Thursday, April 30, 2015


Slides for "The Adaptive Immune System and Artificial Immune Systems" lecture, April 29 2015 online

I485/H400 - Lecture 24 - The Adaptive Immune System and Artificial Immune Systems

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Wednesday, April 29, 2015


links for "Immune System" lecture

Immune System
Overview of the Immune System
Immunology movies at Cells Alive!
Immunobiology animations
An Interpretative Introduction to the Immune System. by S. A. Hofmeyr.
Immunology as information processing. by S. Forrest and S. A. Hofmeyr.
Immune System by Paul Bugl
Gary Carlson Biomedical images
T-Cell Selection Animation
Clonal Selection and Clonal Expansion, by Gary Kaiser

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Bio-inspired computing complete set of lecture notes

All lecture notes, updated for 2015, are now on the course site. All chapters are also available as a single file.

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New lecture notes: Modeling Evolution

7. Modeling Evolution: Evolutionary Computation

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Monday, April 27, 2015


Slides for "Turing’s Tape, Von Neumann and the design principle of open-ended, multi-level complexity", April 27, 2015 lecture online

I485/H400 - Lecture 23 - Turing’s Tape, Von Neumann and the design principle of open-ended, multi-level complexity

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Slides for EXTRA lecture "Swarms, Stigmergy and Collective Intelligence" online

I485/H400 - Lecture 22 - Swarms, Stigmergy, and Collective Intelligence

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Ants Swarm Like Brains Think

"The behavior of each individual in the group is set by the rate at which it meets other ants and a set of basic rules. Its behavior alters that of its neighbors, which in turn affects the original ant, in a classic example of feedback. The result is astonishing, complex behavior." Full article @ Nautilus

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Links for "Self-Reproduction" Lecture

Robot Self-replication
Cornell Creative Machines Lab: Self replication
Stochastic Modular Assembly (Programmable Matter)

An implementation of Von Neumann's Self_reproducing Automata. See Modifications by Tim Hutton.

Self-Reproducing Loops: from Langton's to Evoloop. Hiroki Sayama's Website.

Self-reproducing loops

Langton's Loop Applet .

Bibliography on Self-replicating automata

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Links for "Swarms, Stigmergy and Collective Intelligence" lecture

Ant Colony Optimization Resources
Dynamic Concepts Stigmergy Robots. Report with rules used.

Collective Robotic Intelligence Project (CRIP)
Braitenberg (reactive) Vehicles. A simulation of Braitenberg Vehicles from Rolf Pfeifer's group.

Swarm Paintings and a conceptual update (using pheromone fields by Vitorino Ramos).

IdMind. Leonel Moura's robot art including RAP (Robot Action Painter).

Collective Dynamics
Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks
Mexican Wave
Simulate Escape Panic
Lane Formation in a Street

Collective Dynamics

Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks and Simulation of Multi-lane traffic. A video with stop-and.go dynamics
Mexican Wave
Simulate Escape Panic. Crowd Turbulence
Lane Formation in a Street

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Sunday, April 26, 2015


New Lecture Notes: Von Neumann and Natural Selection

6. Von Neumann and Natural Selection (pdf)

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Slides for "Ant Clustering Algorithm" April 22, 2015 lecture online

H400/I485 - Lecture 21 - Ant Clustering Algorithm

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Tuesday, April 21, 2015


Swarming drones that can float on water

Full news piece @ BBC News

Monday, April 20, 2015


Bacterial Stigmergy: An Organising Principle of Multicellular Collective Behaviours of Bacteria

"The self-organisation of collective behaviours often manifests as dramatic patterns of emergent large-scale order. This is true for relatively “simple” entities such as microbial communities and robot “swarms,” through to more complex self-organised systems such as those displayed by social insects, migrating herds, and many human activities. The principle of stigmergy describes those self-organised phenomena that emerge as a consequence of indirect communication between individuals of the group through the generation of persistent cues in the environment. Interestingly, despite numerous examples of multicellular behaviours of bacteria, the principle of stigmergy has yet to become an accepted theoretical framework that describes how bacterial collectives self-organise. Here we review some examples of multicellular bacterial behaviours in the context of stigmergy with the aim of bringing this powerful and elegant self-organisation principle to the attention of the microbial research community." Full article @ Scientifica

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Slides for "Collective Behavior" April 20, 2015 lecture Online

I485/H400 - Lecture 20 - Collective Behavior

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links for "Collective Behavior" lecture

Artificial Ecosystems
Special Issue on Michael Conrad's Work
Sim Life and Spore (More on Spore).

