Complex Systems Summer School 2015-Tutorials

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Complex Systems Summer School 2015

CSSS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.

You can schedule your own tutorial here, they will be held in the ESL study hall. Please do not schedule during other CSSS Lectures.

try to use this template:

Global Complexity Research/Educational Patterns & Career Pathways

Speaker: Sander Bais, et al.
Date & Time: June 29th, 5:30-7:00 Dinner Take-Out to meet at Main Lecture Hall
Motivation and content: Consider the following excerpts from the founding essay (The Concept of the Institute-1987) by Murray Gell-Mann regarding SFI:

  1. We have an imposing apparatus of professional societies, professional journals, university departments for research and teaching, government funding agencies and peer review committees or sections, all directed toward quality control in the traditional disciplines. In the past ..( this was enough ) to accommodate..the appearance of cross-disciplinary subjects like biochemistry or nuclear engineering. I believe, however, that the current developments in science and scholarship represent a much more rapid and more widespread rearrangement of subjects than we have experienced before..The apparatus we have described needs to change more rapidly and more radically than it is accustomed to doing, and we must understand what would be useful and appropriate changes and how they might be carried out.
  2. The whole pattern of grants and peer review must evolve in ways that are hard to prescribe and even harder to carry out. The journals and professional societies will have to evolve so that the establishment of standards and the conduct of refereeing can be carried out for the new transcendent subjects. All of that will be painful and difficult but exciting.
  3. The fact that natural and social science are redefining themselves seems to create the opportunity for a new kind of institution that would combine the advantages of the open teaching and research environment of the university with the flexibility of interdisciplinary patterns in national laboratories and other dedicated research institutions. What we propose in the creation here in Santa Fe of such an institute...Interdisciplinary appointments, which are often so difficult to make at universities with a traditional structure, would be encouraged..
  4. ( This difficulty... ) has its foundation in a real concern that lies behind the skepticism about academics seeking interdisciplinary appointments. Faculty members are familiar with a certain kind of person who looks to the mathematicians like a good physicist and looks to the physicists like a good mathematician. Very properly, they do not want that kind of person around. In fact, our organization into professions, with professional societies, journals, traditions, and standards of criticism , has much to be said in its favor, because it helps safeguard excellence.
  5. There are some psychologists and pop psychologists who like to place people on a scale running from Apollonian to Dionysian, where, roughly speaking, Apollonians tend to favor logic, rationality and analysis, while Dionysians go in more for intuition, feeling, and synthesis. In the middle are those tortured souls, the Odysseans, who strive for the uniion of both styles. The new institute would have to recruit a number of Odysseans to be successful!
  6. What would be the relation of the network activity of the Institute to the existing academic and industrial organizations to which we all belong? ...if we consider the two operations, building the networks and establishing the permanent Institute, we see that each is very valuable in itself and also that they are mutually beneficial. As the permanent Institute gradually comes into being, there is no reason to believe that the networks will cease to operate. Assuming they are successful, they should presumably continue indefinitely and constitute one of the principal modes of operation of the Institute, adding strength to it, and also to many of the leading academic organizations in this country and to some abroad.
  7. One of the most important questions that we have to address is this: Why not try to accomplish some of our objectives by adding to the activities of an existing university and saving the cost of creating a new institution? Well, I think that the national response to the challenge of the emerging synthesis will consist in great part of steps taken by the universities...But the form of the response, as I indicated before, is not likely to be adequate for a long time.
  8. The typical response of a university to the emergence of a new interdisciplinary subject is to set up a Center in an old Victorian house or a little shed left over from the First or Second World War, funded with soft money and treated to some extent like a stepchild. Wonderful results often emerge from these dilapidated structures, but some of the most talented researchers are not in permanent positions, have little influence on teaching policy, and are far removed from the centers of influence in the institution. Of course, a senior faculty member who has distinguished himself in a particular profession and made a great reputation can afford to shift to a new, interdisciplinary subject. He can sometimes get funding, although that is not very easy. However, the younger people who want to work on the new subject may have great difficulty furthering their careers, unless they wish to spend years becoming famous in some old fashioned field.
  9. It will be a slow and difficult process for each university to change from its old message, "Learn a traditional subject and stick to it," to the new message, "It is all right to learn how to make connections among different subjects." We would like to create here in Santa Fe at least one institution that is free from the drag exerted by past specialization and the tyranny of the department, an institution that would encourage faculty, students and young researchers to make connections.

