Santa Fe Institute Events Wiki - User contributions [en]

Complex Systems Summer School 2012-Tutorials

2012-06-26T01:05:23Z

CRSmith: /* Hierarchical Dirichlet Processes and the Infinite Hidden Markov Model */

{{Complex Systems Summer School 2012}}

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.

==Fractal Tutorial??==

Hi, I have a request for a tutorial: Could anyone who has the expertise please teach a tutorial on fractal theory and codes to generate some?
Thanks! -Jasmeen

==Python online materials==
[Follow up to Ryan's tutorial..]

Here you have some useful online references for getting started in Python.

=== Google's Python Class ===
* A ''[...] free class for people with a little bit of programming experience who want to learn Python. The class includes written materials, lecture videos, and lots of code exercises to practice Python coding [...]''
* http://code.google.com/edu/languages/google-python-class/

=== Numpy, Scipy and Matplotlib tutorials ===
* I.e.: all the things you typically do in Matlab done in Python..
* NumPy tutorial: http://www.scipy.org/Tentative_NumPy_Tutorial
* Matplotlib tutorial: http://matplotlib.sourceforge.net/users/pyplot_tutorial.html
* Numpy for Matlab Users (extremely useful!!!): http://www.scipy.org/NumPy_for_Matlab_Users

=== NetworkX ===
* I.e.: network analysis in Python
* NetworkX tutorial: http://networkx.lanl.gov/tutorial/index.html

=== Enthought Python Distribution ===
* ''The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.''
* It is free (!!!): http://www.enthought.com/products/edudownload.php

=== Additional References ===
* Py4Science: a Starter Kit (by Fernando Perez, U.C. Berkeley)
* http://fperez.org/py4science/starter_kit.html

Hope this helps,

Matteo

==Non-linear measures of correlation==

I have been working on how to quantify the reciprocal interaction of time-series over time. I am using Recurrence Plots (http://www.recurrence-plot.tk/glance.php). If anybody is interested in discussing this method, I am willing to prepare a small tutorial on what recurrence plots are and how I have been using them.

Riccardo (fusaroli@gmail.com)

- Matteo

- Oleksandr krystoferivanov@gmail.com

- Priya

- Friederike

- Miguel

- Vikram

- Hide

==Intro to Philosophy of Science==

Hi All, I've heard some interest in having a more structured/rigorous intro to ideas in the philosophy of science. I'd be happy to briefly explain some of the classic theories as well as some more recent views due to, e.g. Bas Van Fraassen, James Ladyman, Nancy Cartwright, and we could have a small (moderated!) group discussion. Sign up if interested... -Jasmeen

- Hide is interested and has a crush on Engels

- Friederike

- Matteo

- Vikram

- Mikkel

- Mark (!)

-Keegan is down

-Xiaoli

- Georg W.

- Priya

- Miguel

- Oscar

==Markov Chain Monte Carlo==
If anyone is interested in talking more about Bayesian methods and MCMC implementation, I'd be happy to put something together. - Keegan

[[Media: MCMC.pdf|Slides]]

-Hide is interested in this!

-Abby

-Joanne

-Oscar

-Vanessa

-Jasmeen

-Georg

-Nona

-benji

-Riccardo

-Matteo

-Cameron

- Priya

-Xiaoli

- Vikram

- Miguel

==Python, Computational Mechanics, and Information Theory==

There has been interest in more discussion on a number of topics, and so i'm offering to have evening discussions on them. please sign up below so that i can get a feel for the number of people who would be attending. also, please put a preference for what day it should be.

===Python===
Sign up below if you'd like an introduction to basic python programming. Python is a general purpose, very flexible and useful programming language. It is used pretty extensively in scientific computing.

dan wu: wu12345@gmail.com Let me know when we're meeting

- Benji: bzusman@gmail.com 

-Keegan keegan.hines@gmail.com

-Christa (maybe- I'm competent at the very basics, but could still use some help)

- Riccardo: fusaroli@gmail.com

- Oleksandr: krystoferivanov@gmail.com

- Nona: nona.karalashvili@gmail.com

- Xiaoli: xiaolidong2008@gmail.com

- Abby: Abbyhorn@Mit.edu

- Marco: maduenase@gmail.com

- Nick: goudemand at pim dot uzh dot ch

- Fabio: fabio.cresto-aleina@zmaw.de

- Joanne: joannerodrigues@berkeley.edu

- Hide: hi55 at cornell dot edu

- Priya: iitm.priya@gmail.com

- Miguel: miguel.lurgi@icm.csic.es

- Oscar: opatters@asu.edu

- Vanessa: vanferdi at gmail dot com

- Georg G: gmg at stat dot cmu dot edu dot notthelastpart

- Oleksandr: krystoferivanov@gmail.com

===Information Theory===
Interested in turning your data into bits, or seeing how the bits over there are related to the bits over here? If so, sign up below.

- Matteo

- Benji: bzusman@gmail.com

-Keegan keegan.hines@gmail.com

-Riccardo

-Christa

- Katrien

- Xiaoli

- Abby

- Jasmeen

- Hide

- Sanith

- Priya

- Georg W.

- Piotr

- Miguel

- Oscar

- Vanessa

- Nona

- Georg G.

- Oleksandr krystoferivanov@gmail.com

===Computational Mechanics===
If you'd like to know more about epsilon machines, measures of complexity, how to go from a map to a machine, i'm happy to discuss it all. 
- Matteo

Yes please! --Chloe

-Keegan keegan.hines@gmail.com

-Christa

-Xiaoli

-Jasmeen

-Hide

-Sanith

- Priya

- Georg W.

-Piotr

-Ian

- Miguel

- Oscar

- Abby

- Georg G.

- Riccardo.

==Order Book Dynamics: Learn how to trade in 15min==

--I'm happy to repeat this -just get in touch with me.--

If you are curious about how stocks trade and want to try your luck, I'll
be going over some of the basics with a hands-on example.

Meet at 7.30pm in main lecture hall Thursday June 7th. Please make sure
to bring your laptop.

Sanith

==Update==

Hi guys

I guess the main lecture hall is free at 6.30 pm and so we can meet there. I have a small talk through the idea and then maybe we can try out getting bifurcation plots for one or two systems. I use software written in MATLAB for the demo but the idea can be implemented in any software.

Here's a link to the [[software for numerical continuation|http://twr.cs.kuleuven.be//research/software/delay/notice.shtml]]. This software can handle systems with time delays and can be used to obtain the bifurcation behaviour.

(1) Please download the software DDE-BIFTOOL and unzip.

(2) Within the folder, you will find another zipped folder in small case ‘ddebiftool’. Please unzip this into a folder with the same name

(3) Add the location of the folder to the path of MATLAB.
I have also sent out a mail with a zipped folder containing files to get a bifurcation plot for a Rijke tube system.
Do let me know if anyone did not get this.
See you there!

Priya

==An easier way to get a bifurcation plot==

Hey guys
I have been working in the past in obtaining bifurcation plots for different physical systems. There's a better way to get these pictures instead of getting the evolution at every parameter value of interest. This is called ''numerical continuation'' and basically involves tracking a curve. I plan to give a informal talk on how to do this and maybe even a demo on applying this technique on 14th June at 6.30 pm. Do mail me if you are interested at '''iitm.priya@gmail.com''' or sign up below.
[[User:Priya|Priya]]

- [[Ryan James|Ryan]] is interested in this. 
- Riccardo is interested in this. 
- Vikram is interested in this. 
- Matteo is interested in this. 
- Hide is interested in this. 
- Katrien wants to hear more about this. 
- Cameron is interested in this and would like to see [http://itunes.apple.com/us/app/xpp/id433859546?mt=8 this] in action if anyone has an iPad. 
- Oscar is interested in this. 
- Charlie is interested in this. (I've done this once for a paper.) 
- Georg W. is interested in this 

==Using Tisean on R on OS X==
first install TISEAN, like you've done already. Make sure R is up to date (v 2.15).
you can try to install RTisean from CRAN
install.packages("RTisean"); library(RTisean); henon()
But me and Dave both got an error about some bad file name, something about con and something about a long path involving -Tmp-
Solution:
remove.packages("RTisean")
restart R
download this: http://cl.ly/0I0b2P2L311y1q0q0y0n
install it, it changes line 74 of nativeTISEAN.R which has some problems with file handling
If you are golden, then:
> henon()
V1 V2
[1,] -0.1232481 -1.030383

==A conceptual shell==

One thing that I think has been missing from this course is an explicit set of concepts and tools which we can use to relate all of the talks we've been listening to. Last fall, two other graduates students and I taught a survey course on complexity. We put together the following document, which contains one-paragraph summaries of what we felt were the 20 most important concepts that comprised the field of complexity. These were the "glue" that we used to relate all of our lectures and workshops. Most of these will probably be familiar to you, but I think they serve as a nice, concise reference and may be helpful in tying all of this information overload together. One caveat: These are works in progress and are in alphabetical rather than any logical conceptual order.

[[Media:Topics_in_Complexity_Foundational_Definitions.pdf]]

Cheers,
Mark Longo

== Hierarchical Dirichlet Processes and the Infinite Hidden Markov Model ==

Over the past week, I've discussed Hierarchical Dirichlet Processes (HDP) and the Infinite Hidden Markov Model (iHMM) with several of you. Basically, it's the only framework I've come across, aside from Jim Crutchfield's work on the epsilon machine, that offers the diligent student the ability to estimate the hidden states generating one's data, without requiring the analyst a priori specify the number of hidden states (a very nice feature). One of the most significant differences between these approaches is Crutchfield's requires a finite alphabet, whereas HDP is defined in the context of an infinite number of base probability measures (think clustering). I believe they are both worth knowing, and I'm willing to offer a tutorial on the topics of HDP and iHHM. I'm thinking Tuesday at 7pm (after dinner) in the conference room is our best bet. If you are interested, please do have a look at the following paper by Yee Whye Teh:
*[[File:HDP(2005)Teh&Jordan.pdf]]

[1] Y. W. Teh, M. I. Jordan, M. J. Beal, and D. M. Blei, Journal of the American Statistical Association 101, 1566-1581 (2006).

[2] J. P. Huelsenbeck and P. Andolfatto, Genetics 175, 1787-802 (2007).

[3] T. Xu, Z. (Mark) Zhang, P. S. Yu, and B. Long, in 2008 Eighth IEEE International Conference on Data Mining (IEEE, 2008), pp. 658-667.

[4] J. D. McAuliffe, D. M. Blei, and M. I. Jordan, Statistics and Computing 16, 5-14 (2006).

It can get a little abstract, infinite partitions nested in infinite partitions, so try to check it out beforehand if you plan to attend. If you have any questions, fire me an email: jlong29@gmail.com
Thanks,
John

Please sign up:

-[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-Tutorials

2012-06-26T01:00:57Z

CRSmith: /* Hierarchical Dirichlet Processes and the Infinite Hidden Markov Model */

{{Complex Systems Summer School 2012}}

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.

