PhysioDesigner
A modeling tool for multilevel physiological systems

Jan 2014

Version 1.0 beta7

PhysioDesigner 1.0 beta7


1st January, 2014

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0b7". 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 PhysioDesigner1.0b7 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 PhysioDesigner1.0b7 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), 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 OSX 10.8version is principally working on OSX 10.9 well. But There might be some unknown problem. Please consider as a testing version if you want to execute PhysioDesigner OSX 10.8 version on OSX 10.9.

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

A function to extract only parameter values from a model was implemented. The parameter list was saved in PHPL (PH Parameter List markup language) format
It is also possible to import a PHPL file to set the parameter values of the model
Morphospace was enhanced. Three view modes were implemented.
Several bugs were fixed
On ImageViewer
ImageViewer supports Analyze format for all functions of image processing. NIfTI format will be also soon.
Enabled to convert from MATLAB format to Analyze format
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Linux el5.x86_64
Linux el6.x86_64
PhysioDesigner1.0b7_el5.x86_64.rpm
PhysioDesigner1.0b7_el6.x86_64.rpm
Note: These installers for linux are still experimental. If you noticed any problem on the installers, please contact us.


Flint 1.0 beta7


Flint can perform simulations of models created on PhysioDesigner.
Stacks Image 355
Linux el5.x86_64
Linux el6.x86_64
Flint1.0b7_el5.x86_64.zip
Flint1.0b7_el6.x86_64.zip
Note: These installers for linux are still experimental. If you noticed any problem on the installers, please contact us.

Install Note

Mac:
Note 1) To install PhysioDesigner into Mountain Lion (OSX 10.8), 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".

Release Notes

Fixed a bug on calculating initial values of ODEs.
Added the "-headless" option to run a single simulation with a model file.
Fixed a installation process on Windows; now it creates shortcuts to Flint on the Desktop and the Start Menu for every user.
Enabled to detect and warn a circular definition of time units.
Enabled to handle nested conditional equations.