PhysioDesigner
A modeling tool for multilevel physiological systems

Apr 2013

Version 1.0 beta4

PhysioDesigner 1.0 beta4


24th April, 2013

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Note: These installers for linux are still experimental. If you noticed any problem on the installers, please contact us.

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0b4". 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 PhysioDesigner1.0b4 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 PhysioDesigner1.0b4 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".

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 available on Windows 8
Now one in-port can receive multiple inputs (functional edges). How to handle these multiple inputs (sum, multiply and so on) must be defined in the extra-implementation of the physical quantity that receives the inputs. Default is "sum".
In the PhysicalQuantity table at the bottom of the main window, value of static-parameters are now editable.
Now module's color can be selected among 24 colors.
A module including SBML model is now labeled by SBML logo for better visibility.
Instances now can be distinguished by their "label".
Several bugs were fixed.


On ImageViewer
In ImageViewer, synchronized movement among xy, yz, xz and volume views can be done. Drag a mouse pointer with cross hair in a selected view, other viewers move accordingly.
Support of NifTi format file.
Volume representation can be switched between volume rendering view and volume cross-sectional view.
File name, file path and description contents of ImageViewer can be set into a module.


Flint 1.0 beta4


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), 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

Now available on Windows 8
Support for <piecewise> of MathML
Support for <sep/> in <cn> element of MathML
Open a recent model easily via menu "File" > "Recent Models..."
Save and load simulation configuration through menu "File" > "Save configuration" and "Load Configuration"
Export simulation result as a CSV or ISDF file with menu "File" > "Export As"
Improved performance of plotting a line graph with gnuplot
Improved performance of simulation
Fixed memory leaks