==Fractal Tutorial??==

Hi, I have a request for a tutorial: Could anyone who has the expertise please teach a tutorial on fractal theory and codes to generate some?
Thanks! -Jasmeen

==Python online materials==
[Follow up to Ryan's tutorial..]

Here you have some useful online references for getting started in Python.

=== Google's Python Class ===
* A ''[...] free class for people with a little bit of programming experience who want to learn Python. The class includes written materials, lecture videos, and lots of code exercises to practice Python coding [...]''
* http://code.google.com/edu/languages/google-python-class/

=== Numpy, Scipy and Matplotlib tutorials ===
* I.e.: all the things you typically do in Matlab done in Python..
* NumPy tutorial: http://www.scipy.org/Tentative_NumPy_Tutorial
* Matplotlib tutorial: http://matplotlib.sourceforge.net/users/pyplot_tutorial.html
* Numpy for Matlab Users (extremely useful!!!): http://www.scipy.org/NumPy_for_Matlab_Users

=== NetworkX ===
* I.e.: network analysis in Python
* NetworkX tutorial: http://networkx.lanl.gov/tutorial/index.html

=== Enthought Python Distribution ===
* ''The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.''
* It is free (!!!): http://www.enthought.com/products/edudownload.php

=== Additional References ===
* Py4Science: a Starter Kit (by Fernando Perez, U.C. Berkeley)
* http://fperez.org/py4science/starter_kit.html

Hope this helps,

Matteo

==Non-linear measures of correlation==

I have been working on how to quantify the reciprocal interaction of time-series over time. I am using Recurrence Plots (http://www.recurrence-plot.tk/glance.php). If anybody is interested in discussing this method, I am willing to prepare a small tutorial on what recurrence plots are and how I have been using them.

Riccardo (fusaroli@gmail.com)

- Matteo

- Oleksandr krystoferivanov@gmail.com

- Priya

- Friederike

- Miguel

- Vikram

- Hide

==Intro to Philosophy of Science==

Hi All, I've heard some interest in having a more structured/rigorous intro to ideas in the philosophy of science. I'd be happy to briefly explain some of the classic theories as well as some more recent views due to, e.g. Bas Van Fraassen, James Ladyman, Nancy Cartwright, and we could have a small (moderated!) group discussion. Sign up if interested... -Jasmeen

- Hide is interested and has a crush on Engels

- Friederike

- Matteo

- Vikram

- Mikkel

- Mark (!)

-Keegan is down

-Xiaoli

- Georg W.

- Priya

- Miguel

- Oscar

==Markov Chain Monte Carlo==
If anyone is interested in talking more about Bayesian methods and MCMC implementation, I'd be happy to put something together. - Keegan

[[Media: MCMC.pdf|Slides]]

-Hide is interested in this!

-Abby

-Joanne

-Oscar

-Vanessa

-Jasmeen

-Georg

-Nona

-benji

-Riccardo

-Matteo

-Cameron

- Priya

-Xiaoli

- Vikram

- Miguel

==Python, Computational Mechanics, and Information Theory==

There has been interest in more discussion on a number of topics, and so i'm offering to have evening discussions on them. please sign up below so that i can get a feel for the number of people who would be attending. also, please put a preference for what day it should be.

===Python===
Sign up below if you'd like an introduction to basic python programming. Python is a general purpose, very flexible and useful programming language. It is used pretty extensively in scientific computing.

dan wu: wu12345@gmail.com Let me know when we're meeting

- Benji: bzusman@gmail.com 

-Keegan keegan.hines@gmail.com

-Christa (maybe- I'm competent at the very basics, but could still use some help)

- Riccardo: fusaroli@gmail.com

- Oleksandr: krystoferivanov@gmail.com

- Nona: nona.karalashvili@gmail.com

- Xiaoli: xiaolidong2008@gmail.com

- Abby: Abbyhorn@Mit.edu

- Marco: maduenase@gmail.com

- Nick: goudemand at pim dot uzh dot ch

- Fabio: fabio.cresto-aleina@zmaw.de

- Joanne: joannerodrigues@berkeley.edu

- Hide: hi55 at cornell dot edu

- Priya: iitm.priya@gmail.com

- Miguel: miguel.lurgi@icm.csic.es

- Oscar: opatters@asu.edu

- Vanessa: vanferdi at gmail dot com

- Georg G: gmg at stat dot cmu dot edu dot notthelastpart

- Oleksandr: krystoferivanov@gmail.com

===Information Theory===
Interested in turning your data into bits, or seeing how the bits over there are related to the bits over here? If so, sign up below.

- Matteo

- Benji: bzusman@gmail.com

-Keegan keegan.hines@gmail.com

-Riccardo

-Christa

- Katrien

- Xiaoli

- Abby

- Jasmeen

- Hide

- Sanith

- Priya

- Georg W.

- Piotr

- Miguel

- Oscar

- Vanessa

- Nona

- Georg G.

- Oleksandr krystoferivanov@gmail.com

===Computational Mechanics===
If you'd like to know more about epsilon machines, measures of complexity, how to go from a map to a machine, i'm happy to discuss it all. 
- Matteo

Yes please! --Chloe

-Keegan keegan.hines@gmail.com

-Christa

-Xiaoli

-Jasmeen

-Hide

-Sanith

- Priya

- Georg W.

-Piotr

-Ian

- Miguel

- Oscar

- Abby

- Georg G.

- Riccardo.

==Order Book Dynamics: Learn how to trade in 15min==

--I'm happy to repeat this -just get in touch with me.--

If you are curious about how stocks trade and want to try your luck, I'll
be going over some of the basics with a hands-on example.

Meet at 7.30pm in main lecture hall Thursday June 7th. Please make sure
to bring your laptop.

Sanith

==Update==

Hi guys

I guess the main lecture hall is free at 6.30 pm and so we can meet there. I have a small talk through the idea and then maybe we can try out getting bifurcation plots for one or two systems. I use software written in MATLAB for the demo but the idea can be implemented in any software.

Here's a link to the [[software for numerical continuation|http://twr.cs.kuleuven.be//research/software/delay/notice.shtml]]. This software can handle systems with time delays and can be used to obtain the bifurcation behaviour.

(1) Please download the software DDE-BIFTOOL and unzip.

(2) Within the folder, you will find another zipped folder in small case ‘ddebiftool’. Please unzip this into a folder with the same name

(3) Add the location of the folder to the path of MATLAB.
I have also sent out a mail with a zipped folder containing files to get a bifurcation plot for a Rijke tube system.
Do let me know if anyone did not get this.
See you there!

Priya

==An easier way to get a bifurcation plot==

Hey guys
I have been working in the past in obtaining bifurcation plots for different physical systems. There's a better way to get these pictures instead of getting the evolution at every parameter value of interest. This is called ''numerical continuation'' and basically involves tracking a curve. I plan to give a informal talk on how to do this and maybe even a demo on applying this technique on 14th June at 6.30 pm. Do mail me if you are interested at '''iitm.priya@gmail.com''' or sign up below.
[[User:Priya|Priya]]

- [[Ryan James|Ryan]] is interested in this. 
- Riccardo is interested in this. 
- Vikram is interested in this. 
- Matteo is interested in this. 
- Hide is interested in this. 
- Katrien wants to hear more about this. 
- Cameron is interested in this and would like to see [http://itunes.apple.com/us/app/xpp/id433859546?mt=8 this] in action if anyone has an iPad. 
- Oscar is interested in this. 
- Charlie is interested in this. (I've done this once for a paper.) 
- Georg W. is interested in this 

==Using Tisean on R on OS X==
first install TISEAN, like you've done already. Make sure R is up to date (v 2.15).
you can try to install RTisean from CRAN
install.packages("RTisean"); library(RTisean); henon()
But me and Dave both got an error about some bad file name, something about con and something about a long path involving -Tmp-
Solution:
remove.packages("RTisean")
restart R
download this: http://cl.ly/0I0b2P2L311y1q0q0y0n
install it, it changes line 74 of nativeTISEAN.R which has some problems with file handling
If you are golden, then:
> henon()
V1 V2
[1,] -0.1232481 -1.030383

==A conceptual shell==

One thing that I think has been missing from this course is an explicit set of concepts and tools which we can use to relate all of the talks we've been listening to. Last fall, two other graduates students and I taught a survey course on complexity. We put together the following document, which contains one-paragraph summaries of what we felt were the 20 most important concepts that comprised the field of complexity. These were the "glue" that we used to relate all of our lectures and workshops. Most of these will probably be familiar to you, but I think they serve as a nice, concise reference and may be helpful in tying all of this information overload together. One caveat: These are works in progress and are in alphabetical rather than any logical conceptual order.

[[Media:Topics_in_Complexity_Foundational_Definitions.pdf]]

Cheers,
Mark Longo

== Hierarchical Dirichlet Processes and the Infinite Hidden Markov Model ==

Over the past week, I've discussed Hierarchical Dirichlet Processes (HDP) and the Infinite Hidden Markov Model (iHMM) with several of you. Basically, it's the only framework I've come across, aside from Jim Crutchfield's work on the epsilon machine, that offers the diligent student the ability to estimate the hidden states generating one's data, without requiring the analyst a priori specify the number of hidden states (a very nice feature). One of the most significant differences between these approaches is Crutchfield's requires a finite alphabet, whereas HDP is defined in the context of an infinite number of base probability measures (think clustering). I believe they are both worth knowing, and I'm willing to offer a tutorial on the topics of HDP and iHHM. I'm thinking Tuesday at 7pm (after dinner) in the conference room is our best bet. If you are interested, please do have a look at the following paper by Yee Whye Teh:
*[[File:HDP(2005)Teh&Jordan.pdf]]
It can get a little abstract, infinite partitions nested in infinite partitions, so try to check it out beforehand if you plan to attend. If you have any questions, fire me an email: jlong29@gmail.com
Thanks,
John

Please sign up:

-[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-Tutorials

2012-06-26T00:55:10Z

CRSmith: /* Hierarchical Dirichlet Processes and the Infinite Hidden Markov Model */

{{Complex Systems Summer School 2012}}

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.

==Fractal Tutorial??==

Hi, I have a request for a tutorial: Could anyone who has the expertise please teach a tutorial on fractal theory and codes to generate some?
Thanks! -Jasmeen

==Python online materials==
[Follow up to Ryan's tutorial..]

Here you have some useful online references for getting started in Python.

