Formal Systems in Biology
A collection of resources that apply formal systems to model biological processes. Some easily accessible books to understand the general approaches in this field are also included.
McCulloch-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/
Arthur Iberall / Warren McCulloch
Behavioural Model of Man - His Chains Revealed
Stanisław Ulam and Jon Von Neumann
Theory of Self Reproducing 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 Virtual 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
Joseph Henry Woodgers
The Axiomatic Method in Biology (1937)
Louis Kauffman
Vassiliev Knot Invariants and the Structure of RNA folding
Marius Buliga
Chemlambda
For animations, checkout: https://chemlambda.github.io/collection.html
Stefano Maestri and Emaneula Merelli
Process calculi may reveal the equivalence lying at the heart of RNA and proteins
Correction to the article: https://www.nature.com/articles/s41598-019-51082-3
Artem Kaznatcheev
Computational Complexity as an Ultimate Constraint on Evolution
Tweet thread on it here: https://twitter.com/kaznatcheev/status/1102973539634892800
Jeffrey Ventrella
Clusters
Genepool
Programming Languages
https://kappalanguage.org/
The Systems Biology Markup Language
Computation with Crabs
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)
Complex Systems: A Survey
A really good survey of books in complexity science here.
Further Research
- Rashevsky and Rosen
Rashevsky devised the primary model of neural networks which was interpreted using the boolean language by McCullough/Pitts. His student Robert Rosen went on to work on using Category Theory to model biology. These works need to be catalogued here. Herbert Simon was also his student.
There could also be more possible works from the conference where McCullough presented his work and met Pitts.
Sampling of Rashevsky’s work
Topology and life: In search of general mathematical principles in biology and sociology
On relation between sets — 1961
The representation of organisms in terms of predicates — 1965
On relations between sets: II - 1966
A note on relations between sets – 1966
Organismic sets: Outline of a general theory of biological and social organisms - 1967
Organismic sets: II. Some general considerations - 1968
The Geometrization of Biology
Outline of a unified approach to physics, biology and sociology
Sampling of Rosen’s work:
Pattern Generation in Cellular Spaces
Relational Biology and the Origin of Life
On a unified approach to pattern generation
Complexity and System Description
The Chief Abstractions of Biology
Input-Output Systems
The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design
A logical paradox implicit in the notion of a self-reproducing automaton
A relational theory of biology
The representation of biological systems from the standpoint of the theory of categories
- Ilya Pregorine’s Work
- Gregory Chaitin’s work
- Stochastic CFG for RNA
- Zuse-Fredkin thesis / Digital Philosophy
Think I need to mention the work of Zuse-Fredkin thesis along with Ulam-Neumann model.
- Knot Theory for Protein Molecules
- Wang Tiles and DNA
- Molecular Networks and Monomial Ideals
- Computational Modeling, Formal Analysis, and Tools for Systems Biology: Survey
- Luca Cardelli
- Morphism of reaction networks that couple structure to function
Tools
Ready
Ready is a program for exploring continuous and discrete cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes.
Blogs
I should have loved biology
A beautiful piece of writing from James Somers on the rich tapestry of the field of biology and what user interface design might have to offer the field.
(A Bit of) Biological Neural Networks (2018)
A really nice series of articles on the biological aspects of neural networks by Jack Terwilliger