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. 2005 Mar-Apr;12(2):181–199. doi: 10.1197/jamia.M1637

Figure 7.

Figure 7.

The results of experiments performed by the Mobius tool (plotted using Microsoft Excel). Whereas in TimeNET and Genomic Object Net, a single experiment can examine individual places (or sets of places in TimeNET) as a function of time, a Mobius experiment measures the number of tokens in a place or the number of times that a transition was fired at a single point in time or the total or average number over an interval of time. To generate a kinetic profile in Mobius, several experiments need to be executed. On the other hand, in a single experiment in Mobius, the user can vary many structural parameters. However, plots are not generated automatically by Mobius. A: The number of transitions fired as a function of immune_probability with burst size 50. This curve plots the number of two transitions that were fired: Immune_Response and Asexual_Development as a function of the probability of going in the path of an immune response from Place1 of the composed model shown in ▶, rather than executing the other transition that uses Place1 as an input place (MerozoiteInBlood, left-hand SAN in ▶). The parameter burst size indicates the number of tokens that are output by the output gate shown on the left-hand side of ▶. B: Drug effect (cell death as a function of drug dose). C: Inactive drug/drug effect as a function of drug dose. B, C: Results that were generated from simulation of the Gemcitabine model shown in ▶. The plots show token markings as a function of time: the number of tokens at a place that indicates drug effect (CellDeathPlace + Place13) (B) and the ratio of the sum of tokens in the places that indicate inactivated drug (DeactivatedC, DeactivationDrug, InactiveDrug, marked by arrows in ▶) divided by the number of tokens at the place that represents drug effect (CellDeath + Place13) (C). Because the places that indicate inactivated drug include two places that store both drug tokens and cytidine tokens (DeactivatedC, DeactivationDrug), we multiplied the number of tokens stored in those places by the ratio of drug concentration to the concentration of cytidine + drug.