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(2000)]] 7 | ** [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.163.9160&rep=rep1&type=pdf][Information in Biology – Peter Godfrey-Smith (2017)]] 8 | ** [[http://www.irisa.fr/dyliss/public/asiegel/Articles/SchaubSiegelVidela.pdf][Logical Modeling of Biological Systems – Katsumi Inoue, Louis Fariñas]] 9 | -------------------------------------------------------------------------------- /readme.org: -------------------------------------------------------------------------------- 1 | * Formal Systems in Biology 2 | 3 | A collection of resources that apply formal systems to model biological processes. 4 | Some easily accessible books to understand the general approaches in this field are also included. 5 | 6 | ** McCulloch-Pitts Work 7 | 8 | *** [[https://www.cs.cmu.edu/~./epxing/Class/10715/reading/McCulloch.and.Pitts.pdf][A Logical Calculus of the Ideas Immanent in Nervous Activity (1943)]] 9 | [[./img/mccullough-pitts.png]] 10 | 11 | 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. 12 | 13 | An interactive demo of their model is available here: https://justinmeiners.github.io/neural-nets-sim/ 14 | 15 | ** Arthur Iberall / Warren McCulloch 16 | 17 | *** [[https://core.ac.uk/download/pdf/85247309.pdf][Behavioural Model of Man - His Chains Revealed]] 18 | 19 | ** Stanisław Ulam and Jon Von Neumann 20 | 21 | *** [[https://dl.acm.org/doi/book/10.5555/1102024][Theory of Self Reproducing Automata]] 22 | [[./img/neumann.png]] 23 | 24 | *** [[http://web.mit.edu/6.454/www/papers/pierce_1952.pdf][Probabilistic Logics and the Synthesis of reliable organisms from unreliable components (1952)]] 25 | [[./img/neumann-pierce-drawings.png]] 26 | 27 | ** L Systems 28 | 29 | *** [[https://www.sciencedirect.com/science/article/abs/pii/0022519368900799][Mathematical models for cellular interactions in development I (1968)]] 30 | [[./img/lsystem-1.png]] 31 | 32 | *** [[https://www.sciencedirect.com/science/article/abs/pii/0022519368900805][Mathematical models for cellular interactions in development II (1968)]] 33 | [[./img/lsystem-2.png]] 34 | 35 | ** Karl Sims 36 | [[./img/karl-sims.jpg]] 37 | *** [[https://www.karlsims.com/evolved-virtual-creatures.html][Evolved Virtual Creatures (1994)]] 38 | 39 | ** Walter Fontana and Leo Buss (1996) 40 | 41 | *** [[https://scholar.harvard.edu/files/walterfontana/files/objects.pdf][The Barrier of Objects From Dynamical Systems to Bounded Organizations]] 42 | [[./img/fontana-buss.png]] 43 | 44 | ** Regev, Silvermann, Shapiro 45 | 46 | *** [[https://psb.stanford.edu/psb-online/proceedings/psb01/regev.pdf][Representation and Simulation of Biochemical Process Using the Pi Calculus Process Algebra (2001)]] 47 | [[./img/regev-shapiro.png]] 48 | 49 | *** [[https://www.nature.com/articles/419343a.pdf][Cell as Computation (2002)]] 50 | [[./img/regev-shapiro-2.png]] 51 | 52 | *** [[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)]] 53 | 54 | ** Ehud Lamm and Ron Unger 55 | 56 | *** [[http://www.ehudlamm.com/biocomputing.html][Biological Computation]] 57 | [[./img/ehud-lamm.jpg]] 58 | 59 | ** P System 60 | [[./img/p-system.png]] 61 | 62 | ** Alan Turing 63 | 64 | *** [[https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.1952.0012][The Chemical Basis of Morphogenesis (1952)]] 65 | [[./img/reaction-diffusion.png]] 66 | Reaction-Diffusion Systems 67 | 68 | ** Joseph Henry Woodgers 69 | 70 | *** [[https://www.amazon.com/axiomatic-method-biology-Joseph-Woodger/dp/B00085P2C8][The Axiomatic Method in Biology (1937)]] 71 | 72 | ** Louis Kauffman 73 | 74 | [[./img/kauffman-magarshak.png]] 