Santa Fe Institute Events Wiki - User contributions [en]

2011 Presentation Schedule

2011-07-01T04:16:56Z

X14n:

{{Complex Systems Summer School 2011}}

9:00-9:15: "Modeling Marriage Squeeze." Cristina Bradatan, Chris Glazner, Nathan Wang, Cristina Metzger 

9:15-9:30: "A Generalized Model of a Synthetic Genetic-Metabolic Oscillator." Ed Reznik 

9:30-9:45: "Fragility and Food Webs in Southwestern Colorado: an Analysis of Interconnectedness in Castle Rock Pueblo." Stefani & Lydia 

9:45-10:00: Evolution Challenge Question, Sean Roberts and Andrew Tinka 

10:00-10:15: Martin Gould, Sean Roberts 

10:15-10:30: "SFI explanations of music neuroscience." Victor Quintanar-Zilinskas 

10:30-10:45 "The Fifth Rule: an agent-based modeling approach and possible applications based on real data." Elliot Aguilar, Nora Connor, Alejandro Fajardo, Matteo Gagliolo, Josh Garland, Eugenia Polizzi 

10:45-11:00: Break 

11:00-11:15: "Routing for Robustness on Wireless Sensor Networks." Andrew Tinka 

11:15-11:30 Tomas Veloz 

11:30-11:45: "Self-organization in a heterogeneous bacterial biofilm." David Borenstein and Erik Edlund 

11:45-12:00:"The Suicide Model Project." C. Bradatan, J. Garland, C. Gunning, C. Metzger, S. Singh, C. Andris 

12:00-12:15: Break 

12:15-12:30: Network Challenge Question. Michael Johanson, Shweta Singh, Yangjing Long, Guido Montufar, 

12:30-12:45: Complexity Challenge Question, Chris Glazner, Fran Moore, Shweta Singh, Ryan Baird, Jason Veneman, Michael Lightfoot, Lydia Smith, Nini Zhang 

12:45-1:00: "Some genes have many partners: Detecting biological modularity." Aaron Brooks, Antoine Allard and Yangjing Long 

1:00-1:15 "A Cellular Automata Model for Common Pool Resource Management" Zoe Hamstead, Michael Sachs, Nadja Kunz, Alejandro Fajardo 

1:15-1:30 "CSSS (social) network challenge" Anand, Cali, Evelien Van der Hurk, Randy, Taka, Stefani 

Closing:
"Chaotic music generation, aka DJ Chaos(es)" Anna Deluca, Martin Gould, Sean Roberts, Nini Zhang 

Special Presentation

Complex Systems Summer School 2011

2011-07-01T04:10:10Z

X14n: /* WHAT'S NEW?!?! */

{{Complex Systems Summer School 2011}}

Welcome to the 2011 Complex Systems Summer School!

Please stay tuned as we add more content to these pages.

We're looking forward to seeing everyone on June 8th.

David Krakauer,

Program Director, 2011 SFI Complex Systems Summer School

'''Please sign up for [[Alfred Hubler's Nonlinear Dynamics Lab 2011 | Alfred Hubler's Nonlinear Dynamics Lab]]'''

==WHAT'S NEW?!?!==

[[2011 Presentation Schedule]]

Completed versions of the four Complexity labs have been uploaded as PDFs. Find them in the lab section of the complexity module page.

----------------------------

The Participants pages are up! If you haven't done so yet, please login to edit your wiki stub.
At the very least, answer the questions below and post a photo.

Start thinking about what (if any) tutorials or lectures you might want to give to your CSSS-mates, or what kinds of working groups you'd like to see organized.

Questions to get you started:
* What are your main interests? Feel free to include a "pie in the sky" big idea!
* What sort of expertise can you bring to the group?
* What do you hope to get out of the CSSS?
* Do you have any possible projects in mind for the CSSS?

Also, Please visit [http://www.facebook.com/pages/SFI-Complex-Systems-Summer-School/195552467134324?sk=wall&filter=2 the Complex Systems Summer School Facebook Page]

Complex Systems Summer School 2011

2011-06-23T04:14:58Z

X14n: /* WHAT'S NEW?!?! */

{{Complex Systems Summer School 2011}}

Welcome to the 2011 Complex Systems Summer School!

