This repository provides a set of tools for CxSystem2 data analysis, visualization and iterative tasks.

The main files are in the project directory:

• project/project_conf_module.py: conf below, provides the primary interface to work with SystemTools.
• project/project_manager_module.py provides a facade for the rest of the code.

The scripts folder contains the following projects:

This folder contains jupyter notebooks for creating figures for the paper Garnier Artiñano, Tomás, et al. Biophysical parameters control signal transfer in spiking network. Frontiers in Computational Neuroscience 17 (2023) 1011814.

conf module is a script, with context (paths etc.) parameters at the top, and executable statements at the bottom. The executable statements are commented by default. To use the software, uncomment a statement and run the conf file.

* PM.viz.show_spikes(results_filename=file_to_display, savefigname="")
    * PM is a ProjectManager instance
    * viz is a Viz (visualization) instance
    * show_spikes is a viz method showing rasterplot of spikes

• Run it as python project/project_conf_module.py

• We strongly recommend creating a new clean virtual environment with python version 3.9 or higher. Then install the packages from the requirements.txt.

• Install miniconda3
• Open Anaconda Powershell Prompt terminal and navigate to SystemTools\scripts\FCN22
• Run the commands listed in fcn22_environment_installation_commands_conda.txt in the terminal.

• Install Python3 (version 3.9 or higher) in your operating system: The jupyter notebook files were generated with python 3.10 running on Windows 10 and Ubuntu 22.04, and any python installation working on these environments are viable options.

  • Windows Users: There are a few options you can use if your main OS is windows. We strongly recommend Windows Subsystem for Linux (WSL2) shell which is one of the easiest way to get access to an integrated linux environment in Windows. A great tutorial on how to install it is available in Ubuntu website.
  • Linux & Mac Users: You can skip to the next step.

• Check python version in your shell. In this example the version is 3.11 which fulfills the requirement:

  $ python3 --version
  Python 3.11.0rc1
  

• Make sure virtualenv is also installed in your environment:

  python3 -m pip install --user virtualenv
  

• Create a virtual environment for this script:

  $ python3 -m venv ~/FCN2
  

  or for Windows powershell

  python3 -m venv $home/FCN2 
  

• Activate the virtual environment:

  $ source ~/FCN2/bin/activate
  

  or for Windows powershell

  .\FCN2\Scripts\Activate
  

• Go to your SystemTools/scripts/FCN22 folder and install the requirements:

  $ pip install -r requirements.txt
  

• Navigate to the FCN22 folder and run the jupyter lab:

  $ cd SystemTools/scripts/FCN22
  $ jupyter lab --no-browser
  
  [truncated]
  To access the server, open this file in a browser:
          file:///home/username/.local/share/jupyter/runtime/jpserver-7983-open.html
      Or copy and paste one of these URLs:
          http://localhost:8888/...
      or http://127.0.0.1:8888/...
  

• At this point, by clicking on one of the links in the output, you should have access to the notebook.

You can create the html documentation locally with Sphinx using a theme provided by Read the Docs.

• Start terminal and activate the python environment FCN2
• Go to docs folder.
• Type

  make html
  

This creates build/html folder, where the index.html (double click or open from browser) is the root documentation folder.

If you use SystemTools for your work, we kindly ask you to cite any of our related article: Garnier Artiñano, Tomás, et al. Biophysical parameters control signal transfer in spiking network. Frontiers in Computational Neuroscience 17 (2023) 1011814.

You are encouraged to use Github's Issues to report bugs, or request enhancements or new features.

In alphabetical order:

• Vafa Andalibi
• Simo Vanni

• GPL3-Clause