MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics
Fig 3
Stochastic Petri net (SPN) implementation of MGDrivE 2.
(A) Petri net representation of the life history module. The set of purple circles corresponds to places, P, and red rectangles to transitions, T. This Petri net shows a model in which development times for the egg stage are Erlang-distributed with shape parameter n = 2, and for the larval stage are Erlang-distributed with shape parameter n = 3. Population dynamics are derived directly from this graph. E.g. The transition corresponding to oviposition has one edge beginning at F, meaning at least one female mosquito must be present for oviposition to occur. When oviposition occurs, a token is added to E1 (new eggs are laid) and a token is returned to F. (B) Conceptual representation of the SPN software architecture showing the separation between the model representation (blue circles) and set of sampling algorithms (red rectangles). These two components of the codebase meet at the simulation API, enabling users to match models and simulation algorithms interchangeably. Output may be returned as an array in R for exploratory work, or written to CSV files for large simulations.