Cant run or getequations from simbiology file from publication

I have a simbiology file from a published article, so theoretically it should work. I am trying to extract the equations using

bb=sbmlimport('filename')
equations=getequations(bb)

I get a lot of warnings when i import the file ("duplicate reaction names not allowed"), and when i try to get the equations it says "error reported from dimensional analysis". (same error as when attempting to simulate). I tried to verify it, and it gives the same error messages and throws a 1x2191 array of errors. (so every single reaction).

I tried to import using the app, but it crashes when it throws the first warning. This is my first time using simbiology, so perhaps theres some setting or something I'm missing? I'm using matlab R2015b, and I have the toolbox.

Answer 1

[Arthur Goldsipe]

You are getting errors because this is basically an incomplete model. The SBML file does not specify rates for any of the reactions. This means there are no equations to get or simulate.

[Renee]

is there some way I can define the rates? I can't figure out how to look at what they would be named.

[Arthur Goldsipe]

If you know what the rates should be, you can either modify the XML file before loading or the SimBiology model after loading. Please read the documentation on reaction rates for more information.

[Renee]

I managed to find their file provided elsewhere. I exported the equations using smblexport(bb,'simbioeqn.xls'), and.. I cant really see any ODEs or actual equations. The same thing happens in the console. Help?

[Arthur Goldsipe]

Neither file contains equations to describe ODEs. The information you want simply does not exist in the model.

My guess is that this is a model that was created for something like flux balance analysis rather than for dynamic simulations with ODEs.