PhysioDesigner
A modeling tool for multilevel physiological systems

Jan 2013

Version 1.0 beta3

PhysioDesigner 1.0 beta3


5th January, 2013

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0b3". 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 PhysioDesigner1.0b3 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 PhysioDesigner1.0b3 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 be OK to run.

Release Notes

On PhysioDesigner
Component tree was functionally integrated. It is possible to access all properties of modules from the component tree.
Edge dialog was enriched. It is possible to edit physical quantities to be assigned to head or tail of an edge.
Port dialog was enriched. It is possible to assign and create physical quantity to be assigned to a port.
Search function was implemented on the main canvas. Users can reach to a module to edit easily.
Visualization of modules was reimplemented with more effectively.
Canvas is now adjustable.
Search interface of XML Viewer was improved.
Canvas can be exported into image files such as png, jpeg, pdf.
Several bugs were fixed.

On ImageViewer
Analyze format was supported, which is often used for medical images.
Processing speed of MAT format was improved.
Interface was improved by adding menu bar.
Equipped three sectional view-mode and one 3D view-mode.
Screen can be saved into a file with PNG, JPEG, PDF, BMP and TIFF formats.


Flint 1.0 beta3


Flint can perform simulations of models created on PhysioDesigner.

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

New numerical solver 'Adams-Moulton method' was implemented.
An instance's label in PHML appears in resulting output file.
Support MathML expressions max / min / mean used in a model.
A new plot feature (log-scale axes) was implemented.
Fixed several bugs, including CVS exporting on Windows.
Several bugs were fixed.