This menu is used to:

• Set parameters for the computation.
• Begin the computation process.

Computation Mode Button

These buttons let the user switch between two modes of computation:

1. Attractor Analysis
   • Purpose: Identifies all possible attractors of the network and groups them by their behavior classes.
2. Control Computation
   • Purpose: Computes perturbations (groups of variables fixed to Boolean values) that eventually guide the network into a specific attractor (referred to as a phenotype).

Control Settings (For Control Computations)

These settings allow users to limit the results of control computations:

• Minimal Robustness: A percentage value used to filter out perturbations that work for less than the specified percentage of network interpretations.
• Maximal Size: Restricts the size of computed perturbations by limiting the number of variables included.
• Maximal Number of Results: Caps the total number of computed perturbations.

This menu is used for managing communication with the compute engine part of the program. Make sure that the compute engine is running on your machine and that it is operating on the correct port. Port number is by default set to 8000 (address http://localhost:8000). You can change it by rewriting the number at the end of the address under the menu title (for example, to http://localhost:5500).

If you do not have the compute engine downloaded, you can download it using the buttons located at the bottom of the menu. Once downloaded and running, you should be able to connect the compute engine using the Connect button.

If the compute engine is connected, you may also disconnect it using the same button. To the left of the Connect/Disconnect button is a status indicator that displays the current status of the compute engine.

Status Indicator States

• Connected: The compute engine is successfully connected.
• Disconnected: The compute engine is not connected.
• Running: A computation is currently in progress.
• Done: Indicates the completion of the last computation, followed by a timestamp.
• Error: Displays an error message when an issue occurs.

When the computation is running, there is button available to cancel the computation. Additionally, for certain computations, it is possible to open partial results without canceling the computation.

This menu is used for importing and exporting models from files. Currently, the following file formats are supported for import/export:

• .aeon
• .sbml
• .bnet

Additionally, you can import a model from the Local Storage of your browser. The Local Storage should contain the last model that was used with the Aeon tool.

Example models are also available for import to help you get started.

This menu is used for general modifications of the model. You can change the name of the model by clicking the text at the top of the menu. If the name hasn’t been set, the placeholder text (model name) will be displayed.

Below the model name, there is a button to display or hide the model description. When the model description is open, you can modify it by clicking on the description text and editing it directly.

Model Information Overview

• Variables: Number of variables in the model.
• Parameter space size: To Do (information pending).
• Regulations: Number of regulations in the model.
• State space size: Number of possible states in the model.
• Max. in-degree: Maximum number of regulations going into one variable.
• Max. out-degree: Maximum number of regulations going out of one variable.
• Explicit parameters: Undefined parameters appearing in the update functions (e.g., function F(CtrA) has an explicit parameter F(1)). Parameters must be regulators of the variable, and their count can range from 0 to infinity.

Variables Section

The Variables section contains:

• Add Variable button: Adds a new variable.
• Filter Variables text bar: Filters variables by name. For filtering multiple variables, separate names with a comma (,). You can search for variables whose names start with a specific string of characters, even if the name is incomplete. Writing "//target: " followed by variable names finds all regulators of those variables (this works only for complete names).

The largest part of the Variables section consists of widgets for all the variables in the model. Here’s a breakdown of the widget components:

• Display/hide variable information button: Shows or hides details about regulators and the update function of the variable.
• Variable name: Editable name of the variable, which can be changed by clicking on it.
• Change Control-Enabled status button: Toggles the Control-Enabled status of the variable. If the button is yellow, the variable is Control-Enabled (may appear in computed control perturbations). Otherwise, it is Not-Control-Enabled (excluded from control perturbations).
• Change Phenotype button: Toggles the phenotype of the variable:
  • Green: The variable is in the phenotype as true.
  • Red: The variable is in the phenotype as false.
  • Grey: The variable is not part of the phenotype.
• Find node button: Locates and zooms in on the variable's node in the graphical representation of the model.
• Delete variable button: Deletes the variable and all regulations connected to it.
• Regulators menu: Lists all regulators of the variable. You can:
  • Change their observability by clicking on them (non-observable regulations are ignored).
  • Modify their monotonicity by clicking:
    • Activation: Uses the current boolean value of the regulator.
    • Inhibition: Uses the opposite boolean value of the regulator.
    • Unspecified: Computes results for both activation and inhibition.
• Update function input bar: Specifies the update function of the variable. The format is:

