Biology Reference
In-Depth Information
The availability of the algorithm has been confirmed by the results of application to the IL-1 signaling
pathway model.
Using our method, the range of delay times of transitions can be decided by introducing the concept
of probability to the conflict transitions. Our method makes it possible to automatically determine the
delay times of all the transitions representing biological reaction rates in signaling pathways according
to the delay times of reliably determined transitions. In the meanwhile, when several delay times of
the transitions have been given in advance based on confirmed biological facts, the delay time of other
transitions can also be determined mechanically.
The Petri net dealt with in this paper is constrained to an acyclic one without inhibitor arcs. However, it
is obvious that there exist cyclic structures in signaling pathways such as feed-back loops and self-loops.
Therefore, as the future work, we will aim to develop our current method further to deal with the Petri
net model including various kinds of net structures.
ACKNOWLEDGEMENTS
This work was partially supported by Grant-in-Aid for Scientific Research on Priority Areas “Systems
Genomics” (17017008) from Ministry of Education, Culture, Sports, Science and Technology of Japan.
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