Databases and Systems

Availability of the Pathways, Software, and Models
The PUMA (http://www.mcs.anl.gov/home/compbio/PUMA/Production/puma.
html), WIT (http://www.cme.msu.edu/WIT/) [7], and WIT2
(http://www . mcs. anl. gov/home/overbeek/WIT2/CGI/user.cgi) systems were
developed at Argonne National Laboratory in close cooperation with the team of
Evgeni Selkov in Russia. The beta release for WIT2 has been sent to four sites and is
currently available. The first actual release of WIT2 is scheduled for October 1997. It
will include all of the software required to install WIT2 and develop a local Web
server, all of our metabolic reconstructions for organisms with genomes in the
publicly available archives, and detailed instructions for adding any new genomes to
the existing system (perhaps, for local use only). Just as widespread availability of
the Metabolic Pathway Database has stimulated a number of projects relating to the
analysis of metabolic networks, we hope that the availability of WIT2 will foster the
development and open exchange of detailed metabolic reconstructions.
Acknowledgments
R.O. was supported by the U.S. Department of Energy, under Contract W-31-109-
Eng-38. N.L. was supported by the Center for Microbial Ecology at Michigan State
University (DEB 9120006). We also thank the Free Software Foundation and Larry
Wall for their excellent software.
References
1. Badger, J. H., and Olsen, G. J. CRITICA: Coding Region Identification Tool Invoking
Comparative Analysis, Molec. Bil. Evol., 1977, in press.
2. Borodovsky M., and Peresetsky, A. Deriving Non-Homogeneous DNA Markov Chain
Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy. Comput
Chemistry, 18, no. 3, 1994, pp. 259-267.
3. Ellis, L.B.M., and Wackett, L. P. A. Microbial Biocatalysis Database, Soc. Ind. Microb.
News. 45, no. 4, 1995, pp. 167-173.
4. Kanehisa, M., Toward Pathway Engineering: A New Database of Genetic and Molecular
Pathways, Science and Technology Japan, 59, 1996, pp. 34-38.
5. Karp, P, Riley, M., Paley, S., and Pellegrini-Toole, A. EcoCyc: Electronic Encyclopedia
of E. coli Genes and Metabolism, Nucleic Acids Research, 25, no. 1, 1997
6. Nelson, O., Coe, E., and Langdale, J., Genetic Nomenclature Guide. Maize. Trends
Genet., March, 1995, 20-21
7. Overbeek O., Larsen, N., Smith, W., Maltsev, N., and Selkov, E.. Representation of
Function: The Next Step. Gene-COMBIS (on-line): 31 January 1997; Gene 191, no. 1,:
GC1-9
8.
Selkov, E., Basmanova, S., Gaasterland, T., Goryanin, I., Gretchkin, Y., Maltsev, N.,
Nenashev, V., Overbeek, R., .Panushkina, E., Pronevitch, I., Selkov Jr., E.., and Yunus,
I. The Methabolic Pathway Collection from EMP: The Enzymes and Metabolic Pathways
Database. Nucleic Acids Research, 24, no. 1 (database issue), 1996, pp. 26-29.
45