I’d say it’s a pretty even mix of matlab and python. My advisor would be upset if I didn’t plug his framework: https://pysb.org/

As far as textbooks go, I guess I’d recommend Uri Alon’s book: https://www.routledge.com/An-Introduction-to-Systems-Biology...

Full disclosure, I haven’t read it, but I like his research and he’s a good communicator.

It’s tough because it’s a newish field and not super well defined. The frustrating answer is that the best way to understand the field is maybe to read a book about biology, then a book about computational modeling, then a few papers where they put those together.