Update fn ::= true | false | Name | Uninterpreted fn | 
              !Update fn | (Update fn Op Update fn)
Op ::= & | | | => | <=>
Uninterpreted fn ::= Name(Parameters)
Parameters ::= Name | Parameters, Parameters

This menu is used for setting the Control-Enabled status of variables. If a variable is Control-Enabled, it can be fixed to a boolean value during the control process. For simplification, this means that the variable may appear in the computed control perturbations.

Overview

The overview displays the number of Control-Enabled and Not-Control-Enabled variables in the model.

Control-Enabled status Buttons

• Set as Control-Enabled button: Yellow button with a "C" inside. Clicking on it sets all selected variables as Control-Enabled.
• Set as Not-Control-Enabled button: Grey button with a "N" inside. Clicking on it sets all selected variables as Not-Control-Enabled.
• Toggle selected button: Button with a toggle switch icon. It toggles the selection state of variables, making selected variables unselected and vice versa.
• Select all button: Button with lines inside a square. Clicking it selects all variables.
• Deselect all button: Button with crossed lines inside a square. Clicking it deselects all variables.

Filter Variables

Below the buttons, there is a Filter Variables input bar used to filter variables by name. To filter multiple variables, separate names with commas (,). The filter also supports searching for variables whose names start with a specific string of characters (even if incomplete).

Variables Table

The table lists all variables present in the model. Features of the table include:

• Select/Unselect: Click on a variable to select or unselect it. You can also select or unselect multiple variables by dragging over them. Selected variables are highlighted in blue.
• Add into filter button: The first circle to the right of a variable name. Clicking it adds the variable's name to the Filter Variables input bar.
• Control-Enabled indicator: The second circle to the right of a variable name. Its color indicates the variable's Control-Enabled status:
  • Yellow: The variable is Control-Enabled.
  • Grey: The variable is Not-Control-Enabled.

This menu is used for setting the phenotype of the control computation. The phenotype is the desired attractor of the control computation and is defined as a set of variables with desired boolean values.

Overview

The overview shows the number of variables in the phenotype as true, as false, and how many variables in the model are not present in the phenotype.

Phenotype Oscillation

The Phenotype Oscillation button allows you to specify if the perturbations should target an oscillating or non-oscillating phenotype. Phenotype oscillation occurs when the Boolean network cycles between being in the phenotype and not being in the phenotype state. If the phenotype is not oscillating, the Boolean network remains in the phenotype state indefinitely.

The button has the following states:

• Allowed: Computes perturbations for both oscillating and non-oscillating phenotypes.
• Required: Computes perturbations only for oscillating phenotypes.
• Forbidden: Computes perturbations only for non-oscillating phenotypes.

Phenotype Status Buttons

• Add as true button: Green button with a "T" inside. Clicking it adds all selected variables to the phenotype as true.
• Add as false button: Red button with a "F" inside. Clicking it adds all selected variables to the phenotype as false.
• Remove from phenotype button: Grey button with a "N" inside. Clicking it removes all selected variables from the phenotype.

Variable Selection Buttons

• Toggle selected button: Button with a toggle switch. It toggles the selection state of variables, making selected variables unselected and vice versa.
• Select all button: Button with lines inside a square. Clicking it selects all variables.
• Deselect all button: Button with crossed lines inside a square. Clicking it deselects all variables.

Filter Variables

Below the buttons, there is a Filter Variables input bar. It is used to filter variables by name. To filter multiple variables, separate names with commas (,). The filter also supports searching for variables whose names start with a specific string of characters, even if incomplete.

