Formal Systems in Biology
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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
Recommend
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