Thanks for pledging and encouraging others to pledge! Full disclosure: I’m the coordinator for the project. I’ve been having a look through the discussions on your references and I’d offer the following thoughts:
I think Hanson’s three part break down (Computing power, brain scanning, cell modeling) is useful and I agree that cell modeling is an important research investment that has not had enough focus, either academically or industrially. Better cell models is one of the technological advances that OpenWorm helps to address due to its approach to model a complete organism with such few cells.
I would add that none of these discussions seem to pick up on the additional benefits of cell modeling outside of the context of brain emulation, which include advances in complexity science in general, increased potential for tissue regeneration and repair, and better diagnostics and therapies for diseases. Remember, all living things have cells, so advanced cell modeling could give us a debugger and an editor for biology unlike anything we’ve ever seen.
In terms of funding open science via crowd funding as a differential technological development strategy, I would also point out that the results are held in a public commons (GitHub in our case) and this transparency and open access may be an important factor. Work like this is likely going to be done at some point, but if it isn’t publicly funded then it is likely to be privately funded and also privately held, and may add to asymmetrical control over these technologies. Personally, I prefer power to be distributed as a bulwark against tyranny. The more of these technological advances are out in the open, I think, the less likely the power of them will be concentrated in the hands of the few and used improperly.
Hi all,
Glad there’s excitement on this subject. I’m currently coordinating an open source project whose goal is to do a full simulation of the c. elegans (http://openworm.googlecode.com). More on that in a minute.
If you are surveying past c. elegans simulation efforts, you should be sure not to leave out the following:
A Biologically Accurate 3D Model of the Locomotion of Caenorhabditis Elegans, Roger Mailler, U. Tulsa http://j.mp/toeAR8
C. Elegans Locomotion: An integrated Approach—Jordan Boyle, U. Leeds http://j.mp/fqKPEw
Back to Open Worm. We’ve just published a structural model of all 302 neurons (http://code.google.com/p/openworm/wiki/CElegansNeuroML) represented as NeuroML (http://neuroml.org). NeuroML allows the representation of multi-compartmental models of neurons (http://en.wikipedia.org/wiki/Biological_neuron_models#Compartmental_models). We are using this as a foundation to overlay the c. elegans connectivity graph and then add as much as we can find about the biophysics of the neurons. We believe this represents the first open source attempt to reverse-engineer the c. elegans connectome.
One of the comments mentioned Andrey Palyanov’s mechanical model of the c. elegans. He is part of our group and is currently focused on moving to a soft-body simulation framework rather than the rigid one they created here: http://www.youtube.com/watch?feature=player_embedded&v=3uV3yTmUlgo Our first goal is to combine the neuronal model with this physical model in order to go beyond the biophysical realism that has already been done in previous studies. The physical model will then serve as the “read out” to make sure that the neurons are doing appropriate things.
Our roadmap for the project is available here: http://code.google.com/p/openworm/wiki/Roadmap
We have a mailing list here: http://groups.google.com/group/openworm
We have regular meetings on Google+ Hangout. If you want to help, we can surely find a way to include you. If you are interested, please let us know and we’ll loop you in.
Cheers, Stephen