PhysioDesigner
A modeling tool for multilevel physiological systems

Jan 2015

Version 1.1.1

PhysioDesigner 1.1.1


23 January, 2015

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.1.1". 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 PhysioDesigner1.1.1 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 PhysioDesigner1.1 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".

Note 5) PhysioDesigner for OSX 10.9 is principally working on OSX 10.10 well. But There might be some unknown problem. If you notice any problems, it is highly appreciated if you could let us know the problems.

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
・ Bugs on edge rerouting after moving modules out from a parental module were fixed.
・ Models in Sample directory were updated.


On MorphoSpace
・ Now single click on a object selects all objects in the subtree. And the double click can select single object.
Stacks Image 498
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.

Version 1.1

PhysioDesigner 1.1


1st January, 2015

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.1". 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 PhysioDesigner1.1 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 PhysioDesigner1.1 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".

Note 5) PhysioDesigner for OSX 10.9 is principally working on OSX 10.10 well. But There might be some unknown problem. If you notice any problems, it is highly appreciated if you could let us know the problems.

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
[IMPORTANT] From this version, PhysioDesigner saves model in PHZ format, which is a zipped archive file including a model PHML file, and other files such as layout information. Of course PhysioDesigner can load and export a PHML file. 
・ Works on OS X Yosemite.
・ A capsule module can be opened in a new separate window.

Layout information is saved in json file, included in a PHZ file.
・ It is possible to generate thumbnail of SBML model integrated in a module.
・ Better optimization algorithm for drawing edges were implemented.
Visualize the simulation results by coding values using the color of modules and edges.
Output simulation result with color mapping to a movie file.
Edge color setting function in preferences dialog was added.
・ A picture can be set on background of canvas.
A new window opens to edit a submodules under a capsule module.
Turn on/off edge display.
Find destination/origin of a out/in-port.
piccolo2d library was upgraded from 1.3 to 3.0.
Several bugs were fixed.

On MorphoSpace
MorphologyEditor can be called from MorphoSpace directly.
・ Functions to reset camera angle and refresh 2D panels and 3D panel were added.
Zoom in/out of the morphology canvas was improved.
Swapped the single click event with double click event. Now a single click selects a whole module tree under the selected module, and double click selects just the clicked single module.
Several bugs were fixed.

On ImageViewer
・ Speed to select voxels in RAW and VOL images was improved.
Stacks Image 498
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.