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To optimize (1), we proposed a greedy transition algorithm, called Final State Oriented Token Transition.
Implementing the Final State Oriented Token Transition algorithm of (2), we do not expect the final state (treated state) is achieved immediately by transition of a relatively large number of tokens, which will cause a high deviation for the identified numbers of gene or drugs tokens by running the algorithm for 1000 times.
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Input tokens and output tokens from a transition correspond to their arc weights, so the number of input tokens can change when they become output tokens [16].
The effects of drugs on molecule expressions and the associated pathways are simulated by the defined tokens and transitions in different colors in the model.
The number of drug tokens for every transition is determined by two parts, one is the number of drug tokens in the output place that have been transited by its downstream interactions, and another is a randomized number also derived from (3) to indicate how many drug tokens should be transited additionally.
However, modeling real complex systems requires the possibility of transforming the nature of tokens through a transition.
The number of gene tokens for every transition is a randomized number μGamma derived from a Gamma distribution, (3) where k, ϑ are two parameters for scale and shape of the Gamma distribution, and Γ k)= k−1)!
Fourth, the construction of the finite-net process (p = mathrm{INet}(N(m_0))) from the finite P/T net system (N(m_0)) is inaccurate in [18], as Net(p) may have more transitions than (N(m_0)); as the previous construction used too few bound names, it was impossible to link precisely the tokens consumed by a transition to the actual place from which these tokens are to be consumed.
In a timed Petri net, a waiting time is associated with the token, and the corresponding transition can be fired only if the associated waiting time has elapsed (the ribosome moves with the stochastic event rate).
When a transition fires, tokens from substrate pre-places are consumed and tokens representing products fired to post-places; the states of pre-places connected to transitions by read or inhibitor edges are not changed.
Green arcs A G transit gene tokens from input place to transitions or transit gene tokens from transitions to output place.
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