Experiments Panel

The Experiments panel configures the parameters and perturbations for simulations, and provides access to results. The defined biological model features and environmental stimuli combine pairwise to determine the perturbations for a simulation.

This page discusses:

See Also
Map
Configuring Experiments
Experiments
Model Overview Panel

Information

The Information tab allows you to define a title and short description for an experiment. Click to edit existing information.

Outcome Markers

The Outcome Markers tab defines which entities correspond to observable markers for a simulation. The list of available markers displays phenotype entities first, followed by all other entities.

Parameters Configuration

The Parameters Configuration tab defines the features of the biological model and the environmental stimuli to include in simulations.

In Living Map biological model features or environmental stimuli allow you to create control or test conditions, similar to a wet lab experiment. Biological model features reflect patient, cell line, or animal model features, for example loss of a protein function because of a mutation. Environmental stimuli reflect the influence of external factors, typically the inhibition of a protein by a drug.

Command Description


Creates a new group of biological model features or environmental stimuli.
Creates a new biological model feature or environmental stimulus in the selected group.
+ Collapses the group.
- Expands the group.
Deletes the selected features and groups.

Perturbations

The Perturbations tab lists all pairwise combinations of perturbed biological model features and environmental stimuli groups of parameters, defined on the Parameters Configuration tab.

For each combination, the list reports the entities included in the two types of parameters, separated by a vertical line.

The text color of the name of each parameter or group indicates its initial state:

  • Green: control group, with no perturbations
  • Blue: entities initially active
  • Red: entities initially inactive

: Starts a simulation for the perturbation, or all perturbations, and displays the Results tab.

Results

The Results tab displays a heat map for the most recent simulation run from the Perturbations tab.

Each row in the heat map represents either:

  • An individual simulation, displaying the final entity state, if there is more than one set of simulation results available. The steps of the simulation can be investigated by clicking and choosing View Result.
  • A step of the simulation, if only one set of simulation results is available.

Each column in the heat map represents an entity in the pathway model.

Command Description
Displays hidden rows or columns.
Pivots the heat maps.
Shows the legend for the heat map.
Opens the Export as PDF dialog box.
Provides options for sorting or clustering the entities or steps.
for an individual simulation among many Opens a menu to select an option for the row.
for a column Opens a menu to choose to hide the column.
from the options menu for an individual simulation among many Opens the Results Summary with a heat map for this simulation.
in the Results Summary for an individual simulation among many Returns to the full results for all simulations.