add "Modeling Life: The Mathematics of Biological Systems"
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haraldschilly commented
Modeling Life: The Mathematics of Biological Systems 1st ed. 2017 Edition
by Alan Garfinkel (Author), Jane Shevtsov (Author), Yina Guo (Author)
https://www.amazon.com/Modeling-Life-Mathematics-Biological-Systems/dp/3319597302/
Also, +William Stein, the book explicitly uses +Sage Mathematical Software System. Sage has been tremendously useful for our course and some former students have even used it for research.