PhysioDesigner
A modeling tool for multilevel physiological systems

Feb 2016

Version 1.4

PhysioDesigner 1.4

1 February, 2016

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.4". Please move the directory anyplace you want to put. That's all for installation.

Note 1) PhysioDesigner cannot be launched from the dmg mounted volume because of the lack of write permission of the volume. It is necessary to copy PhysioDesigner1.4 directory (which include PhysioDesigner.app, Morphology.app etc) somewhere on your local file system such as /Applications.

Note 2) If launch process fails, please try to remove $Users/.physiodesigner directory where some configuration related to PhysioDesigner are stored. By removing this file, configurations are reset to the default.

Note 3) Directory structure in PhysioDesigner1.4 is crucial for execution of PhysioDesigner.app and other apps. For example, all apps and server directly must be in the same directly.

Note 4) To install PhysioDesigner into OSX 10.8 - OSX 10.11, users need to change the system preferences so that any applications (downloaded from other than Mac App Store) can be installed and executed. Check System Preferences > Security & Privacy > General. "Allow applications downloaded from Anywhere".

Win: Please execute the installer by double clicking it. It installs a couple of necessary libraries such as Python, etc.

Note 1) Windows XP is not supported.

Release Notes


On PhysioDesigner
Now available on Mac OSX 10.11 (El Capitan) and Windows 10.
Java8 can work with PhysioDesigner.
A new type of physical quantity, graph, was added to model discrete state transition.
Improved completion function of PhysioTerminal.
Supported multiple line Python commands in PhysioTerminal.
A gray in/out ports are available to link forwarding edges.
The way to link edges to/from instance modules were improved very much.
 Now a dialog opens to control ports and edges.
Implemented a function to jump a destination/origin module by double clicking module name on the Port table.
Implemented Edit Instance dialog, it can select the voxel file made on Image Viewer.
Now it can directly import BioModels from BioModels Database on the SBML Model dialog.
Time series type of physical-quantity can be searched on the Physical Quantity List dialog.
In the Port dialog, physical-quantity types are shown with physical-quantity's name.
Enriched the information shown in the About dialog.
Several bugs were fixed.

On Image Viewer
Now VTK file of primitive geometry mesh can be set into a module, and shown on Image Viewer.

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Mac OS X 10.7-10.11
PhysioDesigner1.4_osx(version).dmg
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Note: These installers for linux are still experimental. If you noticed any problem on the installers, please contact us.


Flint is necessary for performing simulations of models built on PhysioDesigner.
Don't forget to download Flint. You can download it from here.