Reduction of regulatory graphs

The reduction of regulatory graphs allows to extract a "simplified" regulatory graph where a set of components are hidden. To keep a consistent dynamical behaviour, the logical rules associated with the targets of each hidden component account for the (indirect) effects of its regulators. This construction of reduced models preserves crucial dynamical properties of the original model, including stable states and more complex attractors. Furthermore, the relationship between the attractor configuration of the original model and those of reduced models is formally established.

The reduction tool is available in the Actions menu. It open a configuration dialog in which the user can select the components that will be hidden. Several configuration strategies can be defined. Running the tool leads to the construction of a reduced model where the selected components have been removed.

Some reductions are not possible (an auto-regulated component can not be hidden using this method), if a reduction fails, GINsim will show an error message, listing the components that could not be hidden and proposing to continue with the result of the partial reduction.

Note that in some cases, the reduction may only be possible in a precise order (but the result does not not change with the order). When blocked, GINsim will try alternate orders for the remaining components, but not for the components which have already been succesfully reduced. In such cases, it may be necessary to provide the list of components to reduce in several steps to force the use of the correct order.

Outputs are components which do not regulate others. As such, these components have no impact on the attractors that will be reached in a simulation. These output components can be automatically removed when performing a simulation or some other actions on a model. To instruct GINsim to remove outputs, use the "strip outputs" checkbox next to the perturbation selection box.

The reduction tool can also be used in script mode. It then relies on a previously defined reduction strategy.

This method was implemented in GINsim 2.4. Further information on the algorithm is available in Naldi et al. (TCS 2011).

The support for output stripping was added in GINsim 3.0. Further information is available in Naldi et al. (CMSB 2012).