PhysioDesigner
A modeling tool for multilevel physiological systems

Version 2.0

PhysioDesigner 2.0

29 June, 2017

Install Note


Mac
: From this version, PhysioDesigner for macOS supports OS X Mavericks Lion (10.9) or later.
Once you mount the disk image file you download, you will find a directory named "PhysioDesigner2.0". Please move the directory any place you want to put. That's all for installation.

Attention!! if the PhysioDesigner cannot be launched on 10.12 Sierra)
Because of macOS's (
10.12 Sierra) security policy, a downloaded executable file which is created by non-identified developers will not be executed on macOS anymore. Unfortunately we have not registered to Apple's developer program yet, so PhysioDesigner that you download from this site cannot be launched as it is. But there is ways to sidestep this issue. You need to use two machines, let's call them A and B (and B is your mac on which you want to execute PhysioDesigner).

1. Download a PhysioDesigner file on machine A (with any OS)
2. Put the PhysioDesigner file in a directory under Dropbox.
3. Get the PhysioDesigner file via Dropbox on machine B (your mac) which is linked to your local file system (don't download the file from Dropbox site over the net).
This file is no more a file downloaded from the net, hence can be launched.

There is another way.
1. Download a PhysioDesigner file on machine A (windows or linux).
2. Transfer the PhysioDesigner file to your mac via LAN with smb or nfs, or by scp.


On other mac versions, i.e. 10.9-10.11)
To install PhysioDesigner into OSX 10.9 - 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"
Allow applications downloaded from Anywhere" at Preferences > Security & Privacy > General.


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 PhysioDesigner2.0 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 PhysioDesigner2.0 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) 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-2.0 by rpm command.

Note 4) To launch PhysioDesigner, execute $sh /opt/PhysioDesigner-2.0/PhysioDesigner


Release Notes


On PhysioDesigner
・Now an object database ZODB was employed in PD-API for better performance.
・Improved layout of modules at tree diagram.
・Implemented the re-layout function at tree diagram modules.
・Improved the collapse and expand function of instant modules.
・Implemented a function to create instant modules, which can accept binding information of matrix representation and position information as input and which set it to the coordinate of the instant module.
・Implemented a function to change template module.
・Implemented a function to reset instance modules's property to the template.
・Several minor bugs were fixed


On Image Viewer
・Export an image data (RAW, VOL) from a MAT or an Analyze data.

On Morphology Editor
・Export an image data (RAW, VOL) form Geometry Data(VTK, STML, OBJ).


Files


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Mac OS X 10.9-10.12
PhysioDesigner2.0_osx(version).dmg
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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.