Question about Simbiology Model Publication

Dear All,

I am currently using Simbiolgoy verison 2019a for PK/PD modeling. I was curious if your group has any guidance for how to publish these kinds of Simbiology models. Traditionally, PK/PD manuscripts ask for the code used to generate models. From my understanding, Simbiology is used to generate the ODEs, Fluxes, and initial conditions are via the Equations tab, but is there a way to generate the code behind the model?

Thanks in advance for your help

Answer 1

[Sietse Braakman]

Hi Brett,

There are multiple ways to do this:

1. You can share the .sbproj file - this is the easiest way for others to use your model and be sure they are getting the same results as you are.
2. You can export your model to an SBML file. Several softwares (including SimBiology) support importing SBML files. SBML documentation
3. You can export your model as tables of species, parameters, reactions, compartments, doses, events, etc. That way, other people can (re)construct the model from the same tables again (see attached screenshot).
4. You can write the code to construct the SimBiology model, using the programmatic way to create models - here is an example
5. You can copy/paste the equations or use getequations
6. You could create a web-app to allow end-users to simulation your model through a web

Note that SimBiology is an object based programming environment: as opposed to writing ODEs in a script or function, you construct the model network by creating species, compartments, reactions etc. Each of those components is an object with properties you define (e.g. the reaction has a property ReactionRate). From this network, if constructed correctly ('Verify model' confirms whether you constructed the model correctly) SimBiology creates the set of ODEs. Because of this, you can't "generate the code behind the model". You can however write the code to construct the model (see option 4).

Let me know if that makes sense. Feel free to contact me directly if you have specific questions about one of the options I specified above.

[Brett Fleisher]

I see. This is very helpful. Thanks for the help!