PhysioDesigner
A modeling tool for multilevel physiological systems

Getting started

This document shows how to use PhysioDesigner, starting with an existing model.

Download a model from PHDB at physiome.jp

At http://physiome.jp, there is an open database of models written in PHML. PhysioDesigner can download models directly from physiome.jp and set it on the canvas. Clicking a folder icon with a globe opens a dialog connecting to the PH Database at Physiome.jp. Input a keyword in a text box and click “Search” button to search a model in the database. Target fields for the search can be selected with the check boxes. The search result is shown as a table at the lower half part of the dialog. Select one of model and click “Download” button.
download_model
Then a small dialog pops up to select an action, i.e. newly open the model (“Open” button), add the model to the currently editing model (“Add” button) or cancel the action (“Cancel” button).

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Now we can see one module on the canvas (PhysioCanvas), which is called the root module.

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Let's see the series of manipulation in a movie.

Browse a model on the canvas

There are two ways to show the structure of the model. One is Nesting diagram and the other is Tree diagram.
Clicking a module expands it, and modules located one level below are shown. Clicking again the same module collapses the module and hide modules at the lower level.
On the nesting diagram, modules are shown as follows.
And on the tree diagram, it is like the following.
Physical Quantities are defined in each module characterizing the module quantitatively. For example, physical quantities define constant parameters or states (dynamics variables) used to define dynamics (mainly represented by ordinary differential equations).
A list of physical quantities defined in a module is listed in a table shown at the bottom of the main window. Users can edit the definitions of physical quantities in the table.
Details of how to browse and edit a model will be explained in later sections.

Run a simulation

At the menu bar, selecting a menu “Simulation > Flint” opens Flint with opening the currently editing model on it.

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Then a simulator Flint is launched.

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On the configuration window, users can setup several things, such as numerical integration algorithm, time step, simulation duration, and so on. Usage of Flint will be explained in later sections.

Clicking “Run” button starts simulation. When calculation finishes, a dialog pops up to let users know that it finishes. Then in Plot tag, it is possible to check the time course of each physical quantities. To draw a graph, drag and drop name labels from the Variables list at left side to boxes of Y1 (left) or Y2 (right) ordinates.

FlintScreenSnapz001

If users have already installed gnuplot, which is a free software to draw graphs, “Plot” button calls it to draw more practical graphs. Detailed usage of Flint will be also explained in later section.