Formal Systems in Biology

Formal Systems in Biology

A collection of resources that apply formal systems to model biological processes. Some easily accessible books to understand the general approach to this field might be:

McCullough-Pitts Work

A Logical Calculus of the Ideas Immanent in Nervous Activity (1943)

McCullouch and Pitts study of neurons in biology birthed the pivotal paper that kickstarted A.I., regular languages , and digital computers. It was the only paper included in the EDVAC report by John Von Neumann.

An interactive demo of their model is available here: https://justinmeiners.github.io/neural-nets-sim/

Stainslaw Ulam and Jon Von Neumann

Cellular Automata

Probabilistic Logics and the Synthesis of reliable organisms from unreliable components (1952)

L Systems

Mathematical models for cellular interactions in development I (1968)

Mathematical models for cellular interactions in development II (1968)

Karl Sims

Evolved Virutal Creatures (1994)

Walter Fontana and Leo Buss (1996)

The Barrier of Objects From Dynamical Systems to Bounded Organizations

Regev, Silvermann, Shapiro

Representation and Simulation of Biochemical Process Using the Pi Calculus Process Algebra (2001)

Cell as Computation (2002)

The π-calculus as an abtsraction for biomolecular systems (2004)

Ehud Lamm and Ron Unger

Biological Computation

P System

Alan Turing

The Chemical Basis of Morphogenesis (1952)

Reaction-Diffusion Systems

Marius Buliga

Chemlambda

Jeffrey Ventrella

Clusters

Genepool

Resources to understand the field

Neurocomics (Beginner)

Introducing Evolution (Beginner)

Introducing Genetics (Beginner)

Introducing Epigenetics (Beginner)

Complexity: A Very Short Introduction (Intermediate)

Games of Life (Intermediate)

Books

Computational Methods in Systems Biology (2006)

Prior Art

Ramón y Cayal

Golgi