=== Google's Python Class ===
* A ''[...] free class for people with a little bit of programming experience who want to learn Python. The class includes written materials, lecture videos, and lots of code exercises to practice Python coding [...]''
* http://code.google.com/edu/languages/google-python-class/

=== Numpy, Scipy and Matplotlib tutorials ===
* I.e.: all the things you typically do in Matlab done in Python..
* NumPy tutorial: http://www.scipy.org/Tentative_NumPy_Tutorial
* Matplotlib tutorial: http://matplotlib.sourceforge.net/users/pyplot_tutorial.html
* Numpy for Matlab Users (extremely useful!!!): http://www.scipy.org/NumPy_for_Matlab_Users

=== NetworkX ===
* I.e.: network analysis in Python
* NetworkX tutorial: http://networkx.lanl.gov/tutorial/index.html

=== Enthought Python Distribution ===
* ''The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.''
* It is free (!!!): http://www.enthought.com/products/edudownload.php

=== Additional References ===
* Py4Science: a Starter Kit (by Fernando Perez, U.C. Berkeley)
* http://fperez.org/py4science/starter_kit.html

Hope this helps,

Matteo

==Non-linear measures of correlation==

I have been working on how to quantify the reciprocal interaction of time-series over time. I am using Recurrence Plots (http://www.recurrence-plot.tk/glance.php). If anybody is interested in discussing this method, I am willing to prepare a small tutorial on what recurrence plots are and how I have been using them.

Riccardo (fusaroli@gmail.com)

- Matteo

- Oleksandr krystoferivanov@gmail.com

- Priya

- Friederike

- Miguel

- Vikram

- Hide

==Intro to Philosophy of Science==

Hi All, I've heard some interest in having a more structured/rigorous intro to ideas in the philosophy of science. I'd be happy to briefly explain some of the classic theories as well as some more recent views due to, e.g. Bas Van Fraassen, James Ladyman, Nancy Cartwright, and we could have a small (moderated!) group discussion. Sign up if interested... -Jasmeen

- Hide is interested and has a crush on Engels

- Friederike

- Matteo

- Vikram

- Mikkel

- Mark (!)

-Keegan is down

-Xiaoli

- Georg W.

- Priya

- Miguel

- Oscar

==Markov Chain Monte Carlo==
If anyone is interested in talking more about Bayesian methods and MCMC implementation, I'd be happy to put something together. - Keegan

[[Media: MCMC.pdf|Slides]]

-Hide is interested in this!

-Abby

-Joanne

-Oscar

-Vanessa

-Jasmeen

-Georg

-Nona

-benji

-Riccardo

-Matteo

-Cameron

- Priya

-Xiaoli

- Vikram

- Miguel

==Python, Computational Mechanics, and Information Theory==

There has been interest in more discussion on a number of topics, and so i'm offering to have evening discussions on them. please sign up below so that i can get a feel for the number of people who would be attending. also, please put a preference for what day it should be.

===Python===
Sign up below if you'd like an introduction to basic python programming. Python is a general purpose, very flexible and useful programming language. It is used pretty extensively in scientific computing.

dan wu: wu12345@gmail.com Let me know when we're meeting

- Benji: bzusman@gmail.com 

-Keegan keegan.hines@gmail.com

-Christa (maybe- I'm competent at the very basics, but could still use some help)

- Riccardo: fusaroli@gmail.com

- Oleksandr: krystoferivanov@gmail.com

- Nona: nona.karalashvili@gmail.com

- Xiaoli: xiaolidong2008@gmail.com

- Abby: Abbyhorn@Mit.edu

- Marco: maduenase@gmail.com

- Nick: goudemand at pim dot uzh dot ch

- Fabio: fabio.cresto-aleina@zmaw.de

- Joanne: joannerodrigues@berkeley.edu

- Hide: hi55 at cornell dot edu

- Priya: iitm.priya@gmail.com

- Miguel: miguel.lurgi@icm.csic.es

- Oscar: opatters@asu.edu

- Vanessa: vanferdi at gmail dot com

- Georg G: gmg at stat dot cmu dot edu dot notthelastpart

- Oleksandr: krystoferivanov@gmail.com

===Information Theory===
Interested in turning your data into bits, or seeing how the bits over there are related to the bits over here? If so, sign up below.

- Matteo

- Benji: bzusman@gmail.com

-Keegan keegan.hines@gmail.com

-Riccardo

-Christa

- Katrien

- Xiaoli

- Abby

- Jasmeen

- Hide

- Sanith

- Priya

- Georg W.

- Piotr

- Miguel

- Oscar

- Vanessa

- Nona

- Georg G.

- Oleksandr krystoferivanov@gmail.com

===Computational Mechanics===
If you'd like to know more about epsilon machines, measures of complexity, how to go from a map to a machine, i'm happy to discuss it all. 
- Matteo

Yes please! --Chloe

-Keegan keegan.hines@gmail.com

-Christa

-Xiaoli

-Jasmeen

-Hide

-Sanith

- Priya

- Georg W.

-Piotr

-Ian

- Miguel

- Oscar

- Abby

- Georg G.

- Riccardo.

==Order Book Dynamics: Learn how to trade in 15min==

--I'm happy to repeat this -just get in touch with me.--

If you are curious about how stocks trade and want to try your luck, I'll
be going over some of the basics with a hands-on example.

Meet at 7.30pm in main lecture hall Thursday June 7th. Please make sure
to bring your laptop.

Sanith

==Update==

Hi guys

I guess the main lecture hall is free at 6.30 pm and so we can meet there. I have a small talk through the idea and then maybe we can try out getting bifurcation plots for one or two systems. I use software written in MATLAB for the demo but the idea can be implemented in any software.

Here's a link to the [[software for numerical continuation|http://twr.cs.kuleuven.be//research/software/delay/notice.shtml]]. This software can handle systems with time delays and can be used to obtain the bifurcation behaviour.

(1) Please download the software DDE-BIFTOOL and unzip.

(2) Within the folder, you will find another zipped folder in small case ‘ddebiftool’. Please unzip this into a folder with the same name

(3) Add the location of the folder to the path of MATLAB.
I have also sent out a mail with a zipped folder containing files to get a bifurcation plot for a Rijke tube system.
Do let me know if anyone did not get this.
See you there!

Priya

==An easier way to get a bifurcation plot==

Hey guys
I have been working in the past in obtaining bifurcation plots for different physical systems. There's a better way to get these pictures instead of getting the evolution at every parameter value of interest. This is called ''numerical continuation'' and basically involves tracking a curve. I plan to give a informal talk on how to do this and maybe even a demo on applying this technique on 14th June at 6.30 pm. Do mail me if you are interested at '''iitm.priya@gmail.com''' or sign up below.
[[User:Priya|Priya]]

- [[Ryan James|Ryan]] is interested in this. 
- Riccardo is interested in this. 
- Vikram is interested in this. 
- Matteo is interested in this. 
- Hide is interested in this. 
- Katrien wants to hear more about this. 
- Cameron is interested in this and would like to see [http://itunes.apple.com/us/app/xpp/id433859546?mt=8 this] in action if anyone has an iPad. 
- Oscar is interested in this. 
- Charlie is interested in this. (I've done this once for a paper.) 
- Georg W. is interested in this 

==Using Tisean on R on OS X==
first install TISEAN, like you've done already. Make sure R is up to date (v 2.15).
you can try to install RTisean from CRAN
install.packages("RTisean"); library(RTisean); henon()
But me and Dave both got an error about some bad file name, something about con and something about a long path involving -Tmp-
Solution:
remove.packages("RTisean")
restart R
download this: http://cl.ly/0I0b2P2L311y1q0q0y0n
install it, it changes line 74 of nativeTISEAN.R which has some problems with file handling
If you are golden, then:
> henon()
V1 V2
[1,] -0.1232481 -1.030383

==A conceptual shell==

One thing that I think has been missing from this course is an explicit set of concepts and tools which we can use to relate all of the talks we've been listening to. Last fall, two other graduates students and I taught a survey course on complexity. We put together the following document, which contains one-paragraph summaries of what we felt were the 20 most important concepts that comprised the field of complexity. These were the "glue" that we used to relate all of our lectures and workshops. Most of these will probably be familiar to you, but I think they serve as a nice, concise reference and may be helpful in tying all of this information overload together. One caveat: These are works in progress and are in alphabetical rather than any logical conceptual order.

[[Media:Topics_in_Complexity_Foundational_Definitions.pdf]]

Cheers,
Mark Longo

== Hierarchical Dirichlet Processes and the Infinite Hidden Markov Model ==

Over the past week, I've discussed Hierarchical Dirichlet Processes (HDP) and the Infinite Hidden Markov Model (iHMM) with several of you. Basically, it's the only framework I've come across, aside from Jim Crutchfield's work on the epsilon machine, that offers the diligent student the ability to estimate the hidden states generating one's data, without requiring the analyst a priori specify the number of hidden states (a very nice feature). One of the most significant differences between these approaches is Crutchfield's requires a finite alphabet, whereas HDP is defined in the context of an infinite number of base probability measures (think clustering). I believe they are both worth knowing, and I'm willing to offer a tutorial on the topics of HDP and iHHM. I'm thinking Tuesday at 7pm (after dinner) in the conference room is our best bet. If you are interested, please do have a look at the following paper by Yee Whye Teh:
*[[HDP(2005)Teh&Jordan.pdf‎]]
It can get a little abstract, infinite partitions nested in infinite partitions, so try to check it out beforehand if you plan to attend. If you have any questions, fire me an email: jlong29@gmail.com
Thanks,
John

Please sign up:

-[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-Tutorials

2012-06-19T18:58:20Z

CRSmith: /* Markov Chain Monte Carlo */

{{Complex Systems Summer School 2012}}

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.

==Fractal Tutorial??==

Hi, I have a request for a tutorial: Could anyone who has the expertise please teach a tutorial on fractal theory and codes to generate some?
Thanks! -Jasmeen

==Python online materials==
[Follow up to Ryan's tutorial..]

Here you have some useful online references for getting started in Python.

=== Google's Python Class ===
* A ''[...] free class for people with a little bit of programming experience who want to learn Python. The class includes written materials, lecture videos, and lots of code exercises to practice Python coding [...]''
* http://code.google.com/edu/languages/google-python-class/

=== Numpy, Scipy and Matplotlib tutorials ===
* I.e.: all the things you typically do in Matlab done in Python..
* NumPy tutorial: http://www.scipy.org/Tentative_NumPy_Tutorial
* Matplotlib tutorial: http://matplotlib.sourceforge.net/users/pyplot_tutorial.html
* Numpy for Matlab Users (extremely useful!!!): http://www.scipy.org/NumPy_for_Matlab_Users

=== NetworkX ===
* I.e.: network analysis in Python
* NetworkX tutorial: http://networkx.lanl.gov/tutorial/index.html

=== Enthought Python Distribution ===
* ''The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.''
* It is free (!!!): http://www.enthought.com/products/edudownload.php

=== Additional References ===
* Py4Science: a Starter Kit (by Fernando Perez, U.C. Berkeley)
* http://fperez.org/py4science/starter_kit.html

Hope this helps,

Matteo

==Non-linear measures of correlation==

I have been working on how to quantify the reciprocal interaction of time-series over time. I am using Recurrence Plots (http://www.recurrence-plot.tk/glance.php). If anybody is interested in discussing this method, I am willing to prepare a small tutorial on what recurrence plots are and how I have been using them.

