Model Information
Compartments
Species
Reactions
Input/Output
Parameters
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
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.
Current Known Limitations:
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'.
Model Variables
Change Model Parameters
Import Data
Import Observational Data
Select Parameters to Estimate
Estimation Results
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Reactants
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Products
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Modifiers
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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.
Documentation
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
Authors/Contact
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: rdash@mcw.edu
Scott Terhune: sterhune@mcw.edu
Justin Womack: jwomack@mcw.edu
Viren Shah: virshah@mcw.edu
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.