- “Thought” Processes. This uses NeuroML, which is XML used to define biophysical and anatomical properties of the worm’s neurons. [caption id="attachment_93287" align="alignright" width="300"] The OpenWorm App[/caption]
- A simulation engine called “Gepetto,” which includes a WebGL visualizer. More details below.
- An OpenWorm Browser to let you view a 3D representation of each cell. This is also available as a 99 cent
- iOS app to help fund the project.
- A Fluid Mechanic Simulator to simulate the body of the worm and its environment.
- An Optimization engine using genetic algorithms.
OpenWorm Uses Java to Plunge into Microbiology
These days the worlds of biology, particularly microbiology, and computing are rapidly converging. Biological references made their way into computing a long time ago. We always find bugs in our code, though worms are a lot less common. Equally, the biological world at very low levels has become increasingly computerized, with simulations of protein folding algorithms used to identify possible new drugs. Then there is DNA sequencing that involves searching for nucleotides, the building block molecules of life. That involves string searching algorithms, machine learning and database theory in the growing field of bioinformatics. Now, the ever increasing processing power of silicon has led to the OpenWorm project, an attempt to synthesize a digital nematode, C. elegans. This is short for Caenorhabditis elegans, Greek and Latin words meaning recent, elegant rod-like. It’s better known as a roundworm, one of man’s oldest enemies. Think hookworms and pinworms. The project’s intention is to try and understand how a roundworm works by simulating it digitally from the bottom up. Nematodes have just under 1,000 cells yet they are good at finding food, mates and avoiding predators. How they manage to do this remains something of a mystery, and the hope is that the project will bring new insights. The OpenWorm project has several activities going on in parallel. These look at