PhysioDesigner
A modeling tool for multilevel physiological systems

Mar 2014

Version 1.0 RC1

PhysioDesigner 1.0 RC1


5th March, 2014

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0RC1". 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 PhysioDesigner1.0RC1 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 PhysioDesigner1.0RC1 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. 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

Now Timeseries data can be integrated into the model.
A function to observe the time course on out-ports was implemented!
Morphospace was enhanced. Three view modes were implemented, i.e. By Actor, By Camera, and Walkthrough.
In the Physical Quantity dialog, now auto-completion function of physical quantities name was implemented.
In the Physical Quantity dialog, now if un defined physical quantities are used in a definition of a physical quantity, those undefined physical quantities will be created automatically. Afterwards, users need to modify the information of those automatically created physical quantities properly.
Several bugs were fixed
On ImageViewer
Enabled to convert from OBJ, VTK, STL and VRML (mesh formats) to RAW or VOL (volume formats).
Enabled to mutually convert among OBJ, VTK, STL and VRML.
Create mesh on an object with the RAW or VOL format, and export mesh in the OBJ, STL and VRML formats.
Three view modes for volume objects were implemented, i.e., soft display, clear display and raw voxel display.
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Linux el5.x86_64
Linux el6.x86_64
PhysioDesigner1.0RC1_el5.x86_64.rpm
PhysioDesigner1.0RC1_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 RC1


Flint can perform simulations of models created on PhysioDesigner.
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Linux el5.x86_64
Linux el6.x86_64
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) 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".

Release Notes

Flint now tries to detect and warn a dependency cycle among vairables when calculating initial values of them.
Fix the behaviour of PHML's Delay and DeltaTime functions in the Runge-Kutta 4th case
Fix a broken ISDF timestamp on Windows
It becomes possible to open a new file in which a line graph to be saved at the menu Plot > Target