Variables Table

The table lists all variables in the model. Features of the table include:

• Select/Unselect: Click on a variable to select or unselect it. You can also select/unselect multiple variables by dragging over them. Selected variables are highlighted in blue.
• Add into filter button: The first circle to the right of a variable. Clicking it adds the variable's name to the Filter Variables input bar.
• Phenotype status indicator: The second circle to the right of a variable. Its color indicates the variable's phenotype status:
  • Green: The variable is in the phenotype as true.
  • Red: The variable is in the phenotype as false.
  • Grey: The variable is not present in the phenotype.

This menu is used for changing the visual aspects of the graphical representation of the model.

Layout Section

The Layout section allows you to change the arrangement of nodes in the model. Available layouts include:

• Organic Layout: This layout minimizes overlapping of nodes and regulations for a more natural appearance.
• Hierarchical Layout: Based on the network simplex algorithm, this layout organizes nodes hierarchically.
• Phenotype Layout: A concentric layout that separates nodes into three circles based on the phenotype status of their corresponding variables:
  • The central circle consists of nodes for variables in the phenotype as false.
  • The middle circle consists of nodes for variables in the phenotype as true.
  • The outer circle consists of nodes for variables not present in the phenotype.
• Control-Enabled Layout: A concentric layout that separates nodes into two circles based on the Control-Enabled status of their corresponding variables:
  • The central circle consists of nodes for Not-Control-Enabled variables.
  • The outer circle consists of nodes for Control-Enabled variables.

Highlighting Section

The Highlighting section enables highlighting of nodes based on specific criteria. Options include:

• Show Phenotype: Changes the color of the borders and text of nodes based on the phenotype status of their corresponding variables:
  • Green: Variable is in the phenotype as true.
  • Red: Variable is in the phenotype as false.
  • Grey: Variable is not present in the phenotype.
• Show Control-Enabled: Changes the color of nodes based on the Control-Enabled status of their corresponding variables:
  • Yellow: Variable is Control-Enabled.
  • Grey: Variable is Not-Control-Enabled.

Attractor Analysis Results

On the top of the menu, you can see information about the computation:

• Elapsed: How long the computation took (in seconds).
• Total Number of Classes: Number of different behavior classes found.

The computed classes are displayed in a table with the following columns:

• Behavior Class: Represents, with icons, how the attractors of network interpretations in the class behave. Possible behaviors:
  • Disorder: Two arrows, indicating complex attractor behavior.
  • Oscillation: Cycling arrow, indicating the states oscillate in a circular pattern.
  • Stability: Circle with a dot inside, indicating the attractor stabilizes in one state.
  • Combinations of these behaviors are possible (e.g., a class can include stable and oscillating attractors).
• Witness Count: Number of network interpretations exhibiting this behavior class.
• Witness Button: Opens one random interpretation of the network as a fully parameterized model in a new browser tab.
• Attractor Button: Opens a new inner tab showing the attractors of the behavior class represented as a graph of states.

Below the table, there is an Explore Bifurcation Function button that opens the Attractor Explorer for exploring the computed results using the binary decision graph.

Control Results

At the top of the menu, information about the computation is displayed:

• Elapsed: Computation time in hours:minutes:seconds format.
• Number of Interpretations: Total interpretations of the current Boolean network.
• Number of Perturbations: Number of perturbations found with the current settings.
• Minimal Size: Minimal number of variables in one perturbation.
• Maximal Robustness: The maximum robustness of the perturbations (robustness is the percentage of network interpretations for which the perturbation works).
• Oscillation: Indicates whether perturbations were computed for oscillating or non-oscillating phenotypes:
  • Allowed: Computes perturbations for both oscillating and non-oscillating phenotypes.
  • Required: Computes perturbations only for oscillating phenotypes.
  • Forbidden: Computes perturbations only for non-oscillating phenotypes.

Below the information section, there is a Visualization Options Menu for results computed by the control computation. It includes:

• Table: Opens a new inner tab where computed perturbations are visualized in a table. (Note: If there are more than 1000 results, this may cause performance issues. You can export the results to a .csv file.)