- Experiment
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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
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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
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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
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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.
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