PhysioDesigner
A modeling tool for multilevel physiological systems

Jul 2014

Version 1.0

PhysioDesigner 1.0


1st August, 2014

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0". 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 PhysioDesigner1.0 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 PhysioDesigner1.0 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) and Mavericks (OSX 10.9), 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 10.8 is principally working on OSX 10.9 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) On Windows XP with full windows update, Python 2.7 can cause problem, consequently PhysioDesigner cannot work, because PhysioDesigner depends on Python. So far we could not solve this issue. But if Python can work properly, PhysioDesigner itself should run OK.

Release Notes


On PhysioDesigner

・ From this version OSX 10.6 is not supported any more because now Java7 is used in PhysioDesigner.
・ A new type "timeseries" is added to the types of Physical-quantity to assign time series data to the physical quantity.
・ When a physical quantity’s name was changed, the change is reflected in all definitions of all physical quantities in the same module.
・ Fixed a problem of a definition of condition with '=='.
・ Fixed a problem that an initial value definition vanishes at a certain case.
・ Fixed a problem of Physical-quantity’s name search in Physical Quantity dialog.

On MorphoSpace
・ It can now create an animation with morphological data assigned to modules and using physical quantities to define frame coordinate of modules in two ways:
- If the physical quantities in the frame coordinate are assigned time series data, then MorphoSpace can move morphological data according to the values in the time series data.
- If the physical quantities in the frame coordinate are of state or variable type, MorphoSpace can move morphological data after running simulation. MorphoSpace will find the time series data corresponding to the physical quantities in the simulation data.
・ Now it can output a movie file in the format of MOV, MP4, WMV or AVI.
・ Screen can be exported in a file with PNG, JPEG, PDF, BMP or TIFF format.

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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.