at http://www.mathmlcentral.com, a Web site of Wolfram Research (the company
that produces Mathematica). This site offers three valuable Web services for free: va-
lidating whether a given MathML expression is syntactically correct, rendering of
presentation markup MathML into different graphics formats, and conversion of a
mathematical expression that is given in Mathematica syntax into the different types
of MathML. With this wealth of resources available on the Net, it should be no prob-
lem to master MathML.
448
14 Modeling Tools
References
Bernardinello, L. and de Cindio, F. A survey
of basic net models and modular net classes
(1992) Springer Verlag, Berlin.
Campbell, N.A. and Reece, J.B. Biology (2001)
6th Edition, Benjamin Cummings.
Comisky,W.,Yu, J. and Koza, J.R. Automatic
synthesis of a wire antenna using genetic pro-
gramming (2000) Genetic and Evolutionary
Computation Conference.
Finney, A. and Hucka, M. Systems biology
markup language: Level 2 and beyond (2003)
Biochem. Soc. Trans. 31, 1472–3.
Funahashi, A.,Tanimura, N., Morohashi, M.
and Kitano, H. CellDesigner: a process dia-
gram editor for gene-regulatory and biochem-
ical networks (2003) Biosilico 1, 159–162.
Gibson, M.A. and Bruck, J. Efficient exact sto-
chastic simulation of chemical systems with
many species and many channels (2000) J.
Phys. Chem. 104, 1876–1889.
Gillespie, D.T. Exact stochastic simulation of
coupled chemical reactions (1977) J. Phys.
Chem. 81, 2340–2361.
Gillespie, D.T. Approximate accelerated sto-
chastic simulation of chemically reacting sys-
tems (2001) J. Chem. Phys. 115, 1716–1733.
Hanisch, D., Zimmer, R. and Lengauer,T.
ProML–the protein markup language for spe-
cification of protein sequences, structures and
families (2002) In Silico Biol. 2, 313–24.
Holland, J.H. Adaptation in natural and artifi-
cial systems: An introductory analysis with ap-
plications to biology, control, and artificial in-
telligence (1975) University of Michigan
Press, Ann Arbor, MI.
Hucka, M., Finney, A., Sauro, H.M., Bolouri,
H., Doyle, J. and Kitano, H. The ERATO Sys-
tems Biology Workbench: enabling interaction
and exchange between software tools for com-
putational biology (2002) Pac. Symp. Biocom-
put. 450–61.
Hucka, M., Finney, A., Sauro, H.M., Bolouri,
H., Doyle, J.C., Kitano, H., Arkin, A.P.,
Bornstein, B.J., Bray, D., Cornish-Bowden,
A., Cuellar, A.A., Dronov, S., Gilles, E.D.,
Ginkel, M., Gor,V., Goryanin, II, Hedley,
W.J., Hodgman,T.C., Hofmeyr, J.H., Hun-
ter, P.J., Juty, N.S., Kasberger, J.L., Kreml-
ing, A., Kummer, U., Le Novere, N., Loew,
L.M., Lucio, D., Mendes, P., Minch, E.,
Mjolsness, E.D., Nakayama,Y., Nelson, M.R.,
Nielsen, P.F., Sakurada,T., Schaff, J.C.,
Shapiro, B.E., Shimizu,T.S., Spence, H.D.,
Stelling, J.,Takahashi, K., Tomita, M.,
Wagner, J. and Wang, J. The systems biology
markup language (SBML): a medium for re-
presentation and exchange of biochemical net-
work models (2003) Bioinformatics 19, 524–
31.
Hucka, M., Finney, A., Bornstein, B.J., Keat-
ing, S.M., Shapiro, B.E., Matthews, J., Ko-
vitz, B.L., Schilstra, M.J., Funahashi, A.,
Doyle, J.C. and Kitano, H. Evolving a lingua
franca and associated software infrastructure
for computational systems biology: the Sys-
tems Biology Markup Language (SBML) pro-
ject (2004) Syst. Biol. 1, 41–53.
Ishii, N., Robert, M., Nakayama,Y., Kanai, A.
and Tomita, M. Toward large-scale modeling
of the microbial cell for computer simulation
(2004) J. Biotechnol. 113, 281–94.
Koza, J.R. Genetic programming: On the pro-
gramming of computers by means of natural
selection (1992) MIT Press, Cambridge, MA.
Koza, J.R., Bennett, I.F.H., Andre, D. and
Keane, M.A. Genetic programming III: Dar-
winian invention and problem solving (1999)
Morgan Kaufmann, San Francisco, CA.
Koza, J.R., Mydlowec,W., Lanza, G.,Yu, J. and
Keane, M.A. Reverse engineering and auto-
matic synthesis of metabolic pathways from
observed data using genetic programming