BactAdaptable
The BactAdaptable species derives from the BactEPS species, but adds the ability to change its set of active reactions based on definable conditions. The mechanism for this switching behavior is an ON/OFF state switch, with each state having a particular set of active reactions that are set as inactive when the switch is in the opposite state. You may use local solute concentrations or agent biomass amounts as switch conditions; this example mark-up uses the local oxygen (MyO2) concentration as the switch condition.
The first part of the species mark-up proceeds as for the other types. After all possible reactions have been defined, the reactionSwitch mark-up is used to define the behavior of the switch. The first two sub-mark-ups, whenOff and whenOn, define which reactions will be active for those respective switch states. (Note that it is not necessary to explicitly set an on-state reaction as ‘inactive’ when the switch is in the off-state; the turning on and off of reactions is taken care of automatically.) Each sub mark-up also defines the lag time (switchLag) before the switch is actually put in the relevant position, and is meant to capture microbial metabolic delays. In the example above, when conditions are such that the switch should be put in the ON state, the switch will not actually occur until after a delay of 3 hours; in contrast, the switch will move to the OFF position with no delay because the parameter switchLag is 0 for the whenOff state. (Note that if a switch is triggered but not yet activated because of the lag, a reversal of conditions will cancel the switch request.) Finally, the ON/OFF states each include a color definition, which set what color the agent should be in the POV-Ray output; setting a different color for each switch state is useful in analyzing simulation output.
The onCondition mark-up defines the condition for which the switch will be moved to the ON state, with the opposite condition moving the switch to the OFF state. The attribute type may be either ‘solute’ or ‘biomass’, and sets whether the condition is based on a local solute concentration or the agent’s biomass amount. The name attribute defines the solute or particle type that is used to decide the switch state. For the onCondition mark-up, the switch parameter may be set to either ‘lessThan’ or ‘greaterThan’, and for solutes there is a concentration parameter that is used to set the threshold value. In the example above, the switch will be moved to ON when the local oxygen (MyO2) concentration is below 0.25 mg/L, and will be moved to OFF when the concentration is above that value; these states lead to anaerobic and aerobic growth, respectively. For a switch based on a biomass amount, the onCondition mark-up looks as follows:
The name attribute must refer to one of the particle types defined previously (usually biomass, inert, or capsule), and the mass parameter is specified in femtograms (1 fg = 10-15 g).