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Programming Worms

May 3, 2013

No, not as in malware – a program that replicates itself as it moves from machine to machine – but as in an actual dirt-loving, squirming-about, icky-spaghetti worm.

This link comes off of Boing Boing.  The project is called OpenWorm, and it self-describes as:

OpenWorm is an open source project dedicated to creating the world’s first virtual organism in a computer, a C.elegans nematode. We plan to achieve this goal by 1) bringing together highly motivated scientists and engineers 2) pushing away all the red tape 3) fostering growth of a completely open computational biology community.

So, its not building a real worm – a virtual worm.  The worm they are hoping to replicate – Caenorhabditis elegans – is a nematode worm about 1 mm long; there’s about 1,000 cells in each one of these tiny critters.

How is this being done?  Hard to say.  The project milestones are here … here’s an example:

Muscle Cell model output closely matches that of real data

We will show that we have built a model of C. elegans muscle cell that matches data recorded from the nematode muscle cell. In part, we will use techniques of model optimization to fill in gaps in the model parameter space (deduce unmeasured parameters). The main technical challenge is tuning muscle cell passive properties and building a larger data set (more cell recordings). Mike Vella will take the lead on this.


Do we need virtual worms?  No, not as such – but we need these types of projects, that’s is what science is, right?  There’s too much of the attitude these days that all R & D needs to be dedicated to obvious needs.  I for one think we need more scientia gratia scientiae.

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  1. May 3, 2013 at 4:20 am

    Quick! Alert the virtual tequila industry!

    Seriously, I agree with you. Limiting research to only those things with immediate payback is an inherently limiting approach. Down the road this could have all sorts of implications in biology, engineering, or neurochemistry (to name just a few), but we’ll never find out what they are if we stay focused on the short term view.

  2. May 3, 2013 at 9:58 am

    What could have caused this apparent change in industry where it seems that in the past there was a lot of pure research and today everything is focused for the short term? Is it the stock market that expects quarter to quarter improvements? Is it the greater ability to track investment and return?

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