Selecting Biological Model Features

You can specify which biological model features to include in perturbations during simulations. You cannot add phenotypes or drugs as perturbed biological model features. For nucleic acid entities (Generic DNA, Generic RNA, microRNA, siRNA, or Gene) with constant behavior, you can set their states to knock out or activate (knock in) genes.

See Also
Experiments Panel
Experiments
Selecting Stimuli
Selecting Outcome Markers
  1. For an open pathway model, click in the toolbar.
    The Experiments panel opens with the Information tab active.
  2. Select the Parameters Configuration tab.
  3. In the Biological model features section, click .
    This adds a new group of parameters, with a number to allow later identification. There is always a Control group with no entity features.
  4. With the group selected, click and select the entity to add.

    Note: You can add the same entity in multiple parameter groups, with different characteristics if required.
    Tip: Click to remove a selected entity or group.

  5. Choose the Behavior of the entity for this group.
    • Regulated
    • Constant
  6. Optional: For nucleic acid entities with Constant Behavior and all other entities, choose their Initial State:
    • Active
    • Inactive

    When you add an entity, this is automatically set to its Initial State value, defined in the Model Overview Panel. If you retain the default value, the entity will behave as a control in any simulations.

  7. Optional: For nucleic acid entities with Regulated Behavior, choose their Initial State:
    • Knock-Out - complete deactivation of a gene
    • Knock-In - forced activation of a gene

    When you add an entity and set its Behavior to Constant, this is automatically set to Knock-Out.

  8. Optional: Click with one or more groups selected to add further entities to all selected groups.
  9. Optional: Click to add further groups.

The experiment definition includes the groups of biological model features and their entities. Each combination of a biological model features group and a stimuli group has an item in the Perturbations list. You can run a simulation for each perturbation, for more information see Running Simulations.