Interdisciplinary problems have proliferated and multiplied over the last 30 years since Murray Gell-Mann wrote the founding essay. But as predicted, the traditional institutions have remained siloed within the "tyranny of the department". This 1-1/2 jam-session is to provoke a discussion of where we are, the career-track problems we face, and how best to navigate the rapids ahead. Here are a few ice-breakers to get things started (please edit and add to the list):

  1. Global Similarities & Differences in Educational Cultures, Traditions & Architectures in Science & Tech: Murray Gell-Mann focused primarily on the US institutions. In the interim, the world got flattened. So are the patterns described in the essay above similar or different across the globe. Sander Bais to lead.
  2. Patterns of Complexity Related Strategic Initiatives between Industry & Academia. As Prof. Gell-Mann recognized, while the academia may be one-step removed, the industry doesn't have the luxury of considering the problems it faces in a piece-meal fashion, nicely packable and mappable into the respective departments. But at the same time, the scale at which industry ought to be participating seems to be missing. Why is that?
  3. The task of mapping where all across the globe Complexity Research is being conducted--their strengths & weaknesses & areas of focus. Prof. Gell-Mann architected SFI to be the hub in a hub-and-spoke network. But that network seems to be more or less an invisible college, alive and kicking in small clusters, spread across the globe. What would it take to map this network and make it visible and available?
  4. Patterns of PhD/Post-Doc/Industry Challenges & Pathways: As hinted by Prof. Gell-Mann, the challenges faced by a young PhD in the inter-disciplinary mold are daunting. Specifically, what are these in the current situation. And rather than whining about it, given the tools we have, what creative ways can we come up with to overcome these obstacles


  1. Sander Bais
  2. Song Binyang
  3. Anna Zaytseva
  4. Haitao Shang
  5. Daniel Friedman
  6. Masahiko Haraguchi
  7. Glenn Magerman
  8. Chao Fan
  9. Jarrod J Scott
  10. Tirtha Bandy
  11. John Thomas
  12. Marie-Pierre Hasne

Qualitative Complexity

Speaker: Anna
Date & Time: June 30, 20:00
Location: a room near the Hubler's lab in the lab building
Motivation and content: Hi! I would like to give a talk on qualitative complexity, Tuesday 30: its understanding, implications, data, research, methodology. I will present my own work, where I have two very different cases on e-health technologies and their design in the legal environment of Norway. The research is bottom-up raising information from empirics. The research is qualitative, and it has a set of generated analytic rules, visualizations of complex networks in memories of the cases, non-linearity and attractors. Social elements (humans) generate information in the legal environment and in own past, what constraints what they are doing and ought to do with necessity due to information they generate in the legal environment and in the own past. A dynamic space at the edge in between legal regulation and combination of technological elements I conceptualize as a CAS, and in particular I use “memory” from the formal framework by John Holland. Then, in certain places of my methodology I apply the narrative approach – it is even used to confirm my hypothesis and universality of the methodology, what we can hardly expect for the narrative, but this is true. Come and see what other things are possible except what you already know and bring your questions with you.

Tutorial: Skilled action, complex systems science and the Free Energy Principle

Speaker: Jelle Bruineberg
Date & Time: June 11th, 20:00
Motivation and content: Quite some people seemed to be interested in the "Variational Approaches to Mind and Life" project that we are trying to get of the ground. Apart from this, some people were curious how philosophy relates to complex systems science. I would like to present my own work on skilled action and relate it to complex systems science. After this, I will sketch how the Free Energy Principle (the principle to be studied in the Variational Approaches to Mind and Life group) relates to this work. This is the point, where, I hope, the presentation part will stop and the brainstorm/discussion session will take over.
Prerequisite: Being open to a bit of philosophy :)
Slides: will follow
Paper: [1]

Speaker: Christine Harvey (
Date & Time: June 16th 7pm in Tutorial Room
Motivation and content: Basic introduction to NetLogo for new users/programmers. Quick overview of the screens, language and possibilities. And standard documentation practices for the model. Walkthrough editing a model.
Prerequisite: Download and install NetLogo (
Interested people:

Tutorial: R, EDA, a bit of geo-mapping

Speaker: Brent Schneeman
Date & Time: Monday June 29, 7pm (1900)
Motivation and content: The "Great Circles" t-shirt design generated some interest in how it was done. I'll walk through the code showing how R can access the Google Maps API and generate great circle arcs. Along the way, we'll look at generating simple descriptive plots of a dataset that will likely resonate with you (because you heard Shalizi talk about kernel density estimates). If we're lucky, we'll be able to translate the arcs and the world map longitudinally. A teensy bit of github will also be shown. I do not claim to be any sort of expert in anything demo'ed, but bring your questions anyway.
Prerequisite: Minimal: none, but if you want to type along, install R and RStudio (and maybe git). Maximal: you've checked out the CSSS-geo code from github, OR you've clicked the little "Download ZIP" button (lower right hand side of the CSSS-geo page) and have decompressed into a folder.
Slides: Google
Source Code: CSSS-geo