75 | *** [[http://homepages.math.uic.edu/~kauffman/KauffProteins.pdf][Vassiliev Knot Invariants and the Structure of RNA folding]] 76 | 77 | ** Marius Buliga 78 | 79 | *** [[https://chemlambda.github.io/index.html][Chemlambda]] 80 | [[./img/chemlambda.gif]] 81 | 82 | For animations, checkout: https://chemlambda.github.io/collection.html 83 | 84 | [[https://mbuliga.github.io/quinegraphs/history-of-chemlambda.html][History of the project]] 85 | 86 | ** Stefano Maestri and Emaneula Merelli 87 | *** [[https://www.nature.com/articles/s41598-018-36965-1][Process calculi may reveal the equivalence lying at the heart of RNA and proteins]] 88 | **** Correction to the article: https://www.nature.com/articles/s41598-019-51082-3 89 | 90 | ** Artem Kaznatcheev 91 | *** [[https://www.genetics.org/content/genetics/212/1/245.full.pdf][Computational Complexity as an Ultimate Constraint on Evolution]] 92 | **** Tweet thread on it here: https://twitter.com/kaznatcheev/status/1102973539634892800 93 | 94 | ** Jeffrey Ventrella 95 | 96 | *** [[http://ventrella.com/Clusters/][Clusters]] 97 | [[./img/clusters.png]] 98 | 99 | *** [[http://www.swimbots.com/genepool/][Genepool]] 100 | [[./img/genepool.png]] 101 | 102 | ** Programming Languages 103 | 104 | *** [[https://kappalanguage.org/][https://kappalanguage.org/]] 105 | 106 | [[./img/kappa.png]] 107 | 108 | *** [[http://sbml.org/Main_Page][The Systems Biology Markup Language]] 109 | 110 | ** Computation with Crabs 111 | 112 | [[https://arxiv.org/pdf/1204.1749.pdf][Paper]] 113 | 114 | [[./img/crab-or-gate.png]] 115 | 116 | [[./img/crab-and-gate.png]] 117 | 118 | * Resources to understand the field 119 | 120 | ** [[https://amzn.to/2UrKeRv][Neurocomics]] (Beginner) 121 | [[./img/neurocomics.jpg]] 122 | 123 | ** [[https://amzn.to/37ft4vD][Introducing Evolution]] (Beginner) 124 | [[./img/evolution-graphic-guide.jpg]] 125 | 126 | ** [[https://amzn.to/2A7pWpH][Introducing Genetics]] (Beginner) 127 | [[./img/genetics-graphic-guide.jpg]] 128 | 129 | ** [[https://amzn.to/2BQ1JEL][Introducing Epigenetics]] (Beginner) 130 | [[./img/epigenetics-graphic-guide.jpg]] 131 | 132 | ** [[https://amzn.to/2XQ39rz][Complexity: A Very Short Introduction]] (Intermediate) 133 | [[./img/complexity-a-very-short-introduction.jpg]] 134 | 135 | ** [[https://amzn.to/3dYA0ja][Games of Life]] (Intermediate) 136 | [[./img/games-of-life.jpg]] 137 | 138 | * Books 139 | 140 | ** [[https://link.springer.com/book/10.1007/11885191][Computational Methods in Systems Biology (2006)]] 141 | 142 | ** [[https://arxiv.org/abs/1112.1440][Complex Systems: A Survey]] 143 | A really good survey of books in complexity science here. 144 | 145 | * Further Research 146 | 147 | - Rashevsky and Rosen 148 | 149 | [[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. 150 | 151 | There could also be more possible works from the conference where McCullough presented his work and met Pitts. 152 | 153 | ** Sampling of Rashevsky’s work 154 | 155 | *** [[https://link.springer.com/article/10.1007%2FBF02484495][Topology and life: In search of general mathematical principles in biology and sociology]] 156 | *** [[https://link.springer.com/article/10.1007%2FBF02476737][On relation between sets — 1961]] 157 | *** [[https://link.springer.com/article/10.1007%2FBF02476851][The representation of organisms in terms of predicates — 1965]] 158 | *** [[https://link.springer.com/article/10.1007%2FBF02476395][On relations between sets: II - 1966]] 159 | *** [[https://link.springer.com/article/10.1007%2FBF02477001][A note on relations between sets – 1966]] 160 | *** [[https://link.springer.com/article/10.1007%2FBF02476967][Organismic