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Preface


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 database.

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.


Kiyoshi Kawamura
Department of Biosciences and Informatics,
Faculty of Science and Technology,
Keio University
December 28, 2003



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