Loading SBML Model reports error for displaying diagram (giving blank diagram)

Hello, I am new to Matlab/SimBiology. I have an SBML Model that I am loading into the Model Builder. Upon doing this, I have the following error reported in the main Matlab Command window.

Warning: Error posting 'expressionStatus' for ''. Error from MATLAB: 'Error using SimBiology.web.diagramhandler
Input argument 'element' is invalid.'.' 
> In SimBiology.web.modelhandler
In SimBiology.web.modelhandler
In SimBiology.web.modelhandler
In sbiojsgate (line 27)
In connector.internal.fevalMatlab
In connector.internal.fevalJSON 

The model does complete loading, but the diagram is completely blank. I would like to know what I can do to resolve this, since seeing the diagram would be nice. I would share the SBML file, but it is proprietary, and I do not know what I would do to create an SBML model that produces the same issue.

One other thing that might be helpful is that I am on macOS with an M1 chip.

Thank you

[Florian Augustin]

Hi Anand,

Thank you for reaching out. R2021a should be supported via Rosetta2 on Apple M1. But just to make sure, do you have the option to try out if the issue persists on an Intel processor?

You may be able to import the SBML model on the MATLAB command line first and then open it in the SimBiology app:

>> model = sbmlimport("yourSBMLfile.xml");

>> simbiology(model);

It is likely that the error still persists. So far I haven not seen this error before and have not been able to reproduce it given the information from the error stack. I understand it might not be possible because of IP constraints, but if it is in any form possible, it would be helpful for the investigation to have access to the model. We have options to obfuscate the model before you share it with us. I am not able to contact you on your community profile to talk about options for how to proceed. Please contact me on my community profile or send a message to MathWorks Technical support (please reference this MATLAB Answers post).

Thank you,

Florian

[Anand Jain]

I'm still getting this issue in 2022! This time I have a code as an .sbproj. Again, I cannot share this code.

In SimBiology.web.internal.converter.modelhandler

In SimBiology.web.internal.converter.modelhandler

In SimBiology.web.internal.projectconverter

In SimBiology.web.internal/projectconverter/convertProjects

In SimBiology.web.projecthandler

In SimBiology.web.projecthandler

In SimBiology.web.desktophandler

In SimBiology.web.desktophandler

In sbiojsgate (line 28)

In connector.internal.fevalMatlab

In connector.internal.fevalJSON

Warning: Invalid InitialAmountUni

Also I have noticed that using simbiology 2022 UI significantly slower than previous versions. I don't have time to do a formal check of this, but thought it might be worth sharing.

[Florian Augustin]

Hi Anand,

Thank you for reporting this warning. It is cut off, do you see the full warning message and is it be the following?

Invalid InitialAmountUnits for species. Valid quantity types are amount, mass, and concentration.

If this is case, is your model and diagram loading in the SimBiology app? If this is the case, please check the units on the species in the model. It looks like there is an invalid unit specified on a species that is not of type amount, mass, or concentration.

If the model and diagram are not loading, can you share which MATLAB version you are working with? Is it R2022a or R2022b, and do you have any update releases installed? Can you also share which version of MATLAB the project was saved in? If possible, can you share the full text of the warning? I might be able to find something by inspecting the code.

Also thank you for reporting the performance regression. When loading projects saved in previous versions of MATLAB, SimBiology converts them to the new version, which might take some time. You can try saving/loading the project in the current version. However, please let me know if you can identify areas in the SimBiology apps that are particularly slower than in previous version (and which version you are comparing to), i.e. loading of projects (do you have simulation/optimization results stored in programs?), running of simulations/scans/parameter fits. Any information would help us.

Thank you,

Florian