MOOSEGUI: Graphical interface for MOOSE

H. Chaitanya, Harsha Rani, Subhasis Ray, Upi Bhalla

May 11, 2012

Introduction

The Moose GUI lets you work on chemical and compartmental neuronal models using a common interface framework. This document describes this common framework. In MOOSE 2.0.0, the interface lets you read, run, edit, and write chemical kinetic models, and to read, edit and run neuronal models.

Layout of interface

The MooseGui interface consists of a model view window to the left, occupying most of the screen. To the right there is a panel with controls for viewing and editing model parameters, for configuring plots, and for running the model.

The menu bar

In Ubuntu 12.04, the menu bar appears only when the mouse is in the top menu strip of the screen. In other distributions it should appear over the top of the interface.

The menu bar contains the following entries: File, Edit, View, Solver, Help.

File

Edit

View

This allows one to control display of various parts of the interface.

Solver

The Solver options currently only select between methods for kinetic models. Details are in the chemical kinetics documentation.

Options are:

Help

The Model window

The Model window displays a view of the model structure. These views vary depending on the model type.

3-D display of neuronal models in Neurokit:

The individual compartments of the neuron model can be clicked to select, and when selected, the compartment parameters and variables are displayed in the Property editor described below. For a neuronal or neuronal network model, the window displays a 3-D view of the cell(s) in the model. It does so using OpenGL, which is a standard for displaying 3-D views. In addition, the display sets the color of each compartment based on some variable value, typically Vm, the membrane potential of the compartment. Note the 3-D axis indicators in the bottom left.

The controls for moving the display are as follows:

2-D display of chemical kinetics models in Kinetikit:

For a chemical kinetics network, the window displays a schematic of the chemical reaction system. This is in the tab labeled Kkit Layout. There are distinct icons for molecules, reactions and enzymes, and these are connected by arrows to set up the reaction scheme. Again, any icon can be clicked to select and its parameters and variables come up in the Property editor.

The chemical network is displayed only in 2 dimensions. The controls are correspondingly simpler:

The plot window

The plot window displays time-series plots of the simulation. Plots are color-coded to distinguish them. In the case of the kkit interface the plots take the same color as the molecule pool that they represent.

The plots are done using MatPlotLib, so the usual controls apply. Beneath the plot window there is a little row of icons:

These are the plot controls. If you hover the mouse over them for a few seconds, a function reminder box pops up. The functions as follows:

The side panel

The side panel is located on the right of the screen. It displays three controls: the Property editor, the Plot configuration and the Run control.

Property editor

The Property editor displays parameters and variables of the selected model component (object).

The object many be a compartments of a neuronal model, or pools, reactions, or enzymes in a signaling model.

Plot configuration

The Plot configuration panel lets one set up new plots based on selected objects and their fields.

Simulation control

The Simulation control panel controls how the model is run.