Open the folder created during installation and double-click Main.py. The form, 'Indirect Estimation and Simulation Tool', will open.
From this form the user can load and save data and access all system parameters. Here is a short description of the basic operations that one can perform with this form:
The system holds its data in files in a zip archive. Each file can contain many Projects / Models / Populations using the same or different terminology. The system can load this information and at the end of work the user can save the modified information back to a file. Note that while working with the system the information is never saved to a file until the user specifies the save in this form.
In the event the system does not close properly any modifications made will be lost. A proper exit of the system will ask the user to save the information to file. The automatic backup mechanism during file saving helps track back changes in data and helps maintain integrity.
Note that the system does not lock files after loading them during work. Also note that saving records in the system is not the same as saving the file. Records and entities in other forms are saved to memory rather than to a file. The only way to save to a file is through the main form menu.
For a video demonstration of loading and saving files, click here.
A project is the main entity defined in the system. Projects can be either Simulation Projects or Estimation Projects. Projects can share information such as models or parameters.
All the projects currently loaded in the system are listed in the main form in the project list (A).
To view a project, double click its entry in the list (A) in the main form. The appropriate form will open.
To add a new project to the system, double click the text Add New Project at the top of the list (A). Then select the type of the project from the window that will open. The appropriate form will open.
Simulation Projects or Estimation Projects will have different forms to handle the information in them. See Simulation / Estimation for additional details.
One way to familiarize yourself with the system is to load the test examples file Testing.Zip created by the system during installation. This file provides an implementation of all the simulation examples provided in the test example document SimulationExamples.pdf that is also created by the installation.
Each project is an example from this document. Double clicking on projects listed in (A) will open the project clicked upon. Clicking the buttons marked as (B,C,D,E,F) will allow exploring the underlying data that created these projects.
Before working with the computer system, some preparation is required. This page describes the preparation stages and the workflow with the system from a more abstract view.
When developing a new model or modifying an existing model, it is essential to perform an extensive literature review and to consult with clinical experts who can describe the progression of the disease. During the literature review, it is important to identify studies that provide estimates of the transition probabilities for the progression of the disease through time.
The information from the literature review must be translated into system terminology. This involves identification of important keywords that describe disease progression; these are then used in different categories defined by the computer system:
The identified states and sub-processes should be depicted as boxes in a diagram; the boxes should be connected with arrows to signify transitions between states. Note that at this point, the probabilities of the transitions are considered unknown and denoted by a coefficient. The output of this state may look like:
The statistical information from the literature review should be extracted into the following table.
|Study Reference||From State||To State||At-Risk Population Count||Cumulative Incident Count||Study length|
|Study Name / Short description||Use Model Terminology||Use Model Terminology||Number of subjects in the “From State” who are at risk to enter the “To State”.||Number of Individual that reached the end state by the end of the study||The number of Time steps|
The study data and the model should be entered into the system. Then, the estimation module should be run and as a result the unknown coefficients in the model will be estimated. With this version estimation should be repeated for each sub-process separately. Afterwards, the simulation model is almost ready.
If the model does not require estimation of parameters from studies, then the model can be entered directly as a simulation model to the system as described in Simulation.
See Simulation for details.
It is necessary to specify the population of individuals to whom the simulation should apply. The population should contain information about the initial states of each individual. Also, parameters to be used in the simulation should be defined.
The module can be enhanced by adding rules for updating parameters used in the simulation. The rules can contain:
The simulation can then be performed to predict outcomes of disease progression over the defined population set. After analyzing the results, the simulation can be repeated after changing parameters or using a different population set to reflect different model conditions. Each change in the simulation may require creating a new simulation project. This can be easily done by copying the existing project.