Please stay tuned as we add more content to these pages.

We're looking forward to seeing everyone on June 8th.

David Krakauer,

Program Director, 2011 SFI Complex Systems Summer School

'''Please sign up for [[Alfred Hubler's Nonlinear Dynamics Lab 2011 | Alfred Hubler's Nonlinear Dynamics Lab]]'''

==WHAT'S NEW?!?!==

18:00, 23 June 2011 (UTC) High Performance R! See Tutorial page for details.

00:09, 18 June 2011 (UTC) All Computation lecture slides up.

17:46, 16 June 2011 (UTC) Cris Moore slides up.

15:02, 14 June 2011 (UTC) GML Network of Research Interests Posted under "Projects & Working Groups"

22:14, 13 June 2011 (UTC) Machine Learning readings up.

17:20, 13 June 2011 (UTC) Robustness readings up on Robustness module page

15:37, 13 June 2011 (UTC) Intro Netlogo tutorial linked off of software page

15:15, 13 June 2011 (UTC) New software on software page for networks module.

----------------------------

The Participants pages are up! If you haven't done so yet, please login to edit your wiki stub.
At the very least, answer the questions below and post a photo.

Start thinking about what (if any) tutorials or lectures you might want to give to your CSSS-mates, or what kinds of working groups you'd like to see organized.

Questions to get you started:
* What are your main interests? Feel free to include a "pie in the sky" big idea!
* What sort of expertise can you bring to the group?
* What do you hope to get out of the CSSS?
* Do you have any possible projects in mind for the CSSS?

Also, Please visit [http://www.facebook.com/pages/SFI-Complex-Systems-Summer-School/195552467134324?sk=wall&filter=2 the Complex Systems Summer School Facebook Page]

Complex Systems Summer School 2011-Tutorials

2011-06-23T04:13:51Z

X14n:

{{Complex Systems Summer School 2011}}

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

Also, please post requests for tutorials here.

== High Performance R ==

I (Christian) am leading a "High Performance R" tutorial Thurs 23 June at 6pm in the Great Hall. I'll talk for 30 minutes, and then spend 30 minutes working with folks. If anyone has any general R questions, I'll aim to stick around from 7-7:30 to chat.

You'll get the most out of this if you get the following software up-and-running prior to the meeting.

* R -- http://cran.r-project.org/
* RStudio -- A very nice R environment -- http://www.rstudio.org/
* If you have OSX, please make sure you've installed Xcode.

Make sure you can run Rstudio. Inside Rstudio, do the following:
* Go to the Tools menu
* Select "Install packages"
* Select a mirror in the US
* Install the following packages:
- inline
- Rcpp
- RcppArmadillo
[[User:X14n|X14n]] 04:13, 23 June 2011 (UTC)

==Public Speaking==
Would anyone be interested in a public speaking workshop? More specifically, the public speaking module I'd suggest is on presenting one's research to those who are methodologically but probably not substantively inside one's own field (which is a phenomenon that one observes extensively inside complexity research). I can also offer a more basic public speaking workshop if there's any interest. - Nini

--

I'm down, [Nini]. (JP)

==Complex Systems for the Uninitiated (JP)==

After merely tying the "Best Effort" award at the CSSS/Bread Loaf mixer, I've decided to one-up my competition and see if anyone is interested in hosting "Complex Systems for the Masses" lecture for the Bread Loaf folks. I think it might be fun/helpful to evangelize to the uninitiated.