Riccardo (fusaroli@gmail.com)

- Matteo

- Oleksandr krystoferivanov@gmail.com

- Priya

- Friederike

- Miguel

- Vikram

==Intro to Philosophy of Science==

Hi All, I've heard some interest in having a more structured/rigorous intro to ideas in the philosophy of science. I'd be happy to briefly explain some of the classic theories as well as some more recent views due to, e.g. Bas Van Fraassen, James Ladyman, Nancy Cartwright, and we could have a small (moderated!) group discussion. Sign up if interested... -Jasmeen

- Hide is interested and has a crush on Engels

- Friederike

- Matteo

- Vikram

- Mikkel

- Mark (!)

-Keegan is down

-Xiaoli

- Georg W.

- Priya

- Miguel

==Markov Chain Monte Carlo==
If anyone is interested in talking more about Bayesian methods and MCMC implementation, I'd be happy to put something together. - Keegan

-Hide is interested in this!

-Abby

-Joanne

-Oscar

-Vanessa

-Jasmeen

-Georg

-Nona

-benji

-Riccardo

-Matteo

-Cameron

- Priya

-Xiaoli

- Vikram

- Miguel

==Python, Computational Mechanics, and Information Theory==

There has been interest in more discussion on a number of topics, and so i'm offering to have evening discussions on them. please sign up below so that i can get a feel for the number of people who would be attending. also, please put a preference for what day it should be.

===Python===
Sign up below if you'd like an introduction to basic python programming. Python is a general purpose, very flexible and useful programming language. It is used pretty extensively in scientific computing.

dan wu: wu12345@gmail.com Let me know when we're meeting

- Benji: bzusman@gmail.com 

-Keegan keegan.hines@gmail.com

-Christa (maybe- I'm competent at the very basics, but could still use some help)

- Riccardo: fusaroli@gmail.com

- Oleksandr: krystoferivanov@gmail.com

- Nona: nona.karalashvili@gmail.com

- Xiaoli: xiaolidong2008@gmail.com

- Abby: Abbyhorn@Mit.edu

- Marco: maduenase@gmail.com

- Nick: goudemand at pim dot uzh dot ch

- Fabio: fabio.cresto-aleina@zmaw.de

- Joanne: joannerodrigues@berkeley.edu

- Hide: hi55 at cornell dot edu

- Priya: iitm.priya@gmail.com

- Miguel: miguel.lurgi@icm.csic.es

- Oscar: opatters@asu.edu

- Vanessa: vanferdi at gmail dot com

- Georg G: gmg at stat dot cmu dot edu dot notthelastpart

- Oleksandr: krystoferivanov@gmail.com

===Information Theory===
Interested in turning your data into bits, or seeing how the bits over there are related to the bits over here? If so, sign up below.

- Matteo

- Benji: bzusman@gmail.com

-Keegan keegan.hines@gmail.com

-Riccardo

-Christa

- Katrien

- Xiaoli

- Abby

- Jasmeen

- Hide

- Sanith

- Priya

- Georg W.

- Piotr

- Miguel

- Oscar

- Vanessa

- Nona

- Georg G.

- Oleksandr krystoferivanov@gmail.com

===Computational Mechanics===
If you'd like to know more about epsilon machines, measures of complexity, how to go from a map to a machine, i'm happy to discuss it all. 
- Matteo

Yes please! --Chloe

-Keegan keegan.hines@gmail.com

-Christa

-Xiaoli

-Jasmeen

-Hide

-Sanith

- Priya

- Georg W.

-Piotr

-Ian

- Miguel

- Oscar

- Abby

- Georg G.

- Riccardo.

==Order Book Dynamics: Learn how to trade in 15min==

--I'm happy to repeat this -just get in touch with me.--

If you are curious about how stocks trade and want to try your luck, I'll
be going over some of the basics with a hands-on example.

Meet at 7.30pm in main lecture hall Thursday June 7th. Please make sure
to bring your laptop.

Sanith

==Update==

Hi guys

I guess the main lecture hall is free at 6.30 pm and so we can meet there. I have a small talk through the idea and then maybe we can try out getting bifurcation plots for one or two systems. I use software written in MATLAB for the demo but the idea can be implemented in any software.

Here's a link to the [[software for numerical continuation|http://twr.cs.kuleuven.be//research/software/delay/notice.shtml]]. This software can handle systems with time delays and can be used to obtain the bifurcation behaviour.

(1) Please download the software DDE-BIFTOOL and unzip.

(2) Within the folder, you will find another zipped folder in small case ‘ddebiftool’. Please unzip this into a folder with the same name

(3) Add the location of the folder to the path of MATLAB.
I have also sent out a mail with a zipped folder containing files to get a bifurcation plot for a Rijke tube system.
Do let me know if anyone did not get this.
See you there!

Priya

==An easier way to get a bifurcation plot==

Hey guys
I have been working in the past in obtaining bifurcation plots for different physical systems. There's a better way to get these pictures instead of getting the evolution at every parameter value of interest. This is called ''numerical continuation'' and basically involves tracking a curve. I plan to give a informal talk on how to do this and maybe even a demo on applying this technique on 14th June at 6.30 pm. Do mail me if you are interested at '''iitm.priya@gmail.com''' or sign up below.
[[User:Priya|Priya]]

- [[Ryan James|Ryan]] is interested in this. 
- Riccardo is interested in this. 
- Vikram is interested in this. 
- Matteo is interested in this. 
- Hide is interested in this. 
- Katrien wants to hear more about this. 
- Cameron is interested in this and would like to see [http://itunes.apple.com/us/app/xpp/id433859546?mt=8 this] in action if anyone has an iPad. 
- Oscar is interested in this. 
- Charlie is interested in this. (I've done this once for a paper.) 
- Georg W. is interested in this 

==Using Tisean on R on OS X==
first install TISEAN, like you've done already. Make sure R is up to date (v 2.15).
you can try to install RTisean from CRAN
install.packages("RTisean"); library(RTisean); henon()
But me and Dave both got an error about some bad file name, something about con and something about a long path involving -Tmp-
Solution:
remove.packages("RTisean")
restart R
download this: http://cl.ly/0I0b2P2L311y1q0q0y0n
install it, it changes line 74 of nativeTISEAN.R which has some problems with file handling
If you are golden, then:
> henon()
V1 V2
[1,] -0.1232481 -1.030383

==A conceptual shell==

One thing that I think has been missing from this course is an explicit set of concepts and tools which we can use to relate all of the talks we've been listening to. Last fall, two other graduates students and I taught a survey course on complexity. We put together the following document, which contains one-paragraph summaries of what we felt were the 20 most important concepts that comprised the field of complexity. These were the "glue" that we used to relate all of our lectures and workshops. Most of these will probably be familiar to you, but I think they serve as a nice, concise reference and may be helpful in tying all of this information overload together. One caveat: These are works in progress and are in alphabetical rather than any logical conceptual order.

[[Media:Topics_in_Complexity_Foundational_Definitions.pdf]]

Cheers,
Mark Longo

Talk:Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-13T05:34:07Z

CRSmith: Created page with 'If anyone is interested in the [http://en.wikipedia.org/wiki/Optical_feedback video feedback] experiment, there's a nice presentation [http://www.eudonev.com/physics/vidback_slid…'

If anyone is interested in the [http://en.wikipedia.org/wiki/Optical_feedback video feedback] experiment, there's a nice presentation [http://www.eudonev.com/physics/vidback_slideshow/index.html here] and a list of work on the topic [http://softology.com.au/videofeedback/videofeedback.htm here]. -[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-Tutorials

2012-06-12T20:57:19Z

CRSmith: /* An easier way to get a bifurcation plot */

{{Complex Systems Summer School 2012}}

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.

==Order Book Dynamics: Learn how to trade in 15min==

--I'm happy to repeat this -just get in touch with me.--

If you are curious about how stocks trade and want to try your luck, I'll
be going over some of the basics with a hands-on example.

Meet at 7.30pm in main lecture hall Thursday June 7th. Please make sure
to bring your laptop.

Sanith

==An easier way to get a bifurcation plot==

Hey guys
I have been working in the past in obtaining bifurcation plots for different physical systems. There's a better way to get these pictures instead of getting the evolution at every parameter value of interest. This is called ''numerical continuation'' and basically involves tracking a curve. I plan to give a informal talk on how to do this and maybe even a demo on applying this technique on 14th June at 6.30 pm. Do mail me if you are interested at '''iitm.priya@gmail.com''' or sign up below.
[[User:Priya|Priya]]

- [[Ryan James|Ryan]] is interested in this. 
- Riccardo is interested in this. 
- Vikram is interested in this. 
- Matteo is interested in this. 
- Hide is interested in this. 
- Katrien wants to hear more about this. 
- Cameron is interested in this and would like to see [http://itunes.apple.com/us/app/xpp/id433859546?mt=8 this] in action if anyone has an iPad. 

==Using Tisean on R on OS X==
first install TISEAN, like you've done already. Make sure R is up to date (v 2.15).
you can try to install RTisean from CRAN
install.packages("RTisean"); library(RTisean); henon()
But me and Dave both got an error about some bad file name, something about con and something about a long path involving -Tmp-
Solution:
remove.packages("RTisean")
restart R
download this: http://cl.ly/0I0b2P2L311y1q0q0y0n
install it, it changes line 74 of nativeTISEAN.R which has some problems with file handling
If you are golden, then:
> henon()
V1 V2
[1,] -0.1232481 -1.030383

Complex Systems Summer School 2012-Tutorials

2012-06-12T20:52:00Z

CRSmith: /* An easier way to get a bifurcation plot */

{{Complex Systems Summer School 2012}}

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.

==Order Book Dynamics: Learn how to trade in 15min==

--I'm happy to repeat this -just get in touch with me.--

If you are curious about how stocks trade and want to try your luck, I'll
be going over some of the basics with a hands-on example.

Meet at 7.30pm in main lecture hall Thursday June 7th. Please make sure
to bring your laptop.

Sanith

==An easier way to get a bifurcation plot==

Hey guys
I have been working in the past in obtaining bifurcation plots for different physical systems. There's a better way to get these pictures instead of getting the evolution at every parameter value of interest. This is called ''numerical continuation'' and basically involves tracking a curve. I plan to give a informal talk on how to do this and maybe even a demo on applying this technique on 14th June at 6.30 pm. Do mail me if you are interested at '''iitm.priya@gmail.com''' or sign up below.
[[User:Priya|Priya]]

- [[Ryan James|Ryan]] is interested in this. 
- Riccardo is interested in this. 
- Vikram is interested in this. 
- Matteo is interested in this. 
- Hide is interested in this. 
- Katrien wants to hear more about this. 
- Cameron is interested in this. 

