Additional Resources

All password protected materials available on this website are intended for the
exclusive academic use of students enrolled in this offering (Winter 2022) of CS898.
Accordingly, these materials should not be distributed.

Supporting Files

Supplementary Materials for P Papers

Supplementary Materials for R Papers

Additional Course Related Materials

Examples of Paper Presentations

Examples of Reports

Supporting Files

• Technical Report Style Files (zip)
  

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Supplementary Materials for P Papers

• S. McCloskey, DNA Computing – Complexity & Computability
  Supplementary material for P1.

• R.P. Feynman, "There's plenty of room at the bottom"
  Supplementary material for P1.

• A. Junk and F. Riess, "From an idea to a vision: There's plenty of room at the bottom"
  Supplementary material for P1.

• P. Ball, "Feynman's fancy"
  Supplementary material for P1.

• A.M. Turing, "The chemical basis of morphogenesis"
  Supplementary material for P2, P11 and P20.

• Polymerase Chain Reaction (PCR)
  Supplementary material for P1 and P19.

• Chemistry World, Turing Patterns Show Their Hand in Finger Formation
  Supplementary material for P2, P7 and P11.

• E. Pennisi, "The Allure of Monkeyflowers"
  Supplementary material for P2 and P11.

• J. Raspopovic et al., "Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients"
  Supplementary material for P2, P7 and P11.

• Reaction and Diffusion
  Supplementary material for P2 and P11.

• Reaction and Difusion Simulations
  Supplementary material for P2 and P11.

• S. Atasoy et al., "Human brain networks function in connectome-specific harmonic waves"
  Supplementary material for P2 and P11.

• Schaffer’s F6
  Supplementary material for P3.

• Occam’s razor
  Supplementary material for P3.

• W.T. Reeves, "Particle systems - a technique for modeling a class of fuzzy objects"
  Supplementary material for P3.

• R. Poli, "Analysis of the publications on the applications of particle swarm optimization"
  Supplementary material for P3.

• E. Rashedi et al., "GSA: A gravitational search algorithm"
  Supplementary material for P3.

• A. Hatamlou, "Black hole: A new heuristic optimization approach for data clustering"
  Supplementary material for P3.

• M. Meisel et al., ``A taxonomy of biologically inspired research in computer networking''
  Supplementary material for P3, P4 and P7.

• Ant Colony Simulator
  Supplementary material for P4.

• A. Tero et al., ``Physarum solver: A biologically inspired method of road-network navigation''
  Supplementary material for P5.

• R. Boisseau et al., ``Habituation in non-neural organisms: evidence from slime moulds''
  Supplementary material for P5.

• Afek et al., Supplementary material for P6.

• CompuCell3D
  Supplementary material for P7.

• Cytoscape
  Supplementary material for P7.

• E-Cell System
  Supplementary material for P7.

• T.M. Cickovski et al., "A Framework for three-dimensional simulation of morphogenesis"
  Supplementary material for P7.

• Matlab Code
  Supplementary material for P8.

• K. Sorensen, "Metaheuristics - the metaphor exposed"
  Supplementary material for P8 and P10.

• D. Weyland, "A critical analysis of the harmony search algorithm - How to solve sudoku"
  Supplementary material for P8 and P10.

• P. Barthelemy et al., "A Levy flight for light"
  Supplementary material for P10.

• "FLAME – Flexible Large-Scale Agent Modeling Environment"
  Supplementary material for P9 and P25.

• "Virtual Physiological Human"
  Supplementary material for P9 and P25.

• D. Durstewitz et al. "Neurocomputational models of working memory"
  Supplementary material for P12.

• J.K. Seamans and C.R. Yang, "The principal features and mechanisms of dopamine modulation in the prefrontal cortex"
  Supplementary material for P12.

• Use case: bio-printing for visual designers
  Supplementary video for P13.

• S. Dasgupta et al., Supplementary materials for P14.

• R.F. Service, "Biology's dry future"
  Supplementary material for P15.

• K. Kupferschmidt, "Europe's 2 billion bet on the future"
  Supplementary material for P16.

• K. Kupferschimidt, "Graphene and brain projects win European jackpot"
  Supplementary material for P16.

• E. Underwood, "Brain project draws presidential interest, but mixed reactions"
  Supplementary material for P16.

