PhysioDesigner
A modeling tool for multilevel physiological systems

Apr 2012

Version 1.0 beta

PhysioDesigner 1.0 beta


24th April, 2012

Install Note


Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0". 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 directory because of the lack of write permission of the volume. It is necessary to copy PhysioDesigner1.0b directly (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 store, configurations are reset to the default.

Note 3) Directory structure in PhysioDesigner1.0b is crucial for execution of PhysioDesigner.app and other apps. For example, all apps and server directly must be in the same directly.

Win: Please execute the installer by double clicking it. It installs a couple of necessary libraries such as Python, etc.

Release Notes


・Extra-implementation has been supported in Physical-Quantity dialog (see Documents for how to use).
・Canvas design was simplified.
・The way to search path in XML Viewer was improved. Partial XPath search is available.
・"Open Recent Model" and "Revert to Saved" were added in File menu.
・Delay operator became available for variable-parameter type physical-quantity.

Image viewer:
・ Console window was added. It gives information of a created mesh of the object such as number of nodes, elements and measure of quality of mesh.

Morphology editor:
・ Console window was added. It gives information of a created mesh of the object such as number of nodes, elements and measure of quality of mesh.
・It can create mesh object from primitive geometries.
・VTK file of a created primitive geometry mesh can be generated and it can be saved.
・It is possible to highlight default segments on a primitive object in geometry viewer.
・The way to deal with segments defined on primitive geometries was improved.
・Mesh file conversion from FreeFem++ generated VTK file is supported.


Simulator Flint 1.0 beta


Flint can perform simulations of models created on PhysioDesigner.

Release Notes


Support for random variates based on gamma and poisson distribution.
Support for pseudo random number generator's seed in a PHML model.
Made it possible to select output variables in an SBML model.
Added useful logging on error.
Experimental feature to run simulation at a remote machine on LAN.
Improved performance with large-scale models through better calculation scheduling (thanks to Mr. Okuyama).
Fixed calculation for extra-implementation in parallel simulation (thanks to Mr. Matsui and Yoshikawa ).