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Figure 2 | BMC Systems Biology

Figure 2

From: Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case

Figure 2

A Petri net and its unfolding. A: A Petri net and its unfolding. The net contains 'places' (light blue circles), the model's entities, and 'transitions' (rectangles), which constitute the regulation functions and define the model's dynamics. Arcs connect input places to transitions, and transitions to their output places. Places that receive discrete values are called tokens (blue dots). A transition that is activated, or 'fired', reduces the tokens in its input places and increases the number of tokens in each of its output places. At any time step, every transition that has enough tokens in its input places may be fired. In the example, every transition consumes one token from every input place, and produces one token at every output place. Labels next to thick arrows indicate which transition fired. Transitions t1 and t3 can be fired in alternation indefinitely, whereas no other transition can be fired after t2 has fired. B: Unfolding of the Petri net. Transitions are represented by rectangles, places by circles. The two places p1 and p2 that have tokens in the initial marking in state I are the input-less places of the unfolding. The local configuration of t2 at layer 2 corresponds to the marking 010, i.e. the marking in which only p2 contains a token, corresponding to II in Figure 2A. The local configuration of t3 corresponds to the firing of t1 followed by t3, and to the marking 110, i.e. the initial marking. The instances of t1 and of t2 at layer 6 are cutoff points, since their local configurations' markings are already represented by other local configurations. The graph constitutes a branching process.

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