Neurotransmitter Time Constants (PSCs)

This repository contains the files that generate a reference page for neurotransmitter time constants. It consists of

• data.csv - The data that is used to build the plots and table.
• make_webpage.py - A script that uses template.md to generate a markdown file containing the source for this page.
  • Requires jinja2
• plot_data.py - A script that plots the PSC rise times and decay time constants grouped by receptor type.
  • Requires numpy and matplotlib.
• README.md - This file; describes the repository and how to use it.
• requirements.txt - A list of Python packages required by scripts in this repository. This can be read and used by pip.
• template.md - A file used by jinja2 to generate the webpage.

Installing requirements

In order to use these scripts, you will have to install some Python packages. The easiest way is with:

pip install -r requirements.txt

Depending on your setup, this may fail because older versions of matplotlib require numpy to be installed prior to installation. If the installation fails, install numpy first and then proceed with installation:

pip install numpy
pip install -r requirements.txt

If these instructions are not working for you, try installing Anaconda, which contains all the necessary packages.

Usage

To generate the plots, run

python plot_data.py

This will generate decay.svg and rise.svg, which can be uploaded to the website.

To generate the webpage, run

python make_webpage.py

This will generate neurotransmitter-time-constants-pscs.md, which can be uploaded to the website (for generating http://compneuro.uwaterloo.ca/, it is instead pushed to this git repository).

Contributing

We welcome contributions of any kind! We would especially like to increase the amount of data that we're curating and visualizing. You can suggest a paper for us to look at by filing an issue. Or you can add it in and send us a pull request!

If you would like to add in additional data, add it to data.csv, and add the corresponding source to template.md. If you would like to change the plots, edit plot_data.py. If you would like to change the main table, edit make_webpage.py and template.md. If you would like to change the text on the page, edit template.md.

Credits

• Peter Jones: Wrote the original Matlab script, collected all of the references and data.
• Trevor Bekolay: Converted script to Python.