Let me know if you're interested. It's always fun to watch people's eyes go wide when they learn about completely new and exciting topics. (JP)

--

Not sure if we have many unscheduled evenings. Maybe on Friday night? (JP)

Module:Evolution

2011-06-22T20:41:23Z

X14n: /* Readings */

{{Complex Systems Summer School 2011 Modules}}

Organized by [[David Krakauer]]

==Background==

==Readings==

[[Media:India_pop_gen_handout.pdf | India Handount]]

[[Media:Baum+2005SM.pdf | Baum 2005]]

Module:Evolution

2011-06-22T20:40:55Z

X14n: /* Readings */

{{Complex Systems Summer School 2011 Modules}}

Organized by [[David Krakauer]]

==Background==

==Readings==

[[Media:India_pop_gen_handout.pdf]]

[[File:Baum+2005SM.pdf | Baum 2005]]

Module:Evolution

2011-06-22T20:40:41Z

X14n: /* Readings */

{{Complex Systems Summer School 2011 Modules}}

Organized by [[David Krakauer]]

==Background==

==Readings==

[[Mesi:India_pop_gen_handout.pdf]]

[[File:Baum+2005SM.pdf | Baum 2005]]

Module:Evolution

2011-06-22T20:40:06Z

X14n: /* Readings */

{{Complex Systems Summer School 2011 Modules}}

Organized by [[David Krakauer]]

==Background==

==Readings==

[[File:India_pop_gen_handout.pdf]]

[[File:Baum+2005SM.pdf | Baum 2005]]

Module:Evolution

2011-06-22T20:39:32Z

X14n: /* Readings */

{{Complex Systems Summer School 2011 Modules}}

Organized by [[David Krakauer]]

==Background==

==Readings==

[[File:India_pop_gen_handout.pdf | India handout]]

[[File:Baum+2005SM.pdf | Baum 2005]]

File:Baum+2005SM.pdf

2011-06-22T20:36:56Z

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File:India pop gen handout.pdf

2011-06-22T20:36:08Z

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Module:Robustness

2011-06-20T19:57:26Z

X14n: /* Lab */

{{Complex Systems Summer School 2011 Modules}}

Organized by [[Jessica Flack]]

==Readings==

[[Media:2011RobustnessChapter2_05_31_11.pdf‎ |Robustness in biological and social systems]]

[[Media:Ackleyrobust.pdf‎ |Pursue robust indeﬁnite scalability]]

[[Media:Ackleyrobustnessneumann.pdf‎ |The general and logical theory of automata]]

[[Media:AyFlackKrakauer2007.pdf‎ |Robustness and complexity co-constructed
in multimodal signalling networks]]

[[Media:ErrorAttackNature(2000).pdf‎ |Error and attack tolerance
of complex networks]]

[[Media:Flackniche.pdf‎ |
Policing stabilizes construction of social
niches in primate]]

[[Media:KrakauerAyRobust.pdf |
Geometric robustness theory and biological network]]

==Lab==

[[Media:Robustness_lab.pdf‎ | Robustness Lab]]

[[Media:Data.xls | Data file]]

Module:Robustness

2011-06-20T19:55:56Z

X14n: /* Lab */

Module:Robustness

2011-06-20T19:55:44Z

X14n: /* Lab */

File:Data.xls

2011-06-20T19:55:18Z

X14n: Data file for Robust lab

Data file for Robust lab

Module:Networks

2011-06-14T20:23:35Z

X14n: /* Software */

{{Complex Systems Summer School 2011 Modules}}

Organized by [http://www.santafe.edu/about/people/profile/Mark%20Newman Mark Newman]

==Background==

==Readings==

===Mark Newman===

[http://www.nature.com/nature/journal/v410/n6825/full/410268a0.html S. H. Strogatz, "Exploring complex networks", Nature 410, 268-276 (2001)]

===Cris Moore===

[http://arxiv.org/abs/0811.0484 A. Clauset et al., "Hierarchical structure and the prediction of missing links in networks", Nature 453, 98-101 (2008)]

===Jennifer Dunne===

[http://www.sciencemag.org/content/325/5939/416.full J. Bascompte, "Disentangling the web of life", Science 325, 416-419 (2009)]

==Software==

[http://gephi.org/ Gephi Network Analysis Software]

[http://www.umich.edu/~mejn/netdata/ Network Datasets]

[http://cran.r-project.org/web/packages/igraph/ igraph R package -- reads and writes many network file formats, including GML]

Complex Systems Summer School 2011 (CSSS)

2011-06-13T18:22:06Z

X14n: /* WHAT'S NEW?!?! */

Complex Systems Summer School 2011 (CSSS)

2011-06-13T18:19:58Z

X14n: /* WHAT'S NEW?!?! */

Complex Systems Summer School 2011-Projects & Working Groups

2011-06-13T14:35:28Z

X14n: /* Meeting with Geoffrey West */

{{Complex Systems Summer School 2011}}

If you'd like to work on a project with other members of the group, please use this page to organize your thoughts and efforts. We'll schedule a time when we can show off your work towards the end of the program.

