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.
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 Model window displays a view of the model structure. These views vary depending on the model type.
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:
shift
key and the left mouse button
at the same time.y
and u
are assigned to rotate the display about the vertical axis, otherwise known as pitch.q
and a
control rotation around the horizontal axis, otherwise known as yaw.z
and x
rotate the display around the axis going into the display from your eyes.left mouse button
down and moving the mouse.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:
a
key will fit the entire model into the entire field of view.<
and >
. This resizes the icons while leaving their positions on the screen layout more or less the same.A
key (capital A
) will revert to the original model view including the original icon scaling.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:
left mouse button
, this will zoom in to the specified rectangle so that the plots become bigger. With the right mouse button
, the entire plot display will be shrunk to fit into the specified rectangle..png
file.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
.
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.
The Plot configuration
panel lets one set up new plots based on selected objects and their fields.
Reset
button is hit. When checked, this retains the plots from the previous run.The Simulation control
panel controls how the model is run.
Reset
. This sets:Plotdt
in most cases.