Fitting model on a Debian machine

Hello everyone, I am trying to fit a model of mine on a remote linux machine (Debian GNU/Linux 11 (bullseye)). I'd like to use MATLAB as a command line application and not use a X11 interface. I have not found any tutorial or suggestion in the documentation, as all examples either use the Simbiology app or the 'classical' Desktop version of MATLAB.

I have already installed MATLAB on the server with all necessary add-ons, does someone have suggetions on how to proceed? Also considering that I am working on my local pc for the development nof the model and I need to 'transfer' my data to the MATLAB worksopace on the server.

Answer 1

[Arthur Goldsipe]

If you want to fit a SimBiology model using a command-line function, you can directly call sbiofit (or sbiofitmixed). This is exactly what the SimBiology Model Analyzer App uses. There are examples on each of these ref pages.

[Elisa]

I thing my question was confusing. My main problem is exporting and exporting the model so that I can run sbiofit on the server. I tried with the SBML import/export, but it's giving some problems (for example, I have a parameter called 'ln' that the SBML pipeline translates into the 'log' function'). By searching in the documentation, I found mainly three routes for importing/exporting outside MATLAB workspace:

1. SBML, that gives some problems as said before
2. Excel, but I figured it's not intended for this use, rather to save specific components/variants/doses
3. Translate the model into a .mat file for standalone applications

But none of these three methods seem to be fit to my problem, which is to have an 'agile' import/export pipeline of the model.

[Arthur Goldsipe]

Sorry, I'm still a little confused. Are you running an actual MATLAB installation on the server? Or are you trying to create a standalone executable (using MATLAB Compiler) that you run on the server?

If you're running "normal" MATLAB on the server, you can save your model to a MAT file and load it on the server.

If you're trying to create a standlone executable to run on your server, then things are a lot more complicated. And if I understand what you mean by "agile", this is not supported with the MATLAB Compiler. When using SimBiology with MATLAB Compiler, you cannot load/create "normal" SimBiology models. You can however create a deploy a SimFunction. You can find an example of that here. (You would also need to write your own code for fitting that uses a SimFunction.) The SimFunctions you can load in the app also must be determined at the time you create this executable application. So it may still not be "agile" enough for you.

If this still doesn't make sense, feel free to send a message to me over my MATLAB Answers profile. I can either follow up with you directly or put you in touch with one of the engineers that helps support SimBiology.