==Keywords==

Hey Guys! Some of your research interests have been entered. Hopefully this can give us a better idea of what we are studying, and how we can collaborate for the final challenge. They are organized in a [https://spreadsheets.google.com/spreadsheet/ccc?key=0Ak7533_HL5TadHdhRUFyWGVLRHlmN2liSEVtR2FDUEE&hl=en_US google doc] for sorting, searching etc, and all should have editing privileges. Sorry for typos! Feel free to cut and paste into excel, etc.

CHECK BACK FOR A NETWORK OF OUR INTERESTS!!!!!!

-Clio

==Meeting with Geoffrey West==

A group of us were interested to continue a discussion with Geoffrey West following his lecture this evening. We will be meeting over lunch next Wednesday 15th June at SFI in the medium conference room. Please add your name to the below list if you would like to attend. 
Nadja Kunz 
Martin Hilbert 
Shweta Singh 
Fran Moore 
Matteo Gagliolo 
Kevin Carlson 
Raghad Chawla 
Jacob Jensen 
Cristina Metgher 
Alejandro Fajardo 
Lydia Smith 
Antoine Allard 
Michael Sachs 
Nicolas Paez 
Christian Gunning

Complex Systems Summer School 2011-Software

2011-06-03T01:10:23Z

X14n:

{{Complex Systems Summer School 2011}}

Please download these programs for use during the Summer School.

NetLogo: [http://ccl.northwestern.edu/netlogo/ Download Link]

(Optional Pre-Program) TISEAN 3.0.1 Nonlinear Time Series Analysis Software [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/index.html Download Link]

R Statistical Programming Language: [http://cran.opensourceresources.org/ Download Link]

----

[[User:X14n|X14n]] 01:10, 3 June 2011 (UTC) says:

You might be interested in the following TISEAN-related R packages (the links from the RISEAN page are broken):
* [http://cran.r-project.org/web/packages/tsDyn/index.html tsDyn]
* [http://cran.r-project.org/web/packages/RTisean/index.html RTisean]

Christian Gunning

2011-04-28T04:04:27Z

X14n: /* Personal */

{{Complex Systems Summer School 2011}}

[[File:Eye.jpg]]

==School==

I'm a Ph.D. candidate in the Biology Department at the University of New Mexico in Albuquerque. I study disease ecology, and am a member of the [http://math.unm.edu/~hwearing/researchgroup/index.html Wearing Lab].

==Intellectual Interests==

* Timeseries data analysis
* Dynamical systems modelling
* R programming language
* SQL / database design (postgresql is my favorite)
* Linux and Open Source Software

More info on recent projects can be found here:
[http://helmingstay.blogspot.com blog.x14n.org]

==Personal==

* Beer
* Bikes
* Trees / Plants
* Water

Christian Gunning

2011-04-28T04:03:19Z

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Christian Gunning

2011-04-28T04:01:37Z

X14n:

{{Complex Systems Summer School 2011}}

[[File:Eye.jpg]]

==School==

I'm a Ph.D. candidate in the Biology Department at the University of New Mexico in Albuquerque. I study disease ecology, and am a member of the [http://math.unm.edu/~hwearing/researchgroup/index.html Wearing Lab].

