Experiments

An experiment is a set of perturbations performed during a simulation.

See Also
Introductory Concepts
Experiments Panel
Configuring Experiments
Experiment

An experiment is a set of perturbations and observations applied to a pathway model in order to assess the relevance of a hypothesis, or to explore or generate new hypothesis. Just as in a wet lab, an experiment can gather control and test perturbations. Specific entities (for example, phenotypes) are often useful as observed outcome markers.

Perturbation

A perturbation describes the experimental conditions applied to a pathway model with the purpose of conducting an experiment. Perturbations reflect intrinsic variations of the pathway model, such as those reflecting a genetic mutation in a patient. They also represent the contribution of external factors, such as the inhibition of a receptor by a drug. Perturbations consist of changes in the entities' formulas or their initial states. A qualitative simulation computes the effect of perturbations on the behavior of a pathway model.

The defined perturbed biological model features and environmental stimulus parameters combine pairwise to determine the perturbations for a simulation. During the generation of perturbations, unspecified parameters (either perturbed or environment) are considered control parameters. This means that they reflect the behavior of the pathway model without any change.

Biological Model Feature
A perturbed biological model feature parameter is a group of one or more entities (for example, proteins). A user sets the parameter's properties (initial state and behavior) to reflect the intrinsic behavior of an experimental biological system (for example, a cell line, animal model, or patient). You cannot use phenotype entities as perturbed biological model features.
Environmental Stimulus

An environment stimulus parameter is a group of one or more entities (for example, proteins). A user sets the parameter's properties (initial state and behavior) to they reflect the influence of external factors on an experimental biological system. For example, the effect of a drug or natural ligand when they are not part of the pathway model. You cannot use phenotype entities as environment stimuli parameters.

Observed Parameter

Observed outcome markers are entities selected for the purpose of interpreting the results of an experiment. In a simulation result, the investigation of the intermediate or final states taken by these parameters is required to draw the experiment conclusion. In a pathway model, phenotypes are often the observed entities since they express the cellular outcome of a perturbation.