Control Computation Demonstration

This section provides a step-by-step guide for running an example control computation in Aeon. It covers the setup process, parameter configuration, and execution of the computation.

1. Running Aeon

Default State of Aeon State of the Aeon tool at startup

Aeon can be accessed either through its online version ([URL]) or by downloading and running it locally ([URL]).

2. Connecting the Compute Engine

Open the Compute Engine module from the left panel to check the connection status. If the Compute Engine is not connected, download the appropriate version for the system from the bottom of the module and run it locally.

Download Compute Enging Downloading AEON compute engine.

Open Connection Connecting to a running compute engine.

3. Importing or Creating a Model

A model can be created using the Model Editor or imported through the Import/Export module, both accessible from the left panel. The Import/Export module allows loading a model from local storage or selecting one of the default models available at the bottom of the module.

Import Example Model Import of the G2A example model

4. Setting Control-Enabled Variables

The Control-Enabled Editor module, accessible from the left panel, is used to define which variables are Control-Enabled and can be included in perturbations. By default, variables are set as Control-Enabled unless specified otherwise in the imported model.

To change the Control-Enabled status of multiple variables, select them and use the Control-Enabled status Buttons.

Setting Control-Enabled status Control-Enabled Editor Making Control-Enabled variables Not-Control-Enabled using the Control-Enabled Editor

Alternatively, Control-Enabled status can be modified for individual variables using the Model Editor module.

Setting Control-Enabled status Model Editor Making Control-Enabled variables Not-Control-Enabled using the Model Editor

5. Defining the Phenotype

The Phenotype Editor module, located in the left panel, is used to specify the phenotype of the model by assigning Boolean values to selected variables. By default, variables are not part of the phenotype unless specified in the imported model.

  • To add variables to the phenotype as true, select them and click the green button.
  • To add variables to the phenotype as false, select them and click the red button.
  • To remove variables from the phenotype, select them and click the gray button.

Setting Phenotype Phenotype Editor Setting of the phenotype using the Phenotype Editor

The Model Editor module can also be used to set phenotype values for individual variables.

Setting Phenotype Model Editor Setting of the phenotype using the Model Editor

6. Configuring Computation Limits and Starting the Process

In the Start Computation module, accessible from the left panel, set the computation mode to Control. Under the Control Settings section, configure computation limits:

  • Min Robustness (%) – Minimum percentage of Boolean network interpretations for which perturbations must work.
  • Max Size – Maximum number of variables allowed in a perturbation.
  • Max Number of Results – Maximum number of computed perturbations.

Once parameters are set, start the computation using the button at the bottom of the module.

Limiting and Starting Setting computation limits and starting the computation

7. Viewing Control Results

Once the computation is complete, the Results module opens automatically, displaying a summary of results. If needed, this module can also be accessed from the left panel.

Control Results Control Results Module

The results can be further explored using visualization options or exported for external use.