==Using Tisean on R on OS X==
first install TISEAN, like you've done already. Make sure R is up to date (v 2.15).
you can try to install RTisean from CRAN
install.packages("RTisean"); library(RTisean); henon()
But me and Dave both got an error about some bad file name, something about con and something about a long path involving -Tmp-
Solution:
remove.packages("RTisean")
restart R
download this: http://cl.ly/0I0b2P2L311y1q0q0y0n
install it, it changes line 74 of nativeTISEAN.R which has some problems with file handling
If you are golden, then:
> henon()
V1 V2
[1,] -0.1232481 -1.030383

File:Qihc-arrow.pdf

2012-06-12T19:34:44Z

CRSmith:

File:Qihc arrow.png

2012-06-12T19:34:03Z

CRSmith:

Complex Systems Summer School 2012-TShirts

2012-06-12T19:33:45Z

CRSmith:

{{Complex Systems Summer School 2012}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

Have fun and be creative!

==2012 CSSS T-Shirt Design Submissions==
[[File:Urania.jpg]]

Urania blowing seeds of complexity

This is a draft I prepared a late evening some time before the CSSS. I didn't know at that time that the dorms have muse names and that I'll end up in the Urania...

Urania was the muse of Astronomy and also the Muse of Mathematics. she was often depicted holding a globe in her hands. In this case the cubist face and hands of Urania are borrowed from Picasso and she holds a SFI globe/dandelion flower head, on which she blows in order to disperse the seeds of complexity.

In my view this would need some serious polishing and volunteers to do so are welcome! Feedbacks also!

Cheers, Nick Goudemand

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

[[File:SFI transit small.jpg]]

SFI transit: the next generation of innovation is coming!

One more design.

Cheers, Nick G

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

[[File:SFI transit small 2.jpg]]

SFI transit: the next generation of innovation is coming!

An alternative version of the SFI transit in front of apple design....thanks to Sander for the suggestion.

Nick G
------------------------------------------------------------------------------------------------------

[[File:SFI logo with transit2.jpg]]

Venus transit in front of SFI logo

another proposition: urania in the back and this logo with the Venus transit in the front of Tshirt.

Nick

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

[[File:T shirt.jpg]]

Crystals are a prime manifestation of complexity. The design (front and back) represents crystals grown in cell culture dishes as seen under the microscope. The picture on the right has been mapped on a canvas with polar coordinates to show more symmetrical structure and avoid having a beginning and an end. (One from Georg Weber)

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

Simple Systems Summer School (SSSS) Rejects

(from Charlie)

(not necessarily white; and not necessarily this font and logo)

[[File:SSSSR.png]]

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

Black shirt:

Obviously I am very bad at photoshop, but I hope you get my idea. We can work on the final design with someone with experience in graphics design.

Also, I would like the SFI logo in the back of the shirt, small and up near the neck.

(from Miguel)

[[File:T-shirt.png]]

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

White shirt:

Also needs some refinement with the help of a graphic designer. And we have to narrow down the colors (I didn't know only two colors possible).

Maybe this picture can go in the back and the SFI logo in front in the middle of the chest?

(from Miguel)

[[File:Network-shirt.jpg]]

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

Rossler attractor mountains & sun (rough idea)

[[File:rosslermountain.jpg]]

-Jasmeen

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

Another idea, which someone who knows NetLogo could help me make: a network of all the students in the summer school, connected via project links?? (or some other link?) (N.B. we can only use two colours, so can't have multi-coloured agents.)

-Jasmeen

----
Fractal tree and code

[[File:Fractal_and_code.png]]

-Mark and Nick

----
Mountains and cantor set

[[File:Mountains_and_Cantor_Set.png]]

And another - Sarah's idea.

-Mark

----

[[File:qihc.png]]

[[Cameron Ray Smith|Cameron]]

----

[[File:qihc_arrow.png]]

[[File:qihc-arrow.pdf]]

[[Cameron Ray Smith|Cameron]]

----

=== Complexity Triptych ===

[[File:Tshirt.smt.jpg]]

A triptych. Culture (Native American mural at Bandelier), modeling/mathematics (cellular automata from the Crutchfield lecture), and biology/nature (pigment patterning on Olivia porphyria).

Could use some fine tuning! -- Sarah

Complex Systems Summer School 2012-TShirts

2012-06-12T18:09:17Z

CRSmith:

{{Complex Systems Summer School 2012}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

Have fun and be creative!

==2012 CSSS T-Shirt Design Submissions==
[[File:Urania.jpg]]

Urania blowing seeds of complexity

This is a draft I prepared a late evening some time before the CSSS. I didn't know at that time that the dorms have muse names and that I'll end up in the Urania...

Urania was the muse of Astronomy and also the Muse of Mathematics. she was often depicted holding a globe in her hands. In this case the cubist face and hands of Urania are borrowed from Picasso and she holds a SFI globe/dandelion flower head, on which she blows in order to disperse the seeds of complexity.

In my view this would need some serious polishing and volunteers to do so are welcome! Feedbacks also!

Cheers, Nick Goudemand

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

[[File:SFI transit small.jpg]]

SFI transit: the next generation of innovation is coming!

One more design.

Cheers, Nick G

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

[[File:SFI transit small 2.jpg]]

SFI transit: the next generation of innovation is coming!

An alternative version of the SFI transit in front of apple design....thanks to Sander for the suggestion.

Nick G
------------------------------------------------------------------------------------------------------

[[File:SFI logo with transit2.jpg]]

Venus transit in front of SFI logo

another proposition: urania in the back and this logo with the Venus transit in the front of Tshirt.

Nick

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

[[File:T shirt.jpg]]

Crystals are a prime manifestation of complexity. The design (front and back) represents crystals grown in cell culture dishes as seen under the microscope. The picture on the right has been mapped on a canvas with polar coordinates to show more symmetrical structure and avoid having a beginning and an end. (One from Georg Weber)

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

Simple Systems Summer School (SSSS) Rejects

(from Charlie)

(not necessarily white; and not necessarily this font and logo)

[[File:SSSSR.png]]

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

Black shirt:

Obviously I am very bad at photoshop, but I hope you get my idea. We can work on the final design with someone with experience in graphics design.

Also, I would like the SFI logo in the back of the shirt, small and up near the neck.

(from Miguel)

[[File:T-shirt.png]]

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

White shirt:

Also needs some refinement with the help of a graphic designer. And we have to narrow down the colors (I didn't know only two colors possible).

Maybe this picture can go in the back and the SFI logo in front in the middle of the chest?

(from Miguel)

[[File:Network-shirt.jpg]]

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

Rossler attractor mountains & sun (rough idea)

[[File:rosslermountain.jpg]]

-Jasmeen

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

Another idea, which someone who knows NetLogo could help me make: a network of all the students in the summer school, connected via project links?? (or some other link?) (N.B. we can only use two colours, so can't have multi-coloured agents.)

-Jasmeen

----

[[File:qihc.png]]

[[Cameron Ray Smith|Cameron]]

----

[[File:Qihc-arrow.png]]

[[File:qihc-arrows.pdf]]

[[Cameron Ray Smith|Cameron]]

File:Qihc-arrow.png

2012-06-12T18:08:31Z

CRSmith:

File:Qihc-arrows.png

2012-06-12T17:53:47Z

CRSmith:

Complex Systems Summer School 2012-TShirts

2012-06-12T17:53:16Z

CRSmith:

{{Complex Systems Summer School 2012}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

Have fun and be creative!

==2012 CSSS T-Shirt Design Submissions==
[[File:Urania.jpg]]

Urania blowing seeds of complexity

This is a draft I prepared a late evening some time before the CSSS. I didn't know at that time that the dorms have muse names and that I'll end up in the Urania...

Urania was the muse of Astronomy and also the Muse of Mathematics. she was often depicted holding a globe in her hands. In this case the cubist face and hands of Urania are borrowed from Picasso and she holds a SFI globe/dandelion flower head, on which she blows in order to disperse the seeds of complexity.

In my view this would need some serious polishing and volunteers to do so are welcome! Feedbacks also!

Cheers, Nick Goudemand

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

[[File:SFI transit small.jpg]]

SFI transit: the next generation of innovation is coming!

One more design.

Cheers, Nick G

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

[[File:SFI transit small 2.jpg]]

SFI transit: the next generation of innovation is coming!

An alternative version of the SFI transit in front of apple design....thanks to Sander for the suggestion.

Nick G
------------------------------------------------------------------------------------------------------

[[File:SFI logo with transit2.jpg]]

Venus transit in front of SFI logo

another proposition: urania in the back and this logo with the Venus transit in the front of Tshirt.

Nick

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

[[File:T shirt.jpg]]

Crystals are a prime manifestation of complexity. The design (front and back) represents crystals grown in cell culture dishes as seen under the microscope. The picture on the right has been mapped on a canvas with polar coordinates to show more symmetrical structure and avoid having a beginning and an end. (One from Georg Weber)

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

Simple Systems Summer School (SSSS) Rejects

(from Charlie)

(not necessarily white; and not necessarily this font and logo)

[[File:SSSSR.png]]

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

Black shirt:

Obviously I am very bad at photoshop, but I hope you get my idea. We can work on the final design with someone with experience in graphics design.

Also, I would like the SFI logo in the back of the shirt, small and up near the neck.

(from Miguel)

[[File:T-shirt.png]]

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

White shirt:

Also needs some refinement with the help of a graphic designer. And we have to narrow down the colors (I didn't know only two colors possible).

Maybe this picture can go in the back and the SFI logo in front in the middle of the chest?

(from Miguel)

[[File:Network-shirt.jpg]]

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

Rossler attractor mountains & sun (rough idea)

[[File:rosslermountain.jpg]]

-Jasmeen

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

Another idea, which someone who knows NetLogo could help me make: a network of all the students in the summer school, connected via project links?? (or some other link?) (N.B. we can only use two colours, so can't have multi-coloured agents.)

-Jasmeen

----

[[File:qihc.png]]

[[Cameron Ray Smith|Cameron]]

----

[[File:qihc-arrows.pdf]]

[[File:qihc-arrows.png]]

[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-TShirts

2012-06-12T17:53:03Z

CRSmith:

{{Complex Systems Summer School 2012}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

Have fun and be creative!

==2012 CSSS T-Shirt Design Submissions==
[[File:Urania.jpg]]

Urania blowing seeds of complexity

This is a draft I prepared a late evening some time before the CSSS. I didn't know at that time that the dorms have muse names and that I'll end up in the Urania...

Urania was the muse of Astronomy and also the Muse of Mathematics. she was often depicted holding a globe in her hands. In this case the cubist face and hands of Urania are borrowed from Picasso and she holds a SFI globe/dandelion flower head, on which she blows in order to disperse the seeds of complexity.