• Nengo
  Supplementary videos for P16.

• "The Interactive Fly"
  Supplementary material for P20.

• E. Miller, "Fruit flies and moduli: interactions between biology and mathematics"
  Supplementary material for P20.

• "The seesaw magic book: the computational power of DNA molecules"
  Supplementary material for P22.

• S. Djemame et al., "A multi-agent system for image segmentation a bio-inspired approach"
  Supplementary material for P24.

• R.K.S. Kwan et al., "An extensible MRI simulator for post-processing evaluation"
  Supplementary material for P24.

• "BrainWeb:Simulated Brain Database"
  Supplementary material for P24.

• B. Grabowski ""P<0.05" Might not mean what you think: American Statistical Association clarifies P values"
  Supplementary material for P25 and P30.

• O. Milenkovic et al., "Exabytes in a test tube"
  Supplementary material for P28.

• E.H. Lee et al., "Discover through the computational microscope"
  Supplementary material for P29.

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Supplementary Materials for R Papers

• J. Tisseau, "In vivo, in vitro, in silico, in virtuo"
  Supplementary material for R2.

• M. Viceconti et al., "In silico clinical trials: How computer simulation will transform the biomedical industry"
  Supplementary material for R2.

• M. Klawe and B. Shneiderman, "Crisis and opportunity in computer science"
  Supplementary material for R3.

• M. Minsky, "Form and content in computer science"
  Supplementary material for R3.

• D.T. Gillespie, "A general method for numerically simulating the stochastic time evolution of coupled chemical reactions"
  Supplementary material for R3 and R4.

• D.T. Gillespie, "Exact stochastic simulation of coupled chemical reactions"
  Supplementary material for R3 and R4.

• N. Barnes, "Publish your computer code: it is good enough"
  Supplementary material for R5-R8.

• M. Hutson,"Artificial intelligence faces reproducibility crisis"
  Supplementary material for R5-R8.

• J.P. Mesirov, "Accessible reproducible research"
  Supplementary material for R7.

• R.F. Service, "Coming soon to a lab near you: drag-and-drop virtual worlds"
  Supplementary material for R7.

• Gym Open AI
  Supplementary material for R5-R8.

• OpenML
  Supplementary material for R5-R8.

• S.A. Korecki, "Inspired design: using interdisciplinarity and biomimicry for software innovation"
  Supplementary material for R9 and R10.

• R.J. Sension, "Quantum path to photosynthesis"
  Supplementary material for R11.

• L. Savage, "Artificial photosynthesis: saving solar energy for a rainy day"
  Supplementary material for R11.

• S. Steiner et al., " Organic synthesis in a modular robotic system driven by a chemical programming language"
  Supplementary material for R11.

• A. Zahrt et al., " Prediction of higher-selectivity catalysts by computer-driven workflow and machine learning"
  Supplementary material for R11.

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Additional Course Related Materials

• A.M. Turing, "Mind"

• J. You, "Beyond the Turing test"

• J. Klein, "How the father of computer science decoded nature's mysterious patterns"

• B. Misra and E.C.G. Sudarshan, "The Zeno’s paradox in quantum theory"

• A.R. Mackintosh, "Dr. Atansoff’s computer"

• E.J. Reed et al., "Color of shock waves in photonic crystals"
  

• J.C. Rautio, "The long road to Maxwell's equations"
  

• J. Clear, "First-principles: Ellon Musk on the power of thinking for yourself"
  

• Y. Bar-Cohen, "Biomimetics biologically inspired technologies"

• M. Wilson, "Half of Nobel Prize in Physics honors the inventors of chirped pulse amplification"

• D. Strickland and G. Mourou, "Compression of amplified chirped optical pulses"

• A. Gillis, "Academics beware"

• C. Wilcox, "Rude reviews are pervasive and sometimes harmful, study finds"

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Examples of Paper Presentations

• Example 1: Paper and Presentation (without transcripts).

• Example 2: Paper, Presentation a (without transcripts) and Presentation b (without transcripts).

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Examples of Reports

• Example 1: "Structural Colour of the Blue Morpho Butterfly''

• Example 2: "Cephalopod Inspired Dynamic Camouflage"

• Example 3: "Organizing and Deploying CLBlood", (post-course version)

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