Model Information






Differential Equations

Note that any custom equation will disable that equation to be solved for by the computer. You can choose to allow equation to be generated by adding it below

Latex Document

We currently support loading file types in an r data structure and SBML. While SBML is a common storage language for models, we store model information in .rds format as that allows us to store application specific content.
Import RDS File

Import SBML File
Our SBML importer was created from custom scripts. There are many complexities and variations in SBML files. As such, we note that our importer will fail on some files. We do our best to return where these importers failed, looking to better improve it in the future.

Current Known Limitations:
  • MathML parser cannot read expressions with root and degree (other keywords may be an issue)
  • Models are rendered as unitless. We do not currently parse UnitDefinitions in SBML markup.
  • While we can read function definitions and use those to build equations, we have not currently incorporated a converter to add the functions to the UI. As such, all functions will load as type 'CUSTOM'.

New Window

Model Variables

Change Model Parameters

Import Data

Import Observational Data

Select Parameters to Estimate

Estimation Results



Existing Variables
New Variables

Options below define the base unit that the application will use when generating units for parameters, speices, or other variables. These values can be changed from the base in the variables respective table.


Our current documentation is availble in an online format, word document, and pdf that can be seen/downloaded in the iFrame below.

ReadTheDocs: Documentation webpage hosted at ReadTheDocs
Word Document: Download Documentation

Additionally, please see the following links for more information or other downloading methods:

More Information

To further information on our application/work please visit:

Lab Homepage: Visit Application Homepage at MCW/Marquette Website
GitHub: Visit this Projects GitHub


This application was made in conjuction with the Dash/Terhune labs at the Medical College of Wisconsin.
Lead programmers in the development were Justin Womack and Viren Shah.

Ranjan Dash:
Scott Terhune:
Justin Womack:
Viren Shah:

Special Thanks to CSTI For Server Hosting

We like with to thank the Clinical & Translational Science Institute (CTSI) of Southeast Wisconsin for helping us host this application online. A special thank you to Kent Brodie for helping build the Rshiny server and maintaining the application. Another special thank you to George Kowalski for setting up the Jenkins bot allowing us an easy way to update changes to the application.


This page is meant for developers to be able to quickly/easily see different variables and data structures of the application. Allowing insight, and, hopefully, ease of finding and narrowing down software bugs.



Reset all variables

Reset Latex/Mathjax laws