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data for simulations. Visualizations of the biopathways introduced in this paper will be reported in the
future.
Most of existing biopathways simulation tools only compute time courses of concentration behaviors
of biological objects such as proteins and mRNAs. However, in general, distributions of these biological
objects are not uniform because of compartmentalization. Thus, for more precise simulation, more
complex information such as localization of biological objects and molecular level cell-cell interactions
should be included in simulation models. In order to address this problem, we introduced the concept
of hybrid functional Petri net with extension (HFPNe) and developed “ Genomic Object Net ver.1.0”
based on the notion of HFPNe ( http://www.GenomicObject.Net/ ) . One of the features of HFPNe is that
places of the HFPNe can have several types of data such as integer, real, Boolean, string, and vector.
With this feature, the HFPNe allows us to include the more complex biological information in compu-
tational biopathway models. We will demonstrate modeling methods for describing the computational
biopathway model with Genomic Object Net ver.1.0 in the near future.
ACKNOWLEDGEMENTS
This work was partially supported by the Grand-in-Aid for Scientific Research on Priority Areas
“Genome Information Science” from the Ministry of Education, Culture, Sports, Science and Technology
in Japan.
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