PhysioDesigner
A modeling tool for multilevel physiological systems

Jun 2016

Version 1.5

PhysioDesigner 1.5

30 June, 2016

Install Note


Mac
: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.5". Please move the directory any place 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 PhysioDesigner1.5 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 PhysioDesigner1.5 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.



Linux: Install the rpm package file with usual procedure to use rpm command, such as $rpm -ihv filename.rpm (to newly install), or $rpm -Uhv filename.rpm (to update).

Note 1) This RPM package was created on CentOS 7, and tested on it.

Note 2)
Oracle's Java is necessary. PhysioDesigner cannot work with openJDK which is installed to OS by default. Please visit Oracle's Java site to download JDK. Once installed, if still old java is used, please try to configure "alternatives", with
$sudo alternatives --config java
If openjdk's java is checked with + mark, please select the java installed now. This may help.

Note 3) PhysioDesigner will be installed to /opt/PhysioDesigner-1.5 by rpm command.

Note 4) To launch PhysioDesigner, execute $sh /opt/PhysioDesigner-1.5/PhysioDesigner


Release Notes


On PhysioDesigner
Modified the way to re-layout in nesting diagram.
The position of instance module will be displayed at the place where the mouse was last clicked.
Physical-quantity can be used to specify max delay.
Physical-quantity can be used to specify probability of transition condition of graph definition.
In the node table of graph, node IDs are shown with node’ name.
Several minor bugs were fixed.

On Image Viewer
Supported visible or invisible the edges at the voxel view.
Now it's possible to change the opacity of 3D objects.


Files


Stacks Image 398
Mac OS X 10.7-10.11
PhysioDesigner1.5_osx(version).dmg
Stacks Image 498
Note: This installer for linux CentOS 7 is 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 at GitHub.