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The BioDMET "Quick Start" Guide
A Quick Start Guide is available on-line from this web site. This PDF document provides a brief overview of the BioDMET tool plus a tutorial on how to use it to setup and run a simulation. (Note: the size of the file is approximately 3MB.)
On-line tutorials are available for using specific features of BioDMET.
If you would like more information about installing and using the BioDMET tool, please consult the BioDMET User Manual.
The notes and references for the healthy and diseased host models distributed with BioDMET are available.
Pathogen model notes and references.
Notes on the PK/PD modeling of drug action and the testing of BioDMET.
The BioDMET User Interface
There are four main sections to the user interface. These are the menu bar and tool bar, the model tree view—displaying the simulation configuration information in a hierarchical view, the properties window—which displays property sheets for the currently selected item(s) in the hierarchy display, and the information window—which provides access to additional information on the simulation setup and results.
The top of the interface contains a menu bar and tool
bar. The menu selections and tool bar buttons provide access to the
various features and tools available in the application. Some of the
buttons and menu selections are context sensitive: they can only be
selected depending on what part of the simulation model is being edited.
The left side of the interface contains a tree view of the the simulation setup. The data input to the simulation has a very hierarchical structure. The tree view allows you to view and quickly navigate to components of that structure. The simulation setup includes information on the physiology of the host or hosts being modeled, external agents (e.g. drugs) to be introduced into the host(s) and whose progression through the hosts(s) is being simulated, the enzymes which can react with these agents within the host(s), information on how the agents are administered into the host(s), and finally locations in the host(s) and time steps in the simulation where we want to determine various concentrations of the agent(s). Connections between model components are shown with dashed lines drawn on the right side of the the nodes in the tree view.
Every selectable node in the hierarchy tree has properties associated with it that can be edited to tailor the behavior of the simulation. The Properties Pane in the upper right hand side of the window provides a set of property sheets where such modifications can be made. The Properties Pane contains a number of tabbed views, one for each major type of selectable element in the model hierarchy tree. When a node is selected in the hierarchy, the tabbed property sheet corresponding to the node’s type is brought into view. You can use the property sheet to modify the properties of the selected node.
The information window pane is found at the lower right of the BioDMET user interface. The information pane is used to display other pieces of information to the user, information that is not strictly part of the model hierarchy view or a set f properties for a selected node in the model hierarchy. Like the Properties Pane, the Information Pane contains a number of tabbed views: