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PSFs are created by simulating a perturbation at a single point.
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Each time series experiment consisted in strongly increasing or decreasing the initial expression of about one-third of the genes, thereby simulating a physical or chemical perturbation.
This is done by simulating the model at a point near the equilibrium (1% equilibrium perturbation in the three densities).
We investigated the effects of perturbations by simulating reductions in Dbf4, Cdt1 and Cdc6 in our model.
We do so by simulating in the computer the avalanche of perturbations in the gene expression profile of the genetic networks of these organisms.
Afterwards, as a final step, the algorithm determines which DEPCs are not necessary to be directly perturbed (see Figure 3c) by simulating the network response (according to the model assumed to compute attractors) under perturbation of the minimal combination of genes but the gene belonging to specific DEPCs one at a time.
Below, we address this issue by using simulated perturbation responses of a 10 gene and a 100 gene GRN and compare its performance with that of (stochastic) MRA, SBRA and LMML.
Parry, written by Stanford University psychiatrist Kenneth Colby, simulated a human paranoiac.
As suggested by [ 35], we simulated genetic perturbation by limiting flux through all reactions associated to a specific enzyme by a fixed amount of the wild-type geometric FBA flux (0%, 10%, 90%).
Fig. 2 simulates a targeted event corresponding to an external stimulus, taken as a perturbation of the nontrivial steady state by a momentary increase in the number of osteoclasts.
The dynamics was generated by continuous differential equations with the inclusion of perturbations on the data in order to simulate a physical or chemical intervention.
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