Sydney Brenner said, in his talk at a special session of 14th
International C. elegans Meeting at UCLA in 2003, that he had dreamed
just after the start of his research project to use a computer in the
study of C. elegans. Indeed he wrote by himself computer software to
reconstruct a neural system from cell morphology. He thought that some
principles of neural wiring might be possibly discerned by that work (D.
L. Riddle, T. Blumenthal, B. J. Meyer and J. R. Priess; p3 in C. elegans
II, Cold Spring Harbor Laboratory Press, 1997). I believe that the
studies of synaptic connectivity of neurons in the pharynx by Albertson
and Thomson and those of remaining somatic neurons by White, Southgate,
Thomson and Brenner are in line of that strategy of Sydney Brenner.
For the ultimate success of the strategy, collaboration of neural
anatomist and computer scientist should be extended to studies of
biological implication of the wiring. For that purpose, the illustration
in the papers of above mentioned authors, in which they illustrate
location of synapses on almost all neurons of hermaphrodite, should be
transformed into digital data which is readable by a program for
scientific computation. By the digital data, we can install the neuron
wiring on computers and, by appropriate numerical simulation, the worm
can live on computers.
In 1996, our project entitled by "Study of Biological Information
Systems by Models of Physical Complexity" started under the financial
support from Japan Society of Promotion of Science (Project number:
JSPS-RFTF 96I00102). Members of that research project had been disciplined
in various fields of computational physics and our ultimate goal was
"transplantation of biological information system on a computer". We
have referred to our core project with regard to the nervous system of
C. elegans as Cybernetic C. elegans Program (CCeP). Under that research
program, we digitized some features of the anatomical illustration and
constructed a database to be open to computer scientists. On the way of
this work, we found that there had been already three databases, the
database constructed by Achacoso and Yamamoto, that by Durbin, and that
by WormBase (http://www.wormbase.org)
We, however, found that the
original anatomical data includes more information than that digitized
by those people. In particular, we thought that information of location
of synapses on neurons will become important for the computational
research in future.
In 1998, the first version of the database by CCeP appeared. During our
research program using this database, we discovered that synaptic
connection in ventral cord was doubly counted in that database because
of our erroneous interpretation of tables of synaptic connection in
ventral cord. The correction needed change of structure of the database
and accordingly we should improve policy of constructing the database.
On constructing its first version, we employed the policy that the
database should involve information in the original paper as it stands.
We found during the work that the illustration of anatomical data
includes some evidently erroneous descriptions and some of which is
possibly improved. We, however, did not improve it because we believed
that agreement with the original data is essentially important for the
basic database. It is the work of users to modify the data file
according to their own policy, if they find some inconvenience in the
On constructing the new version of database, another policy is added to
the previous one: The database should provide enough information by
which the nerve ring illustrated in the original paper can be uniquely
reconstructed up to topology. Although precise scale of length is not
known, users can sketch the original illustration from the new version
of database. We expect that such structural information makes the worm
transplanted in computers more realistic.
Dr. J. G. White assisted us on interpreting description in the Table in
the original paper. His assistance was very helpful and fruitful and for
that I express my gratitude to him.
In conclusion, I would like to express my sincere thanks to K. Oshio,
Y. Iwasaki, S. Morita, Y. Osana, S. Gomi, E. Akiyama, K. Omata and K. Oka
for their laborious work and pay my respects to their completion of
constructing the database.
Department of Biosciences and Informatics,
Faculty of Science and Technology,
December 28, 2003