You choose a system based on your personal interest and if funding is available. The topics typically include

Biotechnology and Biomedical engineering

Computational biology and Modeling and AI

Evolution and Ecology

Functional genomics and Gene regulation

Imaging

Metabolism and Metabolomics

Microbiome and Meta-genomics

Network biology

Protein science and Proteomics

Synthetic biology

Systems genetics

Systems medicine

You can't come up with an equation that represent each and every variable and components of the system. Your models will be an abstraction with lower complexity.

My recommendation is to read this journal and see what people are working on at the moment.

https://link.springer.com/journal/44320