Model Perturbations (mutants)

Description

Perturbations are model modifications which enable the definition of variants of the model by applying one or several local changes. They are widely used to describe mutations (often knockouts), but can also be used to define hypothetical components or interactions in a model. BioLQM supports perturbations on components or on interactions, as well as multiple perturbations.

Usage

This modifier requires some configuration. The supported perturbations and the syntax of the parameter string to use in command line or scripting mode are described below. We remind that in command line, the parameter string for perturbations is given in the -m perturbation:parameter, or -p parameter switches. In scripts, it is the last argument in lqm.modifyModel(model, "perturbation", parameter).

Simple perturbations are described as target%restriction, where the target can be a component or an interaction, and the restriction is a fixed value or a range (only for components).

Fix the value of a component

This is the simplest type of perturbation. The function of the selected component will be replaced by a fixed target value. Use A%v to fix the value of component A to value v.

Restrict the value of a multivalued component

A slightly less restrctive perturbation, where the target value of a component is blocked inside a smaller range. When the target value of the component is larger (resp. smaller) than the range, it is replaced by the max (resp. min) bound of the range. Use A%v1:v2 to restrict the value of component A in the range [v1,v2].

Perturbation of an interaction

Remove (or enforce) an interaction from the model. The function of the target component will be modified to always behave as if the source component had the specified value. Use A:B%1 to let B believe that A is always active.

List of perturbations

Define multiple individual perturbations, with a comma-separated list of the above elements. For example A%0,B%1 defines the double knockout of A and B.

Going further

The PerturbationService, instance will provide additional methods to facilitate the manipulation of perturbations from scripts and java code.