PhysioDesigner
A modeling tool for multilevel physiological systems

Version 2.2

PhysioDesigner 2.2

10 May, 2018

Install Note


Mac
: From ver 2.0, PhysioDesigner for macOS supports OS X Mavericks (10.9) or later.

On mac versions, 10.12-10.13
Installation process was changed and improved.
Once you mount the disk image file you download, you will find a directory named "PhysioDesigner2.2". Please move the directory to any place you want to put.

Then, you have to setup the path to find PhysioDesigner API server. To do this,

1. Open Terminal
2. Execute
    $python /(where you put PhysioDesigner)/PhysioDesigner2.2/PD_initial_setup.py

This script would modify the PhysioDesigner configuration file, i.e. ($HOME)/.physiodesigner/physiodesigner.properties

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 PhysioDesigner2.2 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 configurations related to PhysioDesigner are stored. By removing this file, the configurations are reset to the default. And execute PD_initial_setup.py again to setup the path.

Note 3) Directory structure in PhysioDesigner2.2 is crucial for execution of PhysioDesigner.app and other apps in this package. For example, all apps and server directly must be in the same directly.

Note 4) On the Retina MacBook there is a problem on rendering objects in Image Viewer, MorphologyEditor and MorphoSpace. This is due to QVTK widget on retina display. On a 4 panels view window, only lower left panel of figure is actually used for rendering.

The problem is caused by the fact that the retina display has four times higher resolution.
It is possible to sidestep this problem by running the applications in lower resolution mode.

To do this, please follow the following steps:
1. Right click on the *.app file
2. Select "Get Info"
3. Check a box at "Open in low resolution mode"
4. Close the Info window and run program




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-2.2 by rpm command.

Note 4) To launch PhysioDesigner, execute $sh /opt/PhysioDesigner-2.2/PhysioDesigner


Release Notes


On PhysioDesigner
・Install method was improved.
・A bug in PHML API was fixed


Files


Stacks Image 398
Mac OS X 10.9-10.13
PhysioDesigner2.2_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.