jupyter notebook

8. Finally, when you are done using the virtual environment, you can deactivate it:

   .. code-block:: bash

   conda deactivate

.. note::

If something goes wrong inside the virtual environment, you can simply delete it and start over:

.. code-block:: bash

  >> conda deactivate
  >> conda remove --name bmnn --all

More information can be found in the conda documentation <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>_.

.. _setup-jupyter:

Now start a Jupyter notebook Links

Here are some useful links to get started with Python and Brian:

• Python documentation <https://www.python.org/doc>_
• Brian2 documentation <https://brian2.readthedocs.io/en/stable>_
• Jupyter notebook documentation <https://jupyter-notebook.readthedocs.io/en/stable>_
• Matplotlib documentation <https://matplotlib.org/tutorials/index.html>_
• conda documentation <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>_