Collective Behavior
Boids Applet
EPFL Laboratory for Intelligent Systems

Particle Swarm Optimization
Particle Swarm Optimization Paper by Kennedy and Eberhart..
Particle Swarm Optimization Applets.
Particle Swarm Optimization Visualization Applet.
Software Resources for PSO
PSO for prediction of protein-ligand interaction

Termites and Ant Colony Clustering and Sorting
Artificial Termites. Another artificial termine applet.
Mitchel Resnick
termites @ Flake's site
Ant-like task allocation and recruitment in cooperative robots
Bristol Robotics Laboratory.
Swarm Simulation Environment

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Wednesday, April 15, 2015


slides for "Multi-level Selection and Evolutionary Dynamics" April 15, 2015 lecture online

Lecture 19 - Multi-level selection and Evolutionary dynamics

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Tuesday, April 14, 2015


How animals, insects and plants inspire scientists to solve everyday human problems

Biomimicry is the science of using nature to answer problems of modern life - and it is more commonplace than you might suspect. News article @ Mirror Online

Monday, April 13, 2015


slides for "Genetic Encodings" April 13, 2015 lecture online

I485/H400 - Lecture 18 - Genetic Encodings

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Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection

"Ever since Cicero's De Natura Deorum ii.34., humans have been intrigued by the origin and mechanisms underlying complexity in nature. Darwin suggested that adaptation and complexity could evolve by natural selection acting successively on numerous small, heritable modifications. But is this enough? Here, we describe selected studies of experimental evolution with robots to illustrate how the process of natural selection can lead to the evolution of complex traits such as adaptive behaviours." Full paper @ PLOS Biology

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Links for "Genetic Encodings" Lecture

Modeling Evolution

Biomorph Viewer
Genetic Algorithm Viewer
Biomorph game
Biomorphs with Crossover
Icosystem - The Hunch Engine™

Karl Sims Evolving Virtual Creatures:

The Golem Project
Illustrating Evolutionary Computation with Mathematica
LifeSpacies. More. Christa Sommerer

Simple Symbolic Regression Using Genetic Programming à la John Koza
Truck Demo
Genetic Programming Resources
36 Human-Competitive Results Produced by Genetic Programming
Distilling Free-Form Natural Laws from Experimental Data
Eureqa: a software tool for detecting equations and hidden mathematical relationships in data. Older version.

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Lecture Notes Chapter 5: Life is Stranger than Fiction

Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology? (pdf document)

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slides for "Genetic Programming" April 8, 2015 lab and lecture online

I485/H400 - Lecture 19 - Genetic Programming

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Monday, April 06, 2015


Slides for "Genetic algorithms", April 6, 2015 lecture online

I485/H400 - Lecture 16 - Genetic Algorithms

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Links for "Genetic Algorithms" Lecture

Modeling Evolution

From Artificial Evolution to Artificial Life (1999), Tim Taylor's PhD Dissertation. Check his overview of open-ended evolution.
Introduction to Genetic Algorithms
Illustrating Evolutionary Computation with Mathematica

BEACON: Center for the Study of Evolution in Action. biologists, computer scientists, and engineers study evolution as it happens and apply this knowledge to solve real-world problems.

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Wednesday, April 01, 2015


Slides for "Information transmission in Biology: the gene" April 1st, 2015 lecture online

I484/H400 Lecture 15 - Information transmission in Biology: the gene

See also the Scientific American special issue on Darwin and Natural Selection.

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Links for "Information and DNA" Lecture

The virtual Cell
A Tour of the Cell
Inside the Cell
Cell Structure animation
Cell Biology at the Biology Project
More on Cells from Wikipedia
The Cell Image Library and highMag
Colonial Algae

Genetics and Genomics

Watson and Crick's Molecular structure of Nucleic Acids 1953 article
Journey into DNA
Cracking the Code of Life (PBS Show)
Explore a stretch of code
DNA Anatomy
DNA Replication
Transcription and Translation
Mitosis and Meiosis, and a comparison.

"To understand the human genome, researchers must spread their wings to all branches of life". Full editorial @ Nature

A paper about ultraconserved DNA which does not seem to be functional...
Frequent lateral gene transfer

Review of The Music of Life: Biology Beyond the Genome by Denis Noble @ Science

How Evolution Works - Minimalist Videos

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