How do I fix a duplicate name error ?

I am using the simBiology builder app on matlab. I keep receiving an error on one of my models of a duplicate name error ( names are SSRI, SERT, 5-HT ) However, it doesn't say how to fix it. I have to models in this project and only one has this issue. How do I fix it?

Answer 1

[Arthur Goldsipe]

It's hard to know exactly what's going on without more details. Can you share more details? Ideally, can you share the project and the steps we need to follow to reproduce the error?

Without those details, it's hard to know how to help you. But here's what I can say.

As of R2024a, SimBiology no longer allows most components within a model to have the same name. There are a few exceptions (for example, two species can have the same name as long as they're in different compartments). You can read more about that in the SimBiology release notes.

If you open a project that has duplicate names (because it was created in an earlier version that supports them), I expect a warning dialog to appear telling you that these duplicate names have been fixed by renaming some of the components. If that's what you're talking about, you can likely just dismiss the dialog and look at the components that have been renamed.

If you are seeing this error when you are trying to give name a component, you just need to give the component a different name. If you really want the component to have this name, then you need to find out what other component in your model has this name and give it a different name.

[shamma]

I got the warning after I saved the models as a project. I don't really know what I did prior but from what I remember I created the species and the reaction for them and them added the dose for one of them One of the species is also involved in several different reactions. I can attach the project itself if that would be easier to fix the problem?

[Arthur Goldsipe]

Ah, yes. That's the warning dialog I was talking about. As described in the link in that dialog, you loaded a model where multiple components had the same name. Some of them had to get renamed to make the names unique. So if you search your model, you should see that you have something named 5-HT and something else named 5-HT_1. Likewise, SERT and SERT_1, and SSRI and SSRI_1.

So, if you're ok with these new names, then there's no problem to fix. If you don't like those names, you just need to rename them to something else you, but you'll need to give things unique names.

If that doesn't make sense, then go ahead and attach the project. Then I can take a closer look at the specifics of your project.

[shamma]

The file is attached

[Arthur Goldsipe]

Oh, it looks like you are using R2023b. So the first thing to point out is that this version of MATLAB/SimBiology allows components with the same name. You're just getting a warning because these duplicate names will now be allowed in the future (specifically in R2024a). So if you don't plan on updating to R2024a any time soon, you can just ignore this warning.

If you open this project in R2024a, then the duplicate names will get fixed automatically. If you want to get rid of this warning now and make your model compatible with R2024a, the easiest thing would be to export the model to MATLAB and use updateduplicatenames to rename components now.

But if you want to rename the components yourself, here's where the duplicates are:

• 5-HT: You have a species and a parameter with this name.
• SERT: You have a species and a parameter with this name.
• SSRI: You have a species and a dose with this name.

BTW, thanks for sharing this project. It's helpful to see how you are using SimBiology.