We have converted all 302 neurons described in the WormBase Virtual Worm Blender files into multi-compartmental neuronal models described in NeuroML format. We are currently building descriptions of the synaptic junctions and the ion channels for each cell. You can explore the github repository.
We are engineering Geppetto, a Java OSGi 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.
The OpenWorm Browser enables ready access to a cell-by-cell 3D representation of the nematode C. elegans in a WebGL enabled browser. Checkout the source code and find out more on the github repository. We also ported this project to an iOS app to support the project.
We have implemented an algorithm called Smoothed Particle Hydrodynamics (SPH) to simulate the body of the worm and its environment using GPUs. This algorithm has been initially worked out in C++ (with OpenGL visualization), then ported to Java as a bundle for Geppetto, our simulation engine.
The Optimization Engine uses optimization techniques like genetic algorithms to help fill gaps in our knowledge of the electrophysiology of C. elegans muscle cells and neurons. Check out the code on the github repository.