Getting started

Introduction

ESQapp is a graphical user interface (GUI) for working with the projects implemented in the {esqlabsR} package.

Opening the project

ESQapp operates with the projects by loading a valid ProjectConfiguration file. In this example, we will use an example project created by executing

library(esqlabsR)

init_project()

Start the app by calling

ESQapp::run_app()

starting screen

Click on “Select Project Configuration” and select the ProjectConfiguration.xlsx file of your project. The app will load the project and show the contents of the scenario definitions, individuals, populations, and plots.

import project configuration

Design Scenarios

You can browse, edit, add new, or remove existing scenarios. To edit a field, e.g., Scenario_name, double-click on it. To remove a scenario or add a new one, right-click on a row and select “Insert” or “Remove row”.

design scenario

The main properties that can be defined for a scenario are:

• The IndividualId column specifies the individual for a scenario. This column shows a drop-down list with all individuals defined in the Individuals tab. To unassign an individual from a scenario, right-click on the cell and select “Clear”.

• The population is specified for a scenario in the column PopulationId, which shows a drop-down list with all populations defined in the Populations tab. To unassign a population from a scenario, right-click on the cell and select “Clear”.

• To edit the simulation time of the scenario, right click on the SimulationTime entry and select “Enter Simulation Time”.
  
  In the following window, you can edit the output intervals of the simulation.
  
  To add or remove an interval, right click on an existing row. You can define the start and the end time of the interval, define the units, and define the resolution. As the original excel structure do not allow to mix time units for otput intervals definition, all values must be converted to a common unit. This is done automatically to the unit selected by the user, the unit is stored in the read-only column SimulationTimeUnit.

• Output paths are defined in the column OutputPathsIds. When double-clicking on a cell, a list of output paths defined in the OutputPaths tab is presented and the user can select the paths that should be added to the scenario.
  

Individuals

The individuals assigned to the scenarios must be specified in the Individuals tab. To add a new invidividual, right-click on an existing entry and select “Isert row below”. After entering the name of the individual, a new individual parameters sheet is added.

adding-individual-sheet

Currently, definition of protein ontogenies are currently not supported in the App.

Populations

Populations are defined in the Populations tab. Definition of protein ontogenies are currently not supported in the App and must be done in the excel file.

Parameter sets

Parameter sets specified in the column ModelParameterSheets of the Scenarios tab are listed in the tab Parameter sets.

parameter sets

In the current version of the app, it is not possible to add new or to remove the existing sets. This must be performed in the excel file.

To add new entries, right-click on a row and select “Insert row” or “Remove row”.

Applications

Definition of application protocols is not supported yet and must be performed in the excel file.

Plot Results

Definition of the figures within the esqlabsR Plotting Workflow is supported by the ESQapp in the tab Plots.

plots

The DataCombined defining the mappings of simulation results with observer data are specified in the DataCombined tab. The app allows selecting the scenarios defined in the Scenarios tab, and output paths from the Scenarios|OutputPaths list.

Applying the changes

WARNING: Closing the app without saving will loose all changes made to the configurations!

After editing the scenarios, plots, or other configurations, the changes must be saved by clicking on the “Export” button.

export

The changes will be written into the Excel files. Of course, you can still manually edit the Excel files.