In my view this would need some serious polishing and volunteers to do so are welcome! Feedbacks also!

Cheers, Nick Goudemand

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

[[File:SFI transit small.jpg]]

SFI transit: the next generation of innovation is coming!

One more design.

Cheers, Nick G

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

[[File:SFI transit small 2.jpg]]

SFI transit: the next generation of innovation is coming!

An alternative version of the SFI transit in front of apple design....thanks to Sander for the suggestion.

Nick G
------------------------------------------------------------------------------------------------------

[[File:SFI logo with transit2.jpg]]

Venus transit in front of SFI logo

another proposition: urania in the back and this logo with the Venus transit in the front of Tshirt.

Nick

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

[[File:T shirt.jpg]]

Crystals are a prime manifestation of complexity. The design (front and back) represents crystals grown in cell culture dishes as seen under the microscope. The picture on the right has been mapped on a canvas with polar coordinates to show more symmetrical structure and avoid having a beginning and an end. (One from Georg Weber)

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

Simple Systems Summer School (SSSS) Rejects

(from Charlie)

(not necessarily white; and not necessarily this font and logo)

[[File:SSSSR.png]]

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

Black shirt:

Obviously I am very bad at photoshop, but I hope you get my idea. We can work on the final design with someone with experience in graphics design.

Also, I would like the SFI logo in the back of the shirt, small and up near the neck.

(from Miguel)

[[File:T-shirt.png]]

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

White shirt:

Also needs some refinement with the help of a graphic designer. And we have to narrow down the colors (I didn't know only two colors possible).

Maybe this picture can go in the back and the SFI logo in front in the middle of the chest?

(from Miguel)

[[File:Network-shirt.jpg]]

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

Rossler attractor mountains & sun (rough idea)

[[File:rosslermountain.jpg]]

-Jasmeen

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

Another idea, which someone who knows NetLogo could help me make: a network of all the students in the summer school, connected via project links?? (or some other link?) (N.B. we can only use two colours, so can't have multi-coloured agents.)

-Jasmeen

----

[[File:qihc.png]]

[[Cameron Ray Smith|Cameron]]

----

[[File:qihc-arrows.pdf]]
[[File:qihc-arrows.png]]

[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-TShirts

2012-06-12T17:52:31Z

CRSmith:

{{Complex Systems Summer School 2012}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

Have fun and be creative!

==2012 CSSS T-Shirt Design Submissions==
[[File:Urania.jpg]]

Urania blowing seeds of complexity

This is a draft I prepared a late evening some time before the CSSS. I didn't know at that time that the dorms have muse names and that I'll end up in the Urania...

Urania was the muse of Astronomy and also the Muse of Mathematics. she was often depicted holding a globe in her hands. In this case the cubist face and hands of Urania are borrowed from Picasso and she holds a SFI globe/dandelion flower head, on which she blows in order to disperse the seeds of complexity.

In my view this would need some serious polishing and volunteers to do so are welcome! Feedbacks also!

Cheers, Nick Goudemand

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

[[File:SFI transit small.jpg]]

SFI transit: the next generation of innovation is coming!

One more design.

Cheers, Nick G

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

[[File:SFI transit small 2.jpg]]

SFI transit: the next generation of innovation is coming!

An alternative version of the SFI transit in front of apple design....thanks to Sander for the suggestion.

Nick G
------------------------------------------------------------------------------------------------------

[[File:SFI logo with transit2.jpg]]

Venus transit in front of SFI logo

another proposition: urania in the back and this logo with the Venus transit in the front of Tshirt.

Nick

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

[[File:T shirt.jpg]]

Crystals are a prime manifestation of complexity. The design (front and back) represents crystals grown in cell culture dishes as seen under the microscope. The picture on the right has been mapped on a canvas with polar coordinates to show more symmetrical structure and avoid having a beginning and an end. (One from Georg Weber)

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

Simple Systems Summer School (SSSS) Rejects

(from Charlie)

(not necessarily white; and not necessarily this font and logo)

[[File:SSSSR.png]]

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

Black shirt:

Obviously I am very bad at photoshop, but I hope you get my idea. We can work on the final design with someone with experience in graphics design.

Also, I would like the SFI logo in the back of the shirt, small and up near the neck.

(from Miguel)

[[File:T-shirt.png]]

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

White shirt:

Also needs some refinement with the help of a graphic designer. And we have to narrow down the colors (I didn't know only two colors possible).

Maybe this picture can go in the back and the SFI logo in front in the middle of the chest?

(from Miguel)

[[File:Network-shirt.jpg]]

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

Rossler attractor mountains & sun (rough idea)

[[File:rosslermountain.jpg]]

-Jasmeen

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

Another idea, which someone who knows NetLogo could help me make: a network of all the students in the summer school, connected via project links?? (or some other link?) (N.B. we can only use two colours, so can't have multi-coloured agents.)

-Jasmeen

----

[[File:qihc.png]]

[[Cameron Ray Smith|Cameron]]

----

[[File:qihc-arrows.pdf]]

[[Cameron Ray Smith|Cameron]]

File:Qihc-arrows.pdf

2012-06-12T17:51:37Z

CRSmith:

Complex Systems Summer School 2012-TShirts

2012-06-12T17:50:35Z

CRSmith:

{{Complex Systems Summer School 2012}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

Have fun and be creative!

==2012 CSSS T-Shirt Design Submissions==
[[File:Urania.jpg]]

Urania blowing seeds of complexity

This is a draft I prepared a late evening some time before the CSSS. I didn't know at that time that the dorms have muse names and that I'll end up in the Urania...

Urania was the muse of Astronomy and also the Muse of Mathematics. she was often depicted holding a globe in her hands. In this case the cubist face and hands of Urania are borrowed from Picasso and she holds a SFI globe/dandelion flower head, on which she blows in order to disperse the seeds of complexity.

In my view this would need some serious polishing and volunteers to do so are welcome! Feedbacks also!

Cheers, Nick Goudemand

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

[[File:SFI transit small.jpg]]

SFI transit: the next generation of innovation is coming!

One more design.

Cheers, Nick G

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

[[File:SFI transit small 2.jpg]]

SFI transit: the next generation of innovation is coming!

An alternative version of the SFI transit in front of apple design....thanks to Sander for the suggestion.

Nick G
------------------------------------------------------------------------------------------------------

[[File:SFI logo with transit2.jpg]]

Venus transit in front of SFI logo

another proposition: urania in the back and this logo with the Venus transit in the front of Tshirt.

Nick

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

[[File:T shirt.jpg]]

Crystals are a prime manifestation of complexity. The design (front and back) represents crystals grown in cell culture dishes as seen under the microscope. The picture on the right has been mapped on a canvas with polar coordinates to show more symmetrical structure and avoid having a beginning and an end. (One from Georg Weber)

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

Simple Systems Summer School (SSSS) Rejects

(from Charlie)

(not necessarily white; and not necessarily this font and logo)

[[File:SSSSR.png]]

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

Black shirt:

Obviously I am very bad at photoshop, but I hope you get my idea. We can work on the final design with someone with experience in graphics design.

Also, I would like the SFI logo in the back of the shirt, small and up near the neck.

(from Miguel)

[[File:T-shirt.png]]

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

White shirt:

Also needs some refinement with the help of a graphic designer. And we have to narrow down the colors (I didn't know only two colors possible).

Maybe this picture can go in the back and the SFI logo in front in the middle of the chest?

(from Miguel)

[[File:Network-shirt.jpg]]

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

Rossler attractor mountains & sun (rough idea)

[[File:rosslermountain.jpg]]

-Jasmeen

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

Another idea, which someone who knows NetLogo could help me make: a network of all the students in the summer school, connected via project links?? (or some other link?) (N.B. we can only use two colours, so can't have multi-coloured agents.)

-Jasmeen

----

[[File:qihc.png]]

[[Cameron Ray Smith|Cameron]]

----

[[File:qihc-arrows.svg]]

[[Cameron Ray Smith|Cameron]]

Complex Systems Summer School 2012-TShirts

2012-06-12T17:09:33Z

CRSmith:

Complex Systems Summer School 2012-TShirts

2012-06-12T17:02:20Z

CRSmith:

File:Qihc.png

2012-06-12T17:01:04Z

CRSmith:

Robustness of complex networks (project)

2012-06-12T03:54:04Z

CRSmith: /* Participants */

[[File:Zoo.png|thumb|300px|Fig. 1. Zoo of complex networks (an example). Taken from Sol´e and Valverde, 2001.]]
== Problem statement ==
Complex networks have various properties which can be measured in real networks (WWW, social networks, biological networks), e.g. degree distribution, modularity, hierarchy, assortativity etc. Robustness of complex networks is a big question, however only some progress have been done in this direction. For example, it was shown that the scale-free networks are much more topologically robust to random attacks than random networks. Many people claim that various characteristics of complex networks will influence the robustness interdependently. The question I am interested in is how?

== Approach ==
The idea is to generate continuous topology space of various complex networks (networks with different modularity, degree distribution, hierarchy etc) and use it to measure their robustness (see Fig. 1). There are many approaches to measure the robustness of complex networks. For example we can remove edges of vertices of a complex network graph and look at the size of a giant cluster. We can discuss other possibilities.

If you are interested you can contact me directly or via my E-mail: krystoferivanov@gmail.com or via my [[Oleksandr Ivanov|discussion page in CSSS 2012 wiki]].

== Relevant literature ==
* ''Important papers about network generation are highlighted in bold''
* '''[http://www.barabasilab.com/pubs/CCNR-ALB_Publications/199910-15_Science-Emergence/199910-15_Science-Emergence.pdf BA Scale-free network]'''
* '''[http://people.maths.ox.ac.uk/maini/PKM%20publications/195.pdf How to generate Scale-free modular network using preferential attachment]'''
* '''[http://arxiv.org/pdf/cond-mat/0402009v1.pdf Scale-free networks with tunable degree distribution exponents]'''
* '''[http://arxiv.org/pdf/cond-mat/0110452v1.pdf Scale free networks with tunable clustering]'''
* [http://www.barabasilab.com/pubs/CCNR-ALB_Publications/200007-27_Nature-ErrorAttack/200007-27_Nature-ErrorAttack.pdf Error and attack tollerance of complex networks]
* [http://vw.indiana.edu/netsci06/conference/Ng_Structural.pdf Structural Robustness of Complex networks]
* [http://arxiv.org/pdf/cond-mat/0205405.pdf Assortative mixing in networks]
* [http://www.cis.upenn.edu/~mkearns/teaching/NetworkedLife/prefatt.pdf Mean field theory to study scale-free networks]
* [http://www.graphanalysis.org/SIAM-PP08/Leskovic.pdf Kroneker Graphs]
* [http://www.lem.sssup.it/WPLem/files/2011-07.pdf Exact maximum-likelihood method to detect patterns in real networks]
* [http://www-users.york.ac.uk/~lsdc1/SysBiol/kitano.robustness.naturegenetics.2004.pdf Biological robustness]
* [http://arxiv.org/ftp/cond-mat/papers/0202/0202410.pdf Attack vulnerability of complex networks]
* [http://jmvidal.cse.sc.edu/papers/nair11a.pdf Supply Network Topology and Robustness against Disruptions – an investigation using multi agent model]

* [http://arxiv.org/abs/cond-mat/0007235 Random graphs with arbitrary degree distributions and their applications]
* [http://www.pnas.org/content/104/1/36 Resolution limit in community detection] - about a typical modularity measure and its limitations

* Add a relevant paper...