  • Christine
  • Glenn
  • Chris
  • Song Binyang
  • Jakub
  • Alejandro
  • Haitao Shang
  • Jarrod Scott
  • Nilton Cardoso
  • Matt Ingram

Python: A Crash Course

Speaker: Richard Barnes
Date & Time: June 17 @ 7pm
Motivation and content: This tutorial assumes some familiarity with programming and covers basic interaction with Python, pros and cons of using it as a language, and a summary of some of its useful packages. If there are particular things you'd like covered, or if you'd like to co-instruct, drop me a line ( A few people have expressed interest on following up on this tutorial by teaching workshops on specific packages for networking, machine learning, and scientific computation.
Prerequisite: Have Python installed on your computer (Anaconda is an easy way to get this set up). Please have a code editor installed, SublimeText is an excellent choice.
Interested people:

  • Kiki(no background at all)
  • Glenn Magerman (no background, only R, Stata)
  • María Pereda (no background in Python, but I like programming, R, Netlogo, Matlab, C, CUDA)
  • Laurence (no Python, only R, C++, ..)
  • Valery (no background in Pyton, only R and Netlogo)
  • Song Binyang (know a little about Python)
  • Tolga Oztan (some Python, mostly R)
  • Jakub (No python, so far Java, Matlab)
  • Anna(no background in Python, but would love to learn)
  • Sola...(no background in Python. Proficient in STATA) <Ii> Jeroen de Wilde (no background)
  • Alejandro(no background in Python. C and Matlab)
  • Haitao Shang (no background in Python, only know MatLab)
  • Jarrod Scott(a little background in Python, a little better with R)
  • Nilton Cardoso (no background in Python, only R and other stat packages)
  • Urs (very little background in Python, only Matlab)
  • Matt Ingram (R, Stata, some Python)
  • Matt O (R, Mathematica, Matlab)
  • Jun (only C)
  • Brent (very very little Python. R, Java, Scala (someday....))
  • Laura (very little Python mostly R)

    Git: A Crash Course

    Speaker: Richard Barnes
    Date & Time: Monday the 22nd
    Motivation and content: This course will cover the basic concepts of Git. It will walk you through creating a repository, committing changes to your code, and collaborating with others. If there are particular things you'd like covered, or if you'd like to co-instruct, drop me a line (
    Prerequisite: Install SourceTree. Have a code editor, preferably SublimeText, installed.
    Interested people:

  • Kiki (no background at all)
  • Glenn Magerman (no background)
  • Valery (no background)
  • Jakub (Used it once)
  • Will (used a little)
  • Tolga Oztan (used it once)
  • Jim Caton (no background)
  • Alejandro (no background)
  • Haitao Shang (no background)
  • Jarrod Scott (some background)
  • Nilton Cardoso (no backgroung)
  • Urs (no background)
  • Matt Ingram (no background)
  • Laurence (some background)
  • Laura (no background)
  • Juan (used a little)

    Cloud Computing Introduction

    Speaker: Christine Harvey (
    Date & Time: TBD, targeting third or fourth week
    Motivation and content: This will cover an introduction to cloud computing using Amazon Web Services. This will review setting up an AWS account, launching an instance, logging on to the remote computing resource, and we can try to do a little something else as well. Open to suggestions!
    Prerequisite: Amazon account and a credit card (compute time should cost < $1)
    Interested people:

    • Glenn Magerman
    • Chris
    • Valery
    • Jakub
    • Anna
    • Alejandro
    • Haitao Shang
    • Nilton Cardoso
    • Jae
    • Matt Ingram
    • Laurence

    Reproducible Research with iPython Notebooks

    Speaker: Christine Harvey (
    Date & Time: TBD, targeting third or fourth week
    Motivation and content: iPython notebooks are a great way to keep track of your analysis and track data manipulations. Ideal for anyone working with data sets and creating visualizations along the way. More details to follow! Example:
    Prerequisite: Python Install with iPython Notebooks (other packages to be listed). Easiest install is the Anaconda Install (
    Interested people:

    • Glenn Magerman
    • Valery
    • Song Binyang
    • Tolga Oztan
    • Anna
    • Nilton Cardoso
    • Matt Ingram
    • Brent
    • Jakub
    • María Pereda
    • Cobain
    • Laura
    • Ilaria

