Instructor: Luis M. Rocha and Johan Bollen, Center for Complex Networks and Systems, School of Informatics and Computing and Cognitive Science Program, Indiana University

Associate Instructor: Ian Wood

Class Location and Time:Tuesdays and Thursdays, 4:00PM - 5:15PM, Room: Informatics East, 901 E. 10th St., Room 122

Course Description

Description:The course deals with the foundations of Informatics as an interdisciplinary field. We will study concepts such as Information, Technology, Knowledge, Modeling, as well as their impact on science and society. The course will also attempt to define and understand what computational thinking can bring to science and society.

Aims: The course is designed to present and discuss the history, methodology and impact of informatics; students are introduced to various approaches to informatics via the appropriate literature. Finally, students are expected to develop a understanding of what constitutes research in the field, via a familiarization with relevant funding opportunities.


Lecture Outline

Course Evaluation

Assignments and Proposal

Office Hours

Luis Rocha: Wednesdays 2-3:30Pm, 919 E. 10th St, Room #301

Course Materials and Readings

Readings available in the OnCourse Class Folder)

Mandatory articles

week papers
week 1

Heims, S.G. [1991]. The Cybernetics Group. MIT Press. Chapters: 1,2

Gleick, J. [2011]. The Information: A History, a Theory, a Flood. Random House. Chapter 8.

week 2

Weaver, W. [1948]. "Science and Complexity". American Scientist, 36(4): 536-44.

Simon, H.A. [1962]. "The Architecture of Complexity". Proceedings of the American Philosophical Society, 106: pp. 467-482.

Lazebnik, Y [2002]. "Can a biologist fix a radio?--Or, what I learned while studying apoptosis". Cancer Cell, 2(3):179-182.

week 4

Prokopenko, Mikhail, Fabio Boschetti, and Alex J. Ryan. [2009]. "An information-theoretic primer on complexity, self-organization, and emergence. ". Complexity 15(1): 11-28

week 6 & 7

Klir, G.J. [2001]. Facets of systems Science. Springer. Chapters: 1,2,3

Klir, G.J. and D. Elias [2003]. Architecture of Systems Problem Solving. Springer. Chapters: 1,2, 3.1, 3.2, 3.10, 4.1, 4.2

week 10

Coutinho, A. [2003]. "On doing science: a speech by Professor Antonio Coutinho". Economia, 4(1): 7-18, jan./jun. 2003.

Schwartz, M.A. [2008]. "The importance of stupidity in scientific research". Journal of Cell Science, 121: 1771.

week 12 & 13

Sandve, Geir Kjetil, Anton Nekrutenko, James Taylor, and Eivind Hovig. [2013]. "Ten Simple Rules for Reproducible Computational Research." PLoS Computational Biology 9 (10): 4.

Zhang, W. [2014]. "Ten Simple Rules for Writing Research Papers." PLoS Computational Biology 10 (1): e1003453.

Weinberger CJ, Evans JA, Allesina S (2015) Ten Simple (Empirical) Rules for Writing Science. PLoS Comput Biol 11(4): e1004205. doi: 10.1371/journal.pcbi.1004205

Knapp B, Bardenet R, Bernabeu MO, Bordas R, Bruna M, et al. (2015) Ten Simple Rules for a Successful Cross-Disciplinary Collaboration. PLoS Comput Biol11(4): e1004214. doi: 10.1371/journal.pcbi.1004214


Heims, S.G. [1991]. The Cybernetics Group. MIT Press. Chapters: 11, and 12.
McCulloch, W. and W. Pitts [1943], "A Logical Calculus of Ideas Immanent in Nervous Activity". Bulletin of Mathematical Biophysics 5:115-133.
Klir, G.J. [2001]. Facets of systems Science. Springer. Chapters: 8 and 11
Klir, G.J. and D. Elias [2003]. Architecture of Systems Problem Solving. Springer. Chapters: 3 and 4
Aleksander, I. [2002]. Understanding Information Bit by Bitî. In: It must be beautiful : great equations of modern science. G. Farmelo (Ed.), Granta, London.

For Presentations (Choose One)