==Intellectual Interests==

* Timeseries data analysis
* Dynamical systems modelling
* R programming language
* SQL / database design (postgresql is my favorite)

More info on recent projects can be found here:
[http://helmingstay.blogger.com blog.x14n.org]

==Personal==

* Beer.
* Bikes.
* Trees / Plants

Christian Gunning

2011-04-28T04:00:13Z

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Christian Gunning

2011-04-28T03:59:21Z

X14n: intro -- framework

File:Eye.jpg

2011-04-28T03:53:37Z

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Complex Systems Summer School 2011-Participants

2011-04-28T03:50:48Z

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{{Complex Systems Summer School 2011}}

Get to know participants on the [http://www.facebook.com/pages/SFI-Complex-Systems-Summer-School/195552467134324?sk=wall&filter=2 Facebook Complex Systems Summer School Page]

'''Elliot Aguilar,''' City University of New York, Biology

'''Antoine Allard,''' Laval University, Physics

'''Clio Andris,''' MIT, Urban Studies and Planning

'''Joshua Auerbach,''' University of Vermont, Computer Science

'''David Borenstein,''' Princeton University, Quantitative and Computational Biology

'''Cristina Bradatan,''' Texas Tech University, Sociology, Anthropology, and Social Work

'''Amy Braun,''' Stanford University, Neuroscience

'''Aaron Brooks,''' University of Washington, Molecular and Cellular Biology

'''[[Tom Carter]],''' Santa Fe Institute

'''Randy Casstevens,''' George Mason University, Computational Social Science

'''Nora Connor,''' University of Colorado, Boulder, Interdisciplinary Quantitative Biology

'''Stefani Crabtree,''' Washington State University, Anthropology

'''Anna Deluca,''' Centre de Recerca Matematica, Complex Systems Group

'''Erik Edlund,''' Chalmers University of Technology, Energy and Environment

'''Alejandro Fajardo,''' Universidad de los Andes, Biology

'''Alejandro Feged,''' Stanford, Anthropology

'''Matteo Gagliolo,''' VUB, DINF

'''Leonida Gheorghiade,''' University of Guelph, Mathematics and Statistics

'''Martin Gould,''' University of Oxford, Industrial and Applied Mathematics

'''[[John Paul Gonzales]]''' Santa Fe Institute

'''[[Christian Gunning]]''', University of New Mexico, Biology

'''Zoe Hamstead,''' University of Illinois at Chicago, Urban Planning and Policy

'''Kameron Harris,''' University of Vermont, Mathematics and Statistics

'''Martin Hilbert,''' University of Southern California, Annenberg School of Communication

'''Michael Johansson,''' CDC, Division of Vector-Borne Diseases

'''[[Nadja Kunz]],''' University of Queensland, Center for Water in Minerals Industry, Sustainable Minerals Institute

'''Yangjing Long,''' Max Planck Society, Mathematics

'''Cristina Metgher,''' George Mason University, Computational Social Science

'''Frances Moore,''' Stanford Uniiversity, Environment and Resources

'''Anand Murugesan,''' University of Maryland, Agriculture and Resource Economics

'''Gustavo Nicolas Paez Salamanca,'''Universidad de los Andes

'''Eugenia Polizzi di Sorrentino,'''National Research Council, Cognitive Science

'''[[Victor Quintanar-Zilinskas]]''', UC Irvine, Complex Biological Systems

'''[[Ed Reznik]],''' Boston University, Biomedical Engineering

'''Sean Roberts,''' University of Edinburgh, Philosophy, Psychology, and Language Science

'''Michael Sachs,''' University of California Davis, Physics

'''Takao Sasaki,''' Arizona State University, School of Life Sciences

'''Shweta Singh,''' The Ohio State University, Chemical and Biomolecular Engineering

'''Lydia Smith,''' UC Berkeley, Energy and Resources

'''Andrew Tinka,''' UC Berkelet, Electrical Engineering and Computer Science

'''Alexis Akira Toda,''' Yale University, Economics

'''Miles Townes,''' The George Washington University, Political Science

'''Evelien Van der Hurk,''' Erasmus University Rotterdam, Management, Information Science

'''Tomas Veloz,''' University of British Columbia

'''Ninghua Wang,''' San Diego State University, UC Santa Barbara, Geography

'''Wenshuo Zhang,''' University of Illinois at Urbana, Political Science