PhysioDesigner
A modeling tool for multilevel physiological systems

Mar 2015

Version 1.2

PhysioDesigner 1.2

31 March, 2015

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.2". 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 PhysioDesigner1.2 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 PhysioDesigner1.2 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 Mountain Lion (OSX 10.8), Mavericks (OSX 10.9), and Yosemite (OSX 10.10), users need to change the system preferences so that any applications (from other than Mac App Store) can be installed. 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
・ Added a PhyisioDesigner plugin framework was introduced.
・ Now it is possible to observe the time course of variables, at out-ports/in-ports of capsule modules and even on edges.
・ Now capsule modules can be opened in a indepedent new window
・ Implemented a function to find template module from instance modules.
・ Implemented a feature to drag and drop time series data file to integrate.
・ Reset edges as well, when sorting modules.
・ Time series data icon is shown on a module, if it includes.
・ When saving, SBML models, time series/morphological data integrated in the model can be bundled in the PHZ file together.
・ Updated the protocol to receive ISD and CSV file via Garuda platform.
・ Improved the Integrate Timeseries Dialog.
・ Several bugs were fixed.
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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.