celegans CNS sofware?

Leon Avery leon at eatworms.swmed.edu
Fri Sep 1 06:05:20 EST 1995


I tried to e-mail this reply to Aquiles Lima-Rodriguez, but his e-mail
address doesn't seem to be working.  So, with apologies to those who
don't care about the answer, I am posting it in the hope that he will
see it here.


In article <424eaq$b73 at rzsun02.rrz.uni-hamburg.de>, you write:
|> As part of my graduation work in psychology, I´m writing a kind
|> of tool-box program to simulate neural systems. My approach has
|> little to do with typical ""neural"" networks, I´d rather try
|> to describe a chemical reaction and simulate the behavior of
|> real neurons.
|>     I´ve heard that C. elegans would be an even better animal
|> model than Aplysia, because it has a CNS about 300 cells big,
|> *all* cells are known and its behavior it´s relatively simple.
|>     A professor told me that there is a complete description
|> of C. elegans CNS available as software, but I haven´t been able
|> to find it (if it realy exist).  I´m also interested in the 
|> synaptic connections, neurotransmitters involved and learning
|> capabilities (if any :-) ).

I presume you know of the two main published papers: Albertson and
Thomson 1976 for the pharyngeal nervous system and White et al 1986
for the extrapharyngeal.  Richard Durbin, who was a grad student with
John White, made a little database of all the synaptic connections and
a little program to look thing up in it.  He left me a copy but it's
been lost in the many years since.  He probably could still lay his
hands on at least the database, though.  He's at rd at sanger.ac.uk.  In
addition, a guy called Ay typed all the commections in from White et
al, and this was published by CRC Press as "Ay's computer atlas of the
C elegans nervous system", or something like that.  I would go for the
original if I were you.  There is no computerable pharyngeal nervous
system description that I know of, but that is fairly simple: you
could type it in from the paper in a couple hours.

I want to add one thing.  C elegans folk often say that we have a
complete map of the nervous system synaptic connectivity based on EM
reconstructions.  I don't believe this statement, mainly because I and
others have done experiments whose results we could predict based on
the supposedly completely known synaptic connectivity, and the
predictions were wrong.  In addition, some types of synapses would
have been missed with the fixation techniques used in the EM
reconstructions.  When I was a postdoc with John White another
postdoc, Siegfried Hekimi, did some EM with glutaraldehyde fixation
and very thin sections, and saw synapses in at least one pharyngeal
neuron where Albertson and Thomson hadn't reported any.

The EM reconstructions are useful, but their usefulness is often
overstated.

-- 
Leon Avery					   (214) 648-2420 (office)
Department of Biochemistry			            -2768 (lab)
University of Texas Southwestern Medical Center             -8856 (fax)
5323 Harry Hines Blvd				   leon at eatworms.swmed.edu
Dallas, TX  75235-9038			  http://eatworms.swmed.edu/~leon/



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