Caenorhabditis elegans is a species of nematode (roundworms). This little worm has been of great interest because it has a well-structured neural system which is at the same time primitive enough for mapping neuronwise. As a result of the efforts now we have the complete graph of the neurons of this worm. There is even an attempt to simulate both the physics and “brain” of C. elegans called OpenWorm.

On this page you can see a visualization of the brain graph of C. elegans along with a brief description on how one can process the original database of the connections.

Graph of C. elegans Neuron Classes

Original structure of the database:

Connections between cells or cell classes are listed in 3 files:
Albertson_Fig
White_Fig
White_Table

Structure of the database:

name_neurons.txt: similar to the original name_neurons.txt of (1), with the following corrections:
– some classes are missing from the original one, but appear in the files named above (e.g. G)
– some cells appear with a name in the files named above different from the original one (e.g. CEPshDL=CEPDL)
– some classes appear with a name in the files named above different from the original one (e.g. m1=M1)
– we put a # at the end of the corrected lines
ellista.txt: two classes are in the same row if there are any connections between them (without considering the direction or the type of the connection)
– we left out the “-” or the “MUSCLE” classes out from the original database
– the number next to the pair of cells refers to the number of the found connections in the database
foxamok.txt: this text file contains the connection number (degree) of the classes, ordered by name foxamok_ordered.txt: contains the degree of the classes, decreasingly ordered by degree
matrixgyarto.py: the script which created “ellista.txt” from the original database (Ce_synapse)
foxamlalo.py: the script which created “foxamok.txt” and “foxamok_ordered.txt” from “ellista.txt”

Packed data archives are downloadable here:

c_elegans.tar.gz c_elegans.zip

References:

(1) Database of Synaptic Connectivity of C.elegans for Computation, Oshio,Iwasaki, Morita, Osana, Gomi, Akiyama, Omata, Oka, Kawamura, 2003
(2) Albertson, D.G. and Thomson, J.N. 1976. The pharynx of Caenorhabditis elegans. Phil. Trans. R. Soc. Lond. B 275, 297-325.
(3) Oshio, K., Morita, S., Osana, Y., and Oka, K. (1998). “C. elegans synaptic connectivity data”, Technical Report of CCeP, Keio Future, No.1, Keio University.
(4) White, J. G., Southgate, E., Thomson J. N., and Brenner, S. (1986). “The Structure of the Nervous System of the Nematode Caenorhabditis elegans”, Phil. Trans. R. Soc. London, B 314, 1-340.

Eotvos Lorand University PIT Group