sets: Outline of a general theory of biological and social organisms - 1967]] 161 | *** [[https://link.springer.com/article/10.1007%2FBF02476947][Organismic sets: II. Some general considerations - 1968]] 162 | *** [[https://link.springer.com/article/10.1007/BF02477842][The Geometrization of Biology]] 163 | *** [[https://link.springer.com/article/10.1007%2FBF02478215][Outline of a unified approach to physics, biology and sociology]] 164 | 165 | ** Sampling of Rosen’s work: 166 | 167 | *** [[https://link.springer.com/chapter/10.1007/978-94-009-2975-3_35][Pattern Generation in Cellular Spaces]] 168 | *** [[https://link.springer.com/chapter/10.1007/978-1-4684-4640-1_31][Relational Biology and the Origin of Life]] 169 | *** [[https://link.springer.com/article/10.1007/BF02459437][On a unified approach to pattern generation]] 170 | *** [[https://link.springer.com/chapter/10.1007/978-94-010-1239-3_9][Complexity and System Description]] 171 | *** [[https://link.springer.com/article/10.1007/BF02459555][The Chief Abstractions of Biology]] 172 | *** [[https://link.springer.com/chapter/10.1007/978-1-4899-6419-9_8][Input-Output Systems]] 173 | *** [[https://link.springer.com/article/10.1007/BF02477959][The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design]] 174 | *** [[https://link.springer.com/article/10.1007/BF02477897][A logical paradox implicit in the notion of a self-reproducing automaton]] 175 | *** [[https://link.springer.com/article/10.1007/BF02478302][A relational theory of biology]] 176 | *** [[https://link.springer.com/article/10.1007/BF02477890][The representation of biological systems from the standpoint of the theory of categories]] 177 | 178 | - Ilya Pregorine’s Work 179 | 180 | - Gregory Chaitin’s work 181 | 182 | - Stochastic CFG for RNA 183 | 184 | - Zuse-Fredkin thesis / [[https://en.wikipedia.org/wiki/Digital_philosophy][Digital Philosophy]] 185 | Think I need to mention the work of Zuse-Fredkin thesis along with Ulam-Neumann model. 186 | 187 | - Knot Theory for Protein Molecules 188 | 189 | - Wang Tiles and DNA 190 | 191 | - [[https://www.sciencedirect.com/science/article/pii/B9780128140666000064][Molecular Networks and Monomial Ideals]] 192 | 193 | - [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004591][Computational Modeling, Formal Analysis, and Tools for Systems Biology: Survey]] 194 | 195 | - Luca Cardelli 196 | - [[https://dx.doi.org/10.1186/1752-0509-8-84][Morphism of reaction networks that couple structure to function]] 197 | 198 | 199 | ** Tools 200 | 201 | *** [[https://github.com/GollyGang/ready][Ready]] 202 | Ready is a program for exploring continuous and discrete cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes. 203 | 204 | ** Blogs 205 | 206 | *** [[https://jsomers.net/i-should-have-loved-biology/][I should have loved biology]] 207 | 208 | 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. 209 | 210 | *** [[http://jackterwilliger.com/biological-neural-networks-part-i-spiking-neurons/][(A Bit of) Biological Neural Networks (2018)]] 211 | A really nice series of articles on the biological aspects of neural networks by Jack Terwilliger 212 | 213 | ** Talks 214 | 215 | *** [[https://www.hkw.de/en/app/mediathek/video/69773][Giuseppe Longo: Alphabets, Axioms, DNA: On Human Knowledge and the Myth of Alphanumeric Coding]] 216 | 217 | ** Prior Art 218 | 219 | *** [[https://en.wikipedia.org/wiki/Santiago_Ram%C3%B3n_y_Cajal][Ramón y Cajal]] 220 | *** [[https://en.wikipedia.org/wiki/Camillo_Golgi][Camillo Golgi]] 221 | --------------------------------------------------------------------------------