PhysioDesigner
A modeling tool for multilevel physiological systems

Integrate Time Series Data




1. Time series data format


On PhysioDesigner it is possible to integrate time series data, and assign the value in the time series data to a physical quantity.
For now PhysioDesigner supports CSV format and ISD format which is a binary time series data format used by Flint to export simulation results. There is a CSV-ISD converter available at Physiome.jp.

Integrated time series data can be used to drive a mathematical model using experimental data, or to constrain partial dynamics of the model by real dynamics of modeled physiological system.



2. Open dialog


To open the dialog to integrate time series data, select "Timeseries... > Integrate Timeseries".
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Then a dialog to select time series data will open.

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3. Load time series data

In the dialog, it is possible to upload new time series data files and view the new data as well as view the time series data already integrated to the module.

Let's start with uploading a new data file to the dialog.
Click "Add" button at the middle column at the top of the window. Then a file chooser will open.

The data file in ISD format or CSV format can be uploaded.
ISD format is a binary data format used by Flint. Once one data file is selected, it appears in the middle column.
Selecting it, the variables (data) contained in the data file are shown in the rightmost column.

Once selecting one of variables (not ticking in a checkbox) in the rightmost column, graph of the variable is shown in the lower panel. We can check the graph by this way to know if the variable is the one that we want to integrate into the model.

Notice that we can load multiple data files.
In the leftmost column, the time series data which are already integrated in the model is shown.

4. Select data to integrate


To select variables which are going to be integrated, tick in check boxes in the rightmost column. We can select multiple variables.
The number of the selected variables from a data file is shown at the right side of the data file.

Remark that selected variables must be the same length in time to be integrated, otherwise when Integrate button is clicked, a warning dialog pops up saying there are variables with different time length and cannot be integrated.

5. Integrate the data


Once we selected variables that we want to integrate, click Integrate button.
Then a small dialog to merge selected variables into one ISD file. In this dialog we can change variable name not to be overlapped and give a name to the data including those variables.
Then again click Integrate button on the small dialog.
It opens a file chooser in which we should specify a file to save the data.

Notice that even if variables are selected from an existing time series file, the process creates a new data file including only variables selected from the original data file.


6. Assign to Physical Quantity


Now we need to assign the data to a physical quantity to functionally integrate the data with mathematical expressions.
Right click on the module and select "Edit Physical Quantity...".
Create a new physical quantity with the type of "Timeseries", and move to "Implementation" tab.
By default, defintion-type is "assign" with "Teimseries" selected.

Data name is "newdata" which is input in a small dialog when we integrated the time series.
Beneath the name combo box, there is a list of variables included in the time series data named "newdata".

Select one of them, showing a rough graph of the variable in the right panel.

Finally click OK button.