C. elegans Neural Interactome Beta (Python 3.8)

Introduction

C. elegans Neural Interactome is an interactive simulation platform for the neuronal network of Caenorhabditis elegans worm. It incorporates both static connectome and dynamic biophysical processes to simulate/visualize the network dynamics and allow users to interact with the network in real-time via stimuli injection/network modifications. For more detailed information please refer to the published paper in Front.Compute.Neurosci.

Web Interface

Web service running the latest version of Neural Interactome is available at:

http://neuralcode.amath.washington.edu/neuralinteractome

Installation (Windows)

We recommend to install Windows Anaconda for Python 3.8 since it has most of the package necessary for Neural Interactome. Once you install Anaconda, you will have to install the following additional packages through Anaconda prompt:

• pip install flask
• pip install flask-socketio
• pip install eventlet=0.26.0 (Latest version has issues regarding monkey patch in Windows)

Once you have installed these dependencies, unzip the cloned zip file to your desired location. Navigate to the Neural Interactome folder (location of initialize.py) in Anaconda prompt, and type

python initialize.py

This will set up the local Neural Interactome server. Once the server is up, go to the browser and enter your localhost address (127.0.0.1:5000) to access the Neural Interactome.

Installation (Linux/Mac)

For Linux/Mac, if you have Python 3.8 installed, you just make sure that you have all the depenedencies below installed. Once all the dependencies have been installed, navigate inside the Neural Interactome folder (where initialize.py is located) in terminal, and type

python initialize.py

This will set up the local Neural Interactome server. Once the server is up, go to the browser and enter your localhost address (127.0.0.1:5000) to access the Neural Interactome.

Dependencies

• numpy
• scipy
• eventlet
• flask
• flask-socketio

Saving Neural Dynamics Data

For each simulation session, you can save the simulated data for all neurons by either: (i) clicking the reset button or (ii) exiting the localhost web page. The voltage dynamics of all neurons will be saved in .npy format and can be found within installation path/saved_dynamics folder. The file can be loaded directly with Python numpy package using the command np.load('saved_dynamics.npy').

The rows and columns of the saved_dynamics.npy are "timepoints" and "neurons' indices". Each row corresponds to individual time point in 0.01 seconds (10ms) resolution. i.e. row 1 = 0s, row 2 = 0.01s, row 3 = 0.02s ...

Columns are neurons which is ordered from head to tail direction. In order to get their names, please refer to 'neuron_names.txt'.

For further information refer to:

Neural Interactome: Interactive Simulation of a Neuronal System

Jimin Kim, William Leahy, Eli Shlizerman

Published paper: Frontiers in Computational Neuroscience https://www.frontiersin.org/articles/10.3389/fncom.2019.00008/full

The paper has to be cited in any use or modification of the dataset or the code.