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Cardiac Physiome Society workshop: November 6-9, 2017 , Toronto

JSim Model Browser

The Model Browser is an implimentation of the Prefuse Information Visualization Toolkit which reads GraphML data generated by the JSim compiler to graphically represent variables and their dependencies or other relationships between variables.

Contents:

Using the Model Browser

There are currently two types of data relationships that can be graphed: To view a graph of the model data:
  1. Compile a model.
  2. Go to the 'Browser' tab. The Model Browser window will be empty.
  3. Select 'Render' -> 'Data select' -> type of data ('Variables', 'Sequence') from the drop-down menu.
  4. Hit the 'Refresh' button to display the rendering.
Depending on how powerful your computer is and how complicated a model you want graphed, you should see a node -> edge rendering of your data (It may take anywhere from 1 to 60 seconds to render the data).

Interacting with the Browser rendering

After you have rendered the data you can currently interact with it in the following ways: JSim version 2.08 and above: JSim version 2.07 and lower:

Changing Browser data rendering rules

You can change the coloring and shape of the nodes based on data rendering rules which are specified in the 'Render' drop-down menu. Here are the options:

GraphML Output

GraphML is a XML file format for graphs. The JSim compiler generates this file at compile time. To view and/or save the GraphML file for a compiled model, go to the 'Debug' tab from within the JSim UI. From there hit the 'View' drop-down menu and pick 'View GraphML'. The formated file should now be visable. To save, just hit 'File' -> 'Export text'.

The GraphML file generated by JSim may contain multiple graphs.The currently used graphs are the first one ('variables' graph) and the second one (the 'sequence' graph).

Comments or Questions?

[This page was last modified 26Jul12, 1:43 pm.]

Model development and archiving support at physiome.org provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.