PhysioDesigner
A modeling tool for multilevel physiological systems

Sep 2012

Version 1.0 beta2

PhysioDesigner 1.0 beta2


16th September, 2012

Install Note


Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0b2". 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 PhysioDesigner1.0b2 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 PhysioDesigner1.0b2 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


New splash screen.
Garuda enabled; PhysioDesigner can send and receive PHML and SBML models through Garuda protocol.
New method to span an edge from an out-port of a module to an in-port of another module.
A dialog to edit an edge was enriched. Now association between physical quantities can be defined.
Users can directly download models from Physiome.jp into PhysioDesigner canvas
A dialog to view a list of physical quantities in all modules is available. Equations and values defined on physical quantities can be edited.
Modules can be aligned in a line or array in lattice.
Instances are displayed as a bundled form.
Algorithm of drawing modules and edges was improved.
Massive instances can be linked by edges semi-automatically for large scale modeling.
It is possible to create a large model using vol format 3D object and instances.

ImageViewer
Support of vol format file. VTK mesh file can be constructed from the vol format file.
It is possible to convert from obj format file to vol format file.
Improvement of reading procedure of vol/raw and vif/mhd files.
Support obj format to display.
Improvement of tab representation of Extract, Smoothing and Resolution menus for mat format file in ImageViewer dialog.
Show object information.

Show morphology
Multiple number of morphology can be linked and displayed according to the tree structure of modules. For the purpose, Show morphology dialog is added.
Support obj format to display.
Now when a morphology is defined in a module, a physical-quantity is automatically created so that users can practically integrate the morphology in the model.


Simulator Flint 1.0 beta2


Flint can perform simulations of models created on PhysioDesigner.

Release Notes


New logo / splash screen.
Support for PHML's "label" attribute of element.
Support for exponential_variate(lambda), random variate based on exponential distribution.
Command isimc can filter output variables via its "-r" option.
Smooth rendering of line plot on the Plot tab, with optional legend.
Garuda enabled; Flint can load model files passed through Garuda protocol.
Mac OS X Mountain Lion (10.8) package available.