Protocols are used to conduct in-silico experiments; they define the duration of a simulation and any stimuli that are applied. The basic structure of the Protocol panel is the same as the Initial states Panel. On the left is a list of defined protocols that allows to select copy and delete protocols. The main part of the window is used for editing a protocol. Change to value in the field Duration to set the amount of time that will be simulated (This is the time that passes for the simulated cell, the time it takes the computer to do the actual calculations might be longer or shorter that this value. Simmune will always attempt to simulate the specified duration, there is no limit on how long this might take). The add step button allows set the concentration of extra cellular stimuli.
Important
Only well defined complexes and be used as a stimulus, if a complex species appears to be missing from the list of complexes make sure a well defined complex is defined for the missing species.
In the screen-shot below, a stimulus is applied afterat the begining of the simulation. Protocol steps can be deleted by clicking on the waste-bin icon to the left of each protocol step.
