Once a Simmune model is chosen in the Model panel by double clicking it, you can specify the initial state of the simulated cell. Click in tool bar to access the panel. There are two sections in the panel: List of Initial States and Initial State. The latter is used to edit the initial concentration that specify a single initial state. The former allows you to choose an initial state from a list of previously defined states
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"New" initial state
Click the "New" button to create a new initial condition with a default name such as "New Initial Condition". The newly created initial condition is automatically loaded with all concentration values set to "0". The cell's dimensions are set to match a 10 micron diameter sphere.
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Initial states are selected for editing by single-clicking on them. The selected initial state is displayed in bold in the list.
Note
Initial States that are used by a simulation can not be edited, except for their name. This ensures that the results of a simulation are always consistent with the initial concentrations.
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Duplicating an initial state will make a copy that can be edited independently of the original initial state.
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Deleting an initial state will remove it from the list of available initial states, however the data associated will not be lost and simulations referring to the initial state continue to be valid.
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"Initial State Name" field
This field is editable and synchronized to the corresponding name in the list of initial conditions at the left.
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Define complex concentrations and distributions.
The table shows the list of "Well defined Complexes", which can be used to define the initial state of a simulation.
Note
Well defined complexes refer to all the complexes that have no "Don't Care" tag and all binding sites other than those involved in in-complex binding are free ("Unbound").
You can change the concentration of a complex, using the mouse wheel over the concentration column, or by clicking into the corresponding field in the table and entering the number using your keyboard. Besides an initial concentration you can specify a distribution that will be used to modify the initial concentration whenever a parameter variation is called for. The default is that all values are used exactly as entered. All changes to parameters are multiplicative, thus setting a parameter value to two will double the initial concentration. Only initial concentrations that are not 0 can be varied.
