(Mathematical) Logic for Systems Biology (Invited Paper)

Abstract

We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The potential candidate logics should have a traditional proof theoretic pedigree (including a sequent calculus presentation enjoying cut-elimination and focusing), and should come with (certified) proof tools. Beyond providing a reliable framework, this allows the adequate encodings of our biological systems. We present two candidate logics (two modal extensions of linear logic, called HyLL and SELL), along with biological examples. The examples we have considered so far are very simple ones-coming with completely formal (interactive) proofs in Coq. Future works includes using automatic provers, which would extend existing automatic provers for linear logic. This should enable us to specify and study more realistic examples in systems biology, biomedicine (diagnosis and prognosis), and eventually neuroscience.