OpenWorm Building Life Cell By Cell
Written by Lucy Black   
Sunday, 25 May 2014

The nematode worm C. elegans is going where no worm has gone before - into cyberspace. The Open Worm project aims to build a complete and accurate simulation of the first animal to be transferred to code. 

The most important thing about C.elegans is that it has only 1000 cells and only 302 are neurons. We also know a lot about C.elegans because it is easy to work with. Its transparent skin allows cells to be tracked using fluorescent dye as it develops. We not only have its complete genome we have the details of its development at the cellar level including its brain and the 5500 plus connections.




The OpenWorm project aims to make use of this knowledge to create a simulation of the worm working at the level of chemistry making it the first animal to be re-created as software. 

The project has been going a while but it recently made a pitch on Kickstarter for $120,000 to develop the simulation to the point where the neurons control the body of the worm. You can appreciate how big a project this is when you realize that the liquid that the worm is swimming in is provided by a particle based hydrodynamics simulator.

At the moment the project has managed to create a simulation of the worm swimming. It took 47 hours of computing time to simulate one third of a second of worm time. With the funds from the Kickstarter, which was successful, they hope to add the 302 neurons. 



The rewards offered on KickStarter might strike some as bizarre:  T-shirts featuring C.elegans, access to an online version of the simulation called WormSim and an online course on the worm and artificial life in general. WormSim is based on Geppetto, a computational biology simulator, another open source project worth finding out about. 




So why is this a good idea?

The only way of understanding a complex system like C.elegans is to simulate it and see if the simulated worm behaves like the real thing. The Kickstarter campaign mentions curing Alzheimer's or Parkinson's disease, but to be honest this is a step on the way to bigger things. We need to understand the brain of a worm before we can move on to something more complex.

The Kickstarter video gives you an idea of what the objectives are:




It might also give philosophers something to think about - is the simulated worm alive?

Then there is the interesting question of "refactoring" - how much of the system can be modified or simplified without destroying its accuracy.?

The whole idea is intriguing beyond the aspirations of computational biology and perhaps this is what motivated the pledges in the Kickstarter campaign rather then the T Shirts. 





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Last Updated ( Sunday, 25 May 2014 )