GSoC Project Idea 16.3: Web based C. elegans integrated simulation explorer

html5
javascript

#1

The OpenWorm project is building a simulation of the C. elegans in an open science fashion. A prototype of an integrated simulation explorer was presented at the Royal Society of London in January 2018 (screenshot below). The prototype integrates electrophysiology simulation (via C302) and fluid dynamics simulation (via Sibernetic) for the body of C. elegans and makes it available for replay and exploration in a web based environment, based on the Geppetto neuroscience platform. This proposal is about taking that prototype and develop it further making it ready for public consumption.

Aims: The primary project aims are as follows:

  • Develop a web application that will let people create their own worm, visualize it and run multiple simulations.
  • Work on the backend of the application to extract data from Sibernetic and make it available as recordings. Pre-existing prototype code is available as a starting point.
  • Work on the frontend of the application to visualize the nervous system simulation (top left widget in the screenshot) and the body simulation (background canvas). Pre-existing prototype code is available as a starting point.

When this project is complete, the candidate would have reached at least basic aims to enable a release of the application to the OpenWorm community and the C. elegans computational modelling community at large of the web based C. elegans simulation explorer.

Skills: Essential: Javascript, HTML5,

Desired but not essential: React, Three.js, Java, basic computational neuroscience knowledge.

Mentors: Matteo Cantarelli (matteo@openworm.org), Giovanni Idili (giovanni@openworm.org), Stephen Larson (stephen@openworm.org)


#2

A screenshot of the prototype currently existing:


and the link to the full video https://www.youtube.com/watch?v=M0rpT831ngM let me know if you have any questions!
Best of luck with your proposal :slight_smile:
Matteo