    Topological Data Analysis - Persistent homology

    Speaker: Alice Patania
    Date & Time: Sunday, June 21st, 7pm
    Content:The tutorial will be a short introduction to topological data analysis and its applications to complex systems. I will try to illustrate the utility of these class of methods in several real world examples, and give some computational tools to apply them.
    Motivation: Topological Data Analysis is sensitive to both large and small scale patterns that often fail to be detected by other analysis methods, such as principal component analysis, (PCA), multidimensional scaling, (MDS), and cluster analysis. PCA and MDS produce unstructured scatterplots and clustering methods produce distinct, unrelated groups. These methodologies sometimes obscure geometric features that topological methods can capture.
    References: File:Tutorial TDA CSSS.pdf
    Interested people:
    1. Nilton
    2. Jean-Gab
    3. Jakub
    4. Richard
    5. María Pereda
    6. Laura
    7. Matt Ingram
    8. Glenn Magerman
    9. Ilaria
    10. Andy
    11. Chris
    12. Andre
    13. Alejandro
    14. Susanne
    15. Valery

    NetworkX: Exploring Python's network library and what you can do with it

    Speaker: Carolina Mattsson and possibly others (
    Date & Time: Monday June 22- 5:30pm
    Motivation and content: We'll be having four (!) lectures on networks. Thankfully some of those giants on whose shoulders we stand have built excellent libraries in python, R, and C that make playing around with networks a whole lot easier. In this tutorial we'll be digging into python's network library - NetworkX - and some things it can be used for. Network libraries in other languages have similar functionality, so don't let the python scare you. Having this after the network lectures means we can directly incorporate things that Newman talks about. I'll most likely use iPython notebook as a teaching tool, but if you don't want to install we can work around. There are people other than me who also know NetworkX quite well, if that's you and you want to help, just let me know!
    Prerequisites: Some Python knowledge - Richard's tutorial would be enough!
    Interested co-instructors:
    1. Carolina
    2. Daniel C.
    Interested people:
    1. Jakub
    2. Laura
    3. Matt Ingram
    4. Chris
    5. Glenn
    6. John
    7. Alejandro
    8. Will

    Basic examples of dummy variable use in econometrics applied to some Prof. Wooldridge datasets

    Speaker: Nilton Cardoso
    Date & Time: Thu, Jun 25, 7:00 PM
    Contents: Let´s go over some basic examples using Wooldridge´s datasets to illustrate the use of dummy varibales in econometrics.
    Motivation: Dummy variables in econometric models can capture group/ categories effects and are very useful in estimating different patterns within the sample.
    Prerequisite: Install R Studio (; selected csv data from Wooldridge data sets (
    Interested people:
    1. Alice
    2. Sola

    Speaker: Christine Harvey ( and Keith Burghardt (
    Date & Time: 7:00PM, June 16
    Motivation: NetLogo is a powerful tool for Agent-Based Models (ABM) due to its ease to code, simple-to-create visualization tools, and relatively fast computation capabilities. NetLogo is written in Java, which gives this modeling environment great portability at the expense of speed compared to C or Fortran.
    Content: In this talk, I will be reviewing NetLogo for students with mild backgrounds in coding by describing the basic program environment, GUI interface, and ways to reduce performance issues through massive parallelization, and avoiding read/write race conditions that can crop up.
    To Install NetLogo:
    Introduction Walkthrough: Download the guide for the tutorial here: File:NetLogoTutorial.pdf
    Slides Upload: File:NetLogo Review.pdf
    Interested people:
    1. Cobain
    2. Jakub
    3. Nilton
    4. Maggie
    5. Urs
    6. Laurence
    7. Matt H

    An evening of discussing economics with Ole Peters

    Where: Lecture Hall
    When: Tuesday 23'rd @ 7.00PM

    I have bothered several people around campus with the work on utility and economic theory by Ole Peters. Ole is in town and he has courteously agreed to give a talk on his work, this Thursday evening (specific time is yet to be disclosed – but probably around 7).

    Ole will run though some of his work and then we can transcend into an informal discussion about these ideas. If stamina and time allows for it, I am very interested in hearing different opinions on what role theory and modelling has, and should have, in the future of economics.

    Ole has a background in physics and mathematics and I think that people outside economics can appreciate his work too. He’s a fellow at the London Mathmatical Laboratory and an External Professor at SFI.

    Check out his website for both technical articles and more accessible material too. I can highly recommend this talk if you're an economist or just plain interested.