== Learning Python ==
* [http://code.google.com/edu/languages/google-python-class/ Google's Python Class]
* [http://networkx.lanl.gov/tutorial/tutorial.html Networkx Python lybrary]
* [http://networkx.lanl.gov/reference/algorithms.html Networkx graph algorithms]
* [http://networkx.lanl.gov/reference/drawing.html Networkx drawing]

== Participants ==
# [[Oleksandr Ivanov]] - krystoferivanov@gmail.com
# [[Ian Wood]] - ibwood@indiana.edu
# [[Xin Lu]] - xin.lu@ki.se
# [[Duenas-Esterling Marco-Antonio]] - maduenase@gmail.com
# [[Katrien Beuls]] - katrien@ai.vub.ac.be
# [[Cameron Ray Smith]] - [http://www.google.com/recaptcha/mailhide/d?k=01_G1kMsuOrJhiwcXbYs5uYQ==&c=4iKaQQLKYQ-uUaepLzz3_1LdZfwZMM24y5sG4GTjP-4= c...@gmail.com] 

== Source Control ==
I've set up a github repository for any python source we write [https://github.com/ibwood/CSSS-Network-Robustness-Project here].
To figure out how to use Git look [http://git-scm.com/book here]. Chapters 1,2,3, and 5 are particularly relevant, but I can run through the basics with anyone. It's useful to have a source control for both project coordination and backup, and git is very simple once you get the hang of it.

There is a shared folder on skype, please either sign your email in the participant list or drop a email to [[Xin Lu]] to access the generated network data. Dropbox link [https://www.dropbox.com/sh/y6e5ukftde4yt7x/i4ZZ03Yr_5]

== BA algorithm in Python ==
* [http://networkx.lanl.gov/_modules/networkx/generators/random_graphs.html#barabasi_albert_graph Networkx source]

== BA network + modularity ==
* [http://networkx.lanl.gov/_modules/networkx/generators/random_graphs.html#powerlaw_cluster_graph Networkx source]

Bandelier Trip 2012

2012-06-08T07:03:10Z

CRSmith: /* STILL NEEDS A SEAT! */

{{Complex Systems Summer School 2012}}

Please sign up here so we know who's going. 
Also: If you have a car, please let us know. The more cars, the more people. 

We'll meet Saturday at 10:00am in the parking circle.

Please remember to bring a hat, sunscreen, water, hiking shoes, and anything else you'll need for a day out in the field.

If you would like to rent a car please visit the [http://santafe.edu/about/contact/ground/ SFI website] for more info

==Cars:==

===Tom's Sedan: 5 seats===
1. [[Nicholas Allgaier]] 

2. Vikram Vijayaraghavan 

3. Katrien Beuls 

4. Riccardo Fusaroli 

5. Priya Subramanian

===John Paul's Camry: 4 (maybe 5) seats===

1. [[John Paul]] 

2. [[Matteo Chinazzi]] 

3. [[Chloe Lewis]] 

4. [[Xue Feng]] 

5. [[Joanne Rodrigues]] 

===Juniper's Car: 4 seats===

1. Jasmeen Kanwal

2. Sarah Tweedt

3. Mark Longo

4. Hide Inamine

===[http://tuvalu.santafe.edu/events/workshops/index.php/Christa_Brelsford Christa]'s Car: 4 (maybe 5) seats===

1. Christa

2. Nicolas Goudemand

3. Marco

4. [http://tuvalu.santafe.edu/events/workshops/index.php/Xin_Lu Xin]

5(middle seat in a 2 door civic). [[Miguel Lurgi]]

===Charlie's car: 2 seats ===
My car's not that useful for this trip because I took out so many of the seats. I have only two seats besides the driver seat. Better than nothing.

1. Andres Gomez-Lievano

2. Vanessa Ferdinand

===STILL NEEDS A SEAT!===
1. Benji zusman

2. [[Piotr Milanowski | Piotr]]

3. Georg M Goerg

4. Oleksandr Ivanov

5. Ben Althouse

6. Georg Weber

7. Oscar Patterson

8. David Pugh

9. Abby Horn

10. Ian Wood

11. Friederike Greb

12. Jianfeng Xu

13. Tom Fennewald

14. Mikkel Vestergaard

15. Nona Karalashvili

16. Elena del Val

17. Gareth Haslam

18. Cameron Smith

Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-07T05:50:57Z

CRSmith: /* Tuesday, June 12, 6:00pm */

{{Complex Systems Summer School 2012}}

==Thursday, June 7, 6:00pm==

1. Sarah Tweedt 
2. Georg F. Weber 
3. Georg M. Goerg 
4. Mikkel Vestergaard 
5. Friederike Greb 
6. Fabio Cresto Aleina 
7. Benji zusman 
8. Elena del Val 
9. Riccardo Fusaroli 
10. Nick Allgaier 
11. John Long 
12. Sepehr Ehsani 
13. David Pugh 
14. Keegan Hines 
15. Sanith 
16.

==Friday, June 8 7:00am==
PLEASE NOTE THAT THIS IS AN EARLY MORNING CLASS! 
1. Matteo Chinazzi 
2. Nona Karalashvili 
3. Xin Lu 
4. Joanne Rodrigues 
5. Chloe Lewis 
6. Seth Frey 
7. Graham Sack 
8. Piotr Milanowski 
9. Andres Gomez-Lievano 
10.Ian Wood 
11.Gareth Haslam 
12.Christa Brelsford 
13. 
14. 
15. 

==Monday, June 11, 6:00pm==
1. Hidetoshi Inamine 
2. Dan Wu 
3. Xiaoli Dong 
4. Si Tang 
5. Abby Horn 
6. Xue Feng 
7. Priya Subramanian 
8. Oscar Patterson 
9. Vanessa Ferdinand 
10.Tom Fennewald 
11.Jianfeng Xu 
12.Nicolas Goudemand 
13.Katrien Beuls 
14.Charlie Brummitt 
15.Ben Althouse 

==Tuesday, June 12, 6:00pm==
1. Marco Duenas

2. Jasmeen Kanwal 
3. Shawana Wilson 
4. Miguel Lurgi 
5. Vikram Vijayaraghavan 
6. Mark Longo 
7. Oleksandr Ivanov 
8. Jon Stoffel 
9. Daniel Strombom 
10. Cameron Smith 
11. 
12. 
13. 
14. 
15.

Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-07T05:50:41Z

CRSmith: /* Tuesday, June 12, 6:00pm */

{{Complex Systems Summer School 2012}}

==Thursday, June 7, 6:00pm==

1. Sarah Tweedt 
2. Georg F. Weber 
3. Georg M. Goerg 
4. Mikkel Vestergaard 
5. Friederike Greb 
6. Fabio Cresto Aleina 
7. Benji zusman 
8. Elena del Val 
9. Riccardo Fusaroli 
10. Nick Allgaier 
11. John Long 
12. Sepehr Ehsani 
13. David Pugh 
14. Keegan Hines 
15. Sanith 
16.

==Friday, June 8 7:00am==
PLEASE NOTE THAT THIS IS AN EARLY MORNING CLASS! 
1. Matteo Chinazzi 
2. Nona Karalashvili 
3. Xin Lu 
4. Joanne Rodrigues 
5. Chloe Lewis 
6. Seth Frey 
7. Graham Sack 
8. Piotr Milanowski 
9. Andres Gomez-Lievano 
10.Ian Wood 
11.Gareth Haslam 
12.Christa Brelsford 
13. 
14. 
15. 

==Monday, June 11, 6:00pm==
1. Hidetoshi Inamine 
2. Dan Wu 
3. Xiaoli Dong 
4. Si Tang 
5. Abby Horn 
6. Xue Feng 
7. Priya Subramanian 
8. Oscar Patterson 
9. Vanessa Ferdinand 
10.Tom Fennewald 
11.Jianfeng Xu 
12.Nicolas Goudemand 
13.Katrien Beuls 
14.Charlie Brummitt 
15.Ben Althouse 

==Tuesday, June 12, 6:00pm==
1. Marco Duenas

2. Jasmeen Kanwal 
3. shawana Wilson 
4. Miguel Lurgi 
5. Vikram Vijayaraghavan 
6. Mark Longo 
7. Oleksandr Ivanov 
8. Jon Stoffel 
9. Daniel Strombom 
10. Cameron Smith 
11. 
12. 
13. 
14. 
15.

Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-07T05:50:16Z

CRSmith: /* Thursday, June 7, 6:00pm */

{{Complex Systems Summer School 2012}}

==Thursday, June 7, 6:00pm==

1. Sarah Tweedt 
2. Georg F. Weber 
3. Georg M. Goerg 
4. Mikkel Vestergaard 
5. Friederike Greb 
6. Fabio Cresto Aleina 
7. Benji zusman 
8. Elena del Val 
9. Riccardo Fusaroli 
10. Nick Allgaier 
11. John Long 
12. Sepehr Ehsani 
13. David Pugh 
14. Keegan Hines 
15. Sanith 
16.

==Friday, June 8 7:00am==
PLEASE NOTE THAT THIS IS AN EARLY MORNING CLASS! 
1. Matteo Chinazzi 
2. Nona Karalashvili 
3. Xin Lu 
4. Joanne Rodrigues 
5. Chloe Lewis 
6. Seth Frey 
7. Graham Sack 
8. Piotr Milanowski 
9. Andres Gomez-Lievano 
10.Ian Wood 
11.Gareth Haslam 
12.Christa Brelsford 
13. 
14. 
15. 

==Monday, June 11, 6:00pm==
1. Hidetoshi Inamine 
2. Dan Wu 
3. Xiaoli Dong 
4. Si Tang 
5. Abby Horn 
6. Xue Feng 
7. Priya Subramanian 
8. Oscar Patterson 
9. Vanessa Ferdinand 
10.Tom Fennewald 
11.Jianfeng Xu 
12.Nicolas Goudemand 
13.Katrien Beuls 
14.Charlie Brummitt 
15.Ben Althouse 

==Tuesday, June 12, 6:00pm==
1. Marco Duenas

2. Jasmeen Kanwal 
3. shawana Wilson 
4. Miguel Lurgi 
5.Vikram Vijayaraghavan 
6.Mark Longo 
7.Oleksandr Ivanov 
8.Jon Stoffel 
9. Daniel Strombom 
10. 
11. 
12. 
13. 
14. 
15.

Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-07T05:49:57Z

CRSmith: /* Thursday, June 7, 6:00pm */

{{Complex Systems Summer School 2012}}

==Thursday, June 7, 6:00pm==

1. Sarah Tweedt 
2. Georg F. Weber 
3. Georg M. Goerg 
4. Mikkel Vestergaard 
5. Friederike Greb 
6. Fabio Cresto Aleina 
7. Benji zusman 
8. Elena del Val 
9.Riccardo Fusaroli 
10. Nick Allgaier 
11.John Long 
12. Sepehr Ehsani 
13. David Pugh 
14.Keegan Hines 
15.Sanith 
16.

==Friday, June 8 7:00am==
PLEASE NOTE THAT THIS IS AN EARLY MORNING CLASS! 
1. Matteo Chinazzi 
2. Nona Karalashvili 
3. Xin Lu 
4. Joanne Rodrigues 
5. Chloe Lewis 
6. Seth Frey 
7. Graham Sack 
8. Piotr Milanowski 
9. Andres Gomez-Lievano 
10.Ian Wood 
11.Gareth Haslam 
12.Christa Brelsford 
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==Monday, June 11, 6:00pm==
1. Hidetoshi Inamine 
2. Dan Wu 
3. Xiaoli Dong 
4. Si Tang 
5. Abby Horn 
6. Xue Feng 
7. Priya Subramanian 
8. Oscar Patterson 
9. Vanessa Ferdinand 
10.Tom Fennewald 
11.Jianfeng Xu 
12.Nicolas Goudemand 
13.Katrien Beuls 
14.Charlie Brummitt 
15.Ben Althouse 

==Tuesday, June 12, 6:00pm==
1. Marco Duenas

2. Jasmeen Kanwal 
3. shawana Wilson 
4. Miguel Lurgi 
5.Vikram Vijayaraghavan 
6.Mark Longo 
7.Oleksandr Ivanov 
8.Jon Stoffel 
9. Daniel Strombom 
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Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-03T19:37:48Z

CRSmith: /* Thursday, June 7, 6:00pm */

{{Complex Systems Summer School 2012}}

==Thursday, June 7, 6:00pm==

1. Sarah Tweedt 
2. Georg F. Weber 
3. Georg M. Goerg 
4. Cameron Smith 
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==Friday, June 8 7:00am==
PLEASE NOTE THAT THIS IS AN EARLY MORNING CLASS! 
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==Monday, June 11, 6:00pm==
1. Hidetoshi Inamine 
2. Dan Wu 
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15. 

==Tuesday, June 12, 6:00pm==
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Cameron Ray Smith

2012-06-01T16:24:59Z

CRSmith:

[[Image:crs.jpg|thumb|left|alt=Showing off my Finnish heritage.|link=http://gplus.to/cameronraysmith/about|[http://en.wikipedia.org/wiki/Sisu sisu], [https://plus.google.com/u/0/106963659779905379276/about google+]]]

{{Complex Systems Summer School 2012}}

Hello! I am looking forward to meeting everyone in Santa Fe. I am excited to hear about everyone's research and to have the opportunity to work on a project that might be a seed for future collaboration. One short story is that I'm interested in evolution, network science, mathematics, computer science, and language.


A longer story is that in light of an internal struggle that I believe has explicitly confronted thinkers, at the least since [http://en.wikipedia.org/wiki/Critique_of_Pure_Reason Kant], my approach to research teeters about the fulcrum between rationalism and empiricism with respect to the order in which each is applied in attempts to cultivate knowledge.



My scientific research interests began with [http://en.wikipedia.org/wiki/Synthetic_biology synthetic biology] and the study of bacterial [http://en.wikipedia.org/wiki/Quorum_sensing quorum sensing] and broadened from there to include [http://en.wikipedia.org/wiki/Systems_biology systems biology] and the [http://en.wikipedia.org/wiki/Multicellular_organism#Evolutionary_history evolution of multicellularity]. I am now primarily interested in applying, as yet abstract, tools from mathematics and theoretical computer science to a [http://en.wikipedia.org/wiki/Mereology mereological] description of the evolution of hierarchical organization in biological systems that incorporates [http://en.wikipedia.org/wiki/Niche_construction niche construction] with selection in order to derive a more concrete computational model of such. In this context, and being at least a [http://en.wikipedia.org/wiki/Reductionism#Ontological_reductionism_2 token ontological reductionist], I am also interested in the hierarchical relationship between information representation in molecular and linguistic forms as may be addressed at the level of abstraction of [http://en.wikipedia.org/wiki/Semiotics semiotics].



Despite my affinity for abstraction, I have attempted to ground myself to "real" data via collaborations with developmental biologists in the study of genetic regulation of the cellular differentiation process associated with [http://en.wikipedia.org/wiki/Hematopoiesis hematopoiesis], immunologists in the study of synergistic interactions between neutralizing and enhancing antibodies to the [http://en.wikipedia.org/wiki/Anthrax_toxin anthrax toxin], cell biologists in the study of [http://en.wikipedia.org/wiki/Holliday_junction Holliday junction] formation and resolution during [http://en.wikipedia.org/wiki/Meiosis meiosis], and cancer biologists in the study of gene expression variability in a mouse model of colon cancer.

Cameron Ray Smith

2012-06-01T16:22:59Z

CRSmith:

[[Image:crs.jpg|thumb|left|alt=Showing off my Finnish heritage.|link=http://gplus.to/cameronraysmith/about|[http://en.wikipedia.org/wiki/Sisu sisu], [http://gplus.to/cameronraysmith/about google+]]]

{{Complex Systems Summer School 2012}}

Hello! I am looking forward to meeting everyone in Santa Fe. I am excited to hear about everyone's research and to have the opportunity to work on a project that might be a seed for future collaboration. One short story is that I'm interested in evolution, network science, mathematics, computer science, and language.


A longer story is that in light of an internal struggle that I believe has explicitly confronted thinkers, at the least since [http://en.wikipedia.org/wiki/Critique_of_Pure_Reason Kant], my approach to research teeters about the fulcrum between rationalism and empiricism with respect to the order in which each is applied in attempts to cultivate knowledge.



My scientific research interests began with [http://en.wikipedia.org/wiki/Synthetic_biology synthetic biology] and the study of bacterial [http://en.wikipedia.org/wiki/Quorum_sensing quorum sensing] and broadened from there to include [http://en.wikipedia.org/wiki/Systems_biology systems biology] and the [http://en.wikipedia.org/wiki/Multicellular_organism#Evolutionary_history evolution of multicellularity]. I am now primarily interested in applying, as yet abstract, tools from mathematics and theoretical computer science to a [http://en.wikipedia.org/wiki/Mereology mereological] description of the evolution of hierarchical organization in biological systems that incorporates [http://en.wikipedia.org/wiki/Niche_construction niche construction] with selection in order to derive a more concrete computational model of such. In this context, and being at least a [http://en.wikipedia.org/wiki/Reductionism#Ontological_reductionism_2 token ontological reductionist], I am also interested in the hierarchical relationship between information representation in molecular and linguistic forms as may be addressed at the level of abstraction of [http://en.wikipedia.org/wiki/Semiotics semiotics].



Despite my affinity for abstraction, I have attempted to ground myself to "real" data via collaborations with developmental biologists in the study of genetic regulation of the cellular differentiation process associated with [http://en.wikipedia.org/wiki/Hematopoiesis hematopoiesis], immunologists in the study of synergistic interactions between neutralizing and enhancing antibodies to the [http://en.wikipedia.org/wiki/Anthrax_toxin anthrax toxin], cell biologists in the study of [http://en.wikipedia.org/wiki/Holliday_junction Holliday junction] formation and resolution during [http://en.wikipedia.org/wiki/Meiosis meiosis], and cancer biologists in the study of gene expression variability in a mouse model of colon cancer.

User:CRSmith

2012-06-01T16:10:19Z

CRSmith: Created page with 'Cameron Ray Smith'

[[Cameron Ray Smith]]

Cameron Ray Smith

2012-06-01T16:09:29Z

CRSmith: Created page with '[http://en.wikipedia.org/wiki/Sisu sisu] {{Complex Systems Summer Sc…'

[[Image:crs.jpg|thumb|left|alt=Showing off my Finnish heritage.|link=http://gplus.to/cameronraysmith/about|[http://en.wikipedia.org/wiki/Sisu sisu]]]

{{Complex Systems Summer School 2012}}

Hello! I am looking forward to meeting everyone in Santa Fe. I am excited to hear about everyone's research and to have the opportunity to work on a project that might be a seed for future collaboration. One short story is that I'm interested in evolution, network science, mathematics, computer science, and language.


A longer story is that in light of an internal struggle that I believe has explicitly confronted thinkers, at the least since [http://en.wikipedia.org/wiki/Critique_of_Pure_Reason Kant], my approach to research teeters about the fulcrum between rationalism and empiricism with respect to the order in which each is applied in attempts to cultivate knowledge.



My scientific research interests began with [http://en.wikipedia.org/wiki/Synthetic_biology synthetic biology] and the study of bacterial [http://en.wikipedia.org/wiki/Quorum_sensing quorum sensing] and broadened from there to include [http://en.wikipedia.org/wiki/Systems_biology systems biology] and the [http://en.wikipedia.org/wiki/Multicellular_organism#Evolutionary_history evolution of multicellularity]. I am now primarily interested in applying, as yet abstract, tools from mathematics and theoretical computer science to a [http://en.wikipedia.org/wiki/Mereology mereological] description of the evolution of hierarchical organization in biological systems that incorporates [http://en.wikipedia.org/wiki/Niche_construction niche construction] with selection in order to derive a more concrete computational model of such. In this context, and being at least a [http://en.wikipedia.org/wiki/Reductionism#Ontological_reductionism_2 token ontological reductionist], I am also interested in the hierarchical relationship between information representation in molecular and linguistic forms as may be addressed at the level of abstraction of [http://en.wikipedia.org/wiki/Semiotics semiotics].



Despite my affinity for abstraction, I have attempted to ground myself to "real" data via collaborations with developmental biologists in the study of genetic regulation of the cellular differentiation process associated with [http://en.wikipedia.org/wiki/Hematopoiesis hematopoiesis], immunologists in the study of synergistic interactions between neutralizing and enhancing antibodies to the [http://en.wikipedia.org/wiki/Anthrax_toxin anthrax toxin], cell biologists in the study of [http://en.wikipedia.org/wiki/Holliday_junction Holliday junction] formation and resolution during [http://en.wikipedia.org/wiki/Meiosis meiosis], and cancer biologists in the study of gene expression variability in a mouse model of colon cancer.

File:Crs.jpg

2012-06-01T14:29:51Z

CRSmith: