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https://github.com/prathyvsh/formal-systems-in-biology

Application of formal systems to model biological systems
https://github.com/prathyvsh/formal-systems-in-biology

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Application of formal systems to model biological systems

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README 

        
* 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



*** [[https://www.cs.cmu.edu/~./epxing/Class/10715/reading/McCulloch.and.Pitts.pdf][A Logical Calculus of the Ideas Immanent in Nervous Activity (1943)]]

[[./img/mccullough-pitts.png]]



McCullouch and Pitts study of neurons in biology birthed the pivotal paper that kickstarted A.I., [[https://www.rand.org/content/dam/rand/pubs/research_memoranda/2008/RM704.pdf][regular languages]], and digital computers. It was the only paper included in [[http://abelgo.cn/cs101/papers/Neumann.pdf][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



*** [[https://core.ac.uk/download/pdf/85247309.pdf][Behavioural Model of Man - His Chains Revealed]]



** Stanisław Ulam and Jon Von Neumann



*** [[https://dl.acm.org/doi/book/10.5555/1102024][Theory of Self Reproducing Automata]]

[[./img/neumann.png]]



*** [[http://web.mit.edu/6.454/www/papers/pierce_1952.pdf][Probabilistic Logics and the Synthesis of reliable organisms from unreliable components (1952)]]

[[./img/neumann-pierce-drawings.png]]



** L Systems



*** [[https://www.sciencedirect.com/science/article/abs/pii/0022519368900799][Mathematical models for cellular interactions in development I (1968)]]

[[./img/lsystem-1.png]]



*** [[https://www.sciencedirect.com/science/article/abs/pii/0022519368900805][Mathematical models for cellular interactions in development II (1968)]]

[[./img/lsystem-2.png]]



** Karl Sims

[[./img/karl-sims.jpg]]

*** [[https://www.karlsims.com/evolved-virtual-creatures.html][Evolved Virtual Creatures (1994)]]



** Walter Fontana and Leo Buss (1996)



*** [[https://scholar.harvard.edu/files/walterfontana/files/objects.pdf][The Barrier of Objects From Dynamical Systems to Bounded Organizations]]

[[./img/fontana-buss.png]]



** Regev, Silvermann, Shapiro



*** [[https://psb.stanford.edu/psb-online/proceedings/psb01/regev.pdf][Representation and Simulation of Biochemical Process Using the Pi Calculus Process Algebra (2001)]]

[[./img/regev-shapiro.png]]



*** [[https://www.nature.com/articles/419343a.pdf][Cell as Computation (2002)]]

[[./img/regev-shapiro-2.png]]



*** [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.1.4739&rep=rep1&type=pdf][The π-calculus as an abtsraction for biomolecular systems (2004)]]



** Ehud Lamm and Ron Unger



*** [[http://www.ehudlamm.com/biocomputing.html][Biological Computation]]

[[./img/ehud-lamm.jpg]]



** P System

[[./img/p-system.png]]



** Alan Turing



*** [[https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.1952.0012][The Chemical Basis of Morphogenesis (1952)]]

[[./img/reaction-diffusion.png]]

Reaction-Diffusion Systems



** Joseph Henry Woodgers



*** [[https://www.amazon.com/axiomatic-method-biology-Joseph-Woodger/dp/B00085P2C8][The Axiomatic Method in Biology (1937)]]



** Louis Kauffman



[[./img/kauffman-magarshak.png]]

*** [[http://homepages.math.uic.edu/~kauffman/KauffProteins.pdf][Vassiliev Knot Invariants and the Structure of RNA folding]]



** Marius Buliga



*** [[https://chemlambda.github.io/index.html][Chemlambda]]

[[./img/chemlambda.gif]]



For animations, checkout: https://chemlambda.github.io/collection.html



[[https://mbuliga.github.io/quinegraphs/history-of-chemlambda.html][History of the project]]



** Stefano Maestri and Emaneula Merelli

*** [[https://www.nature.com/articles/s41598-018-36965-1][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

*** [[https://www.genetics.org/content/genetics/212/1/245.full.pdf][Computational Complexity as an Ultimate Constraint on Evolution]]

**** Tweet thread on it here: https://twitter.com/kaznatcheev/status/1102973539634892800



** Jeffrey Ventrella



*** [[http://ventrella.com/Clusters/][Clusters]]

[[./img/clusters.png]]



*** [[http://www.swimbots.com/genepool/][Genepool]]

[[./img/genepool.png]]



** Programming Languages



*** [[https://kappalanguage.org/][https://kappalanguage.org/]]



[[./img/kappa.png]]



*** [[http://sbml.org/Main_Page][The Systems Biology Markup Language]]



** Computation with Crabs



[[https://arxiv.org/pdf/1204.1749.pdf][Paper]]



[[./img/crab-or-gate.png]]



[[./img/crab-and-gate.png]]



* Resources to understand the field



** [[https://amzn.to/2UrKeRv][Neurocomics]] (Beginner)

[[./img/neurocomics.jpg]]



** [[https://amzn.to/37ft4vD][Introducing Evolution]] (Beginner)

[[./img/evolution-graphic-guide.jpg]]



** [[https://amzn.to/2A7pWpH][Introducing Genetics]] (Beginner)

[[./img/genetics-graphic-guide.jpg]]



** [[https://amzn.to/2BQ1JEL][Introducing Epigenetics]] (Beginner)

[[./img/epigenetics-graphic-guide.jpg]]



** [[https://amzn.to/2XQ39rz][Complexity: A Very Short Introduction]] (Intermediate)

[[./img/complexity-a-very-short-introduction.jpg]]



** [[https://amzn.to/3dYA0ja][Games of Life]] (Intermediate)

[[./img/games-of-life.jpg]]



* Books



** [[https://link.springer.com/book/10.1007/11885191][Computational Methods in Systems Biology (2006)]]



** [[https://arxiv.org/abs/1112.1440][Complex Systems: A Survey]]

A really good survey of books in complexity science here.



* Further Research



- Rashevsky and Rosen



[[https://en.wikipedia.org/wiki/Nicolas_Rashevsky][Rashevsky]] devised the [[https://doi.org/10.1002%2Fjhbs.1094][primary model of neural networks]] which was interpreted using the boolean language by McCullough/Pitts. His student [[https://en.wikipedia.org/wiki/Robert_Rosen_(theoretical_biologist)][Robert Rosen]] went on to work on using Category Theory to model biology. These works need to be catalogued here. [[https://en.wikipedia.org/wiki/Herbert_A._Simon][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



*** [[https://link.springer.com/article/10.1007%2FBF02484495][Topology and life: In search of general mathematical principles in biology and sociology]]

*** [[https://link.springer.com/article/10.1007%2FBF02476737][On relation between sets — 1961]]

*** [[https://link.springer.com/article/10.1007%2FBF02476851][The representation of organisms in terms of predicates — 1965]]

*** [[https://link.springer.com/article/10.1007%2FBF02476395][On relations between sets: II - 1966]]

*** [[https://link.springer.com/article/10.1007%2FBF02477001][A note on relations between sets – 1966]]

*** [[https://link.springer.com/article/10.1007%2FBF02476967][Organismic sets: Outline of a general theory of biological and social organisms - 1967]]

*** [[https://link.springer.com/article/10.1007%2FBF02476947][Organismic sets: II. Some general considerations - 1968]]

*** [[https://link.springer.com/article/10.1007/BF02477842][The Geometrization of Biology]]

*** [[https://link.springer.com/article/10.1007%2FBF02478215][Outline of a unified approach to physics, biology and sociology]]



** Sampling of Rosen’s work:



*** [[https://link.springer.com/chapter/10.1007/978-94-009-2975-3_35][Pattern Generation in Cellular Spaces]]

*** [[https://link.springer.com/chapter/10.1007/978-1-4684-4640-1_31][Relational Biology and the Origin of Life]]

*** [[https://link.springer.com/article/10.1007/BF02459437][On a unified approach to pattern generation]]

*** [[https://link.springer.com/chapter/10.1007/978-94-010-1239-3_9][Complexity and System Description]]

*** [[https://link.springer.com/article/10.1007/BF02459555][The Chief Abstractions of Biology]]

*** [[https://link.springer.com/chapter/10.1007/978-1-4899-6419-9_8][Input-Output Systems]]

*** [[https://link.springer.com/article/10.1007/BF02477959][The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design]]

*** [[https://link.springer.com/article/10.1007/BF02477897][A logical paradox implicit in the notion of a self-reproducing automaton]]

*** [[https://link.springer.com/article/10.1007/BF02478302][A relational theory of biology]]

*** [[https://link.springer.com/article/10.1007/BF02477890][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 / [[https://en.wikipedia.org/wiki/Digital_philosophy][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



- [[https://www.sciencedirect.com/science/article/pii/B9780128140666000064][Molecular Networks and Monomial Ideals]]



- [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004591][Computational Modeling, Formal Analysis, and Tools for Systems Biology: Survey]]



- Luca Cardelli

- [[https://dx.doi.org/10.1186/1752-0509-8-84][Morphism of reaction networks that couple structure to function]]



** Tools



*** [[https://github.com/GollyGang/ready][Ready]]

Ready is a program for exploring continuous and discrete cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes.



** Blogs



*** [[https://jsomers.net/i-should-have-loved-biology/][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.



*** [[http://jackterwilliger.com/biological-neural-networks-part-i-spiking-neurons/][(A Bit of) Biological Neural Networks (2018)]]

A really nice series of articles on the biological aspects of neural networks by Jack Terwilliger



** Talks



*** [[https://www.hkw.de/en/app/mediathek/video/69773][Giuseppe Longo: Alphabets, Axioms, DNA: On Human Knowledge and the Myth of Alphanumeric Coding]]



** Prior Art



*** [[https://en.wikipedia.org/wiki/Santiago_Ram%C3%B3n_y_Cajal][Ramón y Cajal]]

*** [[https://en.wikipedia.org/wiki/Camillo_Golgi][Camillo Golgi]]