Geppetto Simulation Engine

In order to allow the world to play with the model easily, we are engineering Geppetto, an open-source modular platform to enable multi-scale and multi-algorithm interactive simulation of biological systems. Geppetto features a built-in WebGL visualizer that offers out-of-the-box visualization of simulated models right in the browser. You can read about architectural concepts and learn more about the different plug-in bundles we are working on.

Geppetto, is written in Java and leverages technologies like OSGi, Spring Framework, OpenCL and Maven.

Geppetto’s frontend is written using THREE.js and WebGL. Back-end / front-end communication happens via JSON messages through WebSocket.

The engine runs on on Eclipse Virgo WebServer deployed on an Amazon Elastic Compute Cloud Linux instance.

Previous accomplishments

  • Past releases of Geppetto

Current roadmap

STORY: Worm wiggling in the browser

As a user, I want to see the proof of concept sibernetic worm in my web browser so that anyone around the world can play with it.

Practically, this means porting the proof of concept scene into Geppetto.

STORY: Interactive worm wiggling in browser

As a user, I want to be able to see a visualization of the proof of concept worm wiggling in my web browser and be able to perturb it in a manner that causes the wiggling to change in a realistic manner.

This milestone suggests interactivity via Geppetto. The kind of perturbation is not defined yet– ideally we should aim for the simplest kind we can think of that gives the user an interface to make modifications.

Issues list

The issues related to Geppetto are distributed across different repositories.

Issues related to general functionalities that need to be added to support the OpenWorm simulation are found here.

Issues related to the platform in general are found here.

Ultimately every module of Geppetto has issues of its own, see the list of repositories below.

The issues are so splitted to allow capturing different granularities, having both issues that reflect what macro functionalities need to be added in the OpenWorm and Geppetto repository and having detailed close-to-the-code bugs in the individual repositories.

Associated Repositories

Repository Description Language
org.gepetto Geppetto Main Bundle and packaging Java
org.geppetto.solver.sph PCI SPH Solver bundle for Geppetto Java
org.geppetto.simulator.jlems jLEMS based simulator for Geppetto Java
org.geppetto.model.neuroml NeuroML Model Bundle for Geppetto Java
org.geppetto.core Geppetto core bundle Java
org.geppetto.frontend Geppetto frontend bundle - Web application Java
org.geppetto.testbackend Geppetto test backend for Geppetto Java
org.geppetto.simulator.sph SPH Simulator bundle for Geppetto Java
org.geppetto.simulation Generic simulation bundle for Geppetto Java
org.geppetto.model.sph PCI SPH Model Bundle for Geppetto Java
org.geppetto.samples Sample simulations for Geppetto Descriptive
org.geppetto.templatebundle Template bundle Java