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systematic behavior of the genes and proteins forming the complex p53-MDM2-p19ARF, as demonstrated
in this paper. Simulations can reduce the number of biological experiments and save the costs from both
sides of expense and time.
As demonstrated in this paper, the description of biological pathways with HFPN allows the biological
pathways to be simulated directly, since HFPN includes dynamic elements (transitions) at which reaction
speeds are assigned as well as static elements (places) which represent the states of substances such as
concentration. We have developed the automatic conversion systems of biological pathways in KEGG
and TRANSPATH into HFPN models [Nagasaki
et al.
, 2004]. By incorporating dynamic parameters
such as reaction speeds of translation and complex formation from the knowledge of biologists and/or
information in the literature into the converted HFPN models, the HFPN models become simulatable on
Cell Illustrator (
http://www.fqspl.com.pl/?a=product view&id=20&lang=en
).
We have recently developed a new biological pathway description format in XML called Cell System
Markup Language (CSML) (
http://www.csml.org/
). By using the CSML and this conversion system, we
are now working on the construction of a simulatable pathway database.
ACKNOWLEDGEMENTS
This work is partially supported by the Grand-in-Aid for Scientific Research on Priority Areas
17014067 and 17017007 from the Ministry of Education, Culture, Sports, Science and Technology
in Japan.
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