  • Adamic, Lada A., Thomas M. Lento, Eytan Adar, and Pauline C. Ng. [2014]. "Information Evolution in Social Networks”. arXiv:1402.6792
  • Barabasi and Albert (1999) Emergence of Scaling in Random Networks, Science 296 (5439)
  • Eytan Bakshy, Solomon Messing, and Lada A. Adamic [2015] "Exposure to ideologically diverse news and opinion on Facebook." Science 5 June 2015: 348 (6239), 1130-1132.
  • Luís M. A. Bettencourt at al (2007) - Growth, innovation, scaling, and the pace of life in cities, PNAS, vol. 104 no. 17 7301-7306 + Shalizi, C.R. [2011]. "Scaling and Hierarchy in Urban Economies.",
  • Bollen J, Crandall D, Junk D, Ding Y, Borner K. [2014] “From funding agencies to scientific agency: Collective allocation of science funding as an alternative to peer review”. EMBO Rep. DOI: 10.1002/embr.201338068 and
  • Bollen, J., Huina Mao, Xiao-Jun Zeng (2011). Twitter mood predicts the stock market, JCS
  • C. Cattuto, V. Loreto, L. Pietronero [2007] "Semiotic dynamics and collaborative tagging", PNAS 104(17), 1461
  • G.L. Ciampaglia, P. Shiralkar, L.M. Rocha, J. Bollen, F. Menczer, A. Flammini [2015]. “Computational fact checking from knowledge networks.” PLoS One. 10(6): e0128193. doi:10.1371/journal.pone.0128193.
  • Clark, A. [2003]. Natural-Born Cyborgs: Minds, technologies and the Future of Human Intelligence. Oxford University Press. Chapters 2 and 6
  • Eiben. A. and Jim Smith [2015]. "From evolutionary computation to the evolution of things." Nature 521, 476–482. doi:10.1038/nature14544
  • Freeth, Tony. 2014. “Eclipse Prediction on the Ancient Greek Astronomical Calculating Machine Known as the Antikythera Mechanism.” PloS One 9 (7) (January): e103275. doi:10.1371/journal.pone.0103275.
  • Jeremy A. Frimer, Karl Aquino, Jochen E. Gebauer, Luke (Lei) Zhu, and Harrison Oakes [2015] "A decline in prosocial language helps explain public disapproval of the US Congress" PNAS 2015 112 (21) 6591-6594; doi:10.1073/pnas.1500355112
  • Helbing, Dirk, Dirk Brockmann, Thomas Chadefaux, Karsten Donnay, Ulf Blanke, Olivia Woolley-Meza, Mehdi Moussaid, et al. [2015]. "How to Save Human Lives with Complexity Science". Journal of Statistical Physics. 158 (3): 735-781.
  • Heylighen, Francis. 2015. “Stigmergy as a Universal Coordination Mechanism: Components, Varieties and Applications.” In Human Stigmergy: Theoretical Developments and New Applications (Studies in Applied Philosophy, Epistemology and Rational Ethics), edited by Ted; Lewis and Leslie Marsh, In Press.
  • Hughes (2009) Quantification of artistic style through sparse coding analysis in the drawings of Pieter Bruegel the Elder. PNAS 107(4):1279–1283
  • Kolchinsky, A., M. P. Van Den Heuvel, A. Griffa, P. Hagmann, L.M. Rocha, O. Sporns, J. Goni [2014]."Multi-scale Integration and Predictability in Resting State Brain Activity". Frontiers in Neuroinformatics, 8:66.
  • Thomas S. Kuhn (1970). Logic of discovery or Psychology of Research.
  • Kull, Deacon, Pattee, Kauffman[2012] . Approaches to biosemiotics. In Gatherings in Biosemiotics. Eds. S Rattasepp and T. Bennett. University of Tartu Press.
  • Yann LeCun, Yoshua Bengio and Geoffrey Hinton [2015]. "Deep learning" Nature 521, 436–444 (28 May 2015) doi:10.1038/nature14539
  • Danielle Li and Leila Agha [20150. "Big names or big ideas: Do peer-review panels select the best science proposals?" Science 24 April 2015: 348 (6233), 434-438.
  • Markov, Igor L. 2014. “Limits on Fundamental Limits to Computation.” Nature 512 (7513) (August 13): 147–154. doi:10.1038/nature13570.
  • Marques-Pita, M. and L.M. Rocha [2013]. "Canalization and control in automata networks: body segmentation in Drosophila Melanogaster". PLoS ONE, 8(3): e55946.
  • Piantadosi, S. T.,et al (2011). Word lengths are optimized for efficient communication. PNAS, 108(9), 3526–3529.
  • Karl Popper (1963). Science: Conjecture and refutations.
  • Radicchi, F. (2008) Universality of citation distributions: Toward an objective measure of scientific impact. PNAS 105(45): 17268–17272.
  • Rubenstein, M., A. Cornejo, and R. Nagpal. 2014. “Programmable Self-Assembly in a Thousand-Robot Swarm.” Science 345 (6198) (August 14): 795–799.
  • Suzuki, R. et al (2006) Information entropy of humpback whale songs, J. Acoust. Soc. Am, 199(3), March
  • Scheffer (2009) Early-warning signals for critical transitions. Nature 461, 53-59 - doi:10.1038/nature08227
  • Wasserman, M., X.H.T. Zeng, and L.A.N. Amaral [2015]. “Cross-evaluation of metrics to estimate the significance of creative works”. PNAS 112 (5) 1281-1286, doi:10.1073/pnas.1412198112

Last Modified: August 23, 2016