Santa Fe Institute Events Wiki - User contributions [en]

Complex Systems Summer School 2012-Project Presentations

2012-06-27T02:40:02Z

CLewis: /* How Does a Stochastic Environment affect Community Assembly? */

{{Complex Systems Summer School 2012}}

Use this space to post project presentations and outlines. Include group members, a brief outline, and your slides.

=== Price-time Dynamics of Contracts Traded on Prediction Markets ===

Joanne, Vikram, Matteo, Sanith

Prediction markets have been shown to outperform traditional methods of polls and opinion surveys in forecasting future events. The futures contracts traded in these markets assess the expectation of occurrence of a variety of events spread across multiple domains (political, economic, entertainment, financial and weather). We explore the feasibility of 'predicting' the outcome of binary true/false prediction market contracts ahead of their expiry date using a neural-network based machine learning approach. In addition we focus on the characteristics of political-based contracts to establish whether they exhibit characteristic 'fundamental' properties.

=== How Complex Languages Replicate through Simple Brains ===

Katrien, Vanessa, Sandro, Cameron, Jasmeen

Through the use of an iterated learning experiment, we investigated the transmission of a "high entropy", randomised initial language through successive generations of participants. We want to see what features of the language replicated most easily, and what structure emerged by the end of the chain. Our hypothesis is that the language converges to a "low entropy" equilibrium state with a minimal number of words, morphemes, and form-meaning distinctions.

=== Collaboration in times of stress: an Agent Based Modelling approach ===

Fabio Cresto Aleina, Elena del Val, Tom Fennewald and Friederike Greb

We want to investigate the influence of exogenous stress on cooperative behaviour. We propose an agent based model in which the agents can be interpreted as farmers living in a water limited environment. With changes in precipitation patterns, the farmers undergo stress, and we observe how this impacts relationships among farmers and their properties.

=== Simple variation of the logistic map as a model to invoke questions on cellular protein trafficking ===
(Sepehr Ehsani, http://arxiv.org/abs/1206.5557)

Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown aspects of a biological system cannot provide more information about the set of biologically meaningful (e.g., 'hidden') states of the system than could be understood by the designer of the model ab initio. Here, the case is made for the utilization of such models to shift from a 'predictive' to a 'questioning' nature, and a simple natural-logarithm variation of the logistic polynomial map is presented that can invoke questions about protein trafficking in eukaryotic cells.

===Changes in Social Network Structure in Response to Crisis: Using Twitter data to Explore the Effect of the Tōhoku Earthquake.===

Christa Brelsford and Xin Lu

Abstract:
We use twitter data from 7 days before and after the Tōhoku Earthquake to explore how cooperation rates, social network structure and connectivity, and social network vulnerability changed in Japan in response to the disaster. An English language data set is collected for the same time period to use as a control. Data is collected for a period of 96 hours starting from March 4th 2011 2:46pm JST and for 96 hours beginning March 11th 2011 2:46 pm JST. The rate of cooperative behavior, measured by the occurrence of helping words in tweets increases slightly in the English dataset and by an order of magnitude in the Japanese dataset. A network analysis is also performed. Network edges are retweets and direct messages. In future work, we hope to explore whether problem solving capacity in a social system changes in response to crises, based on changes in the rate of cooperation and information transfer in a network.

=== The CSSS Network ===

Tom & Riccardo (with JP and others)

We will investigate the questions you are dying to know: What interesting interactions are revealed from the first 3 weeks of the Complex System Summer School survey? Have barriers between academic disciplines been broken down? Do power laws fit the data!? ...

Let us know if you have specific questions or if you would like to be involved in data analysis!

=== Is there a method in the madness? the dynamic structures of human language use ===

Priya and Riccardo

Psychiatric anecdotal reports point to the monotony, lack of emotion and sometimes intelligibility in many clinical populations. Linear measures of fluency and prosody, however, present only controversial differences between patients and healthy controls and only in unnatural phonations (i.e. say "aaaaa" for 30 secs).
We therefore go complex and chaotic on a set of more ecological recordings and transcriptions from 4 clinical populations (Asperger's, Schizophrenics, Depressed and Right Hemisphere Damage patients) as well as from healthy controls.
We then set a classifier-driven race: will non-linear analyses outcompete linear analyses in discriminating between pathologies?

=== Escaping the Poverty Trap: Modeling the Interplay Between Economic Growth and the Ecology of Infectious Disease ===

Georg, Ben, Laurent, Oscar

The dynamics of economies and infectious disease are inexorably linked: economic well-being influences health (sanitation, nutrition, etc) and health influences economic well-being (labor productivity lost to sickness and disease). Often societies are locked into "poverty traps" of poor health and poor economy. Here, we demonstrate poverty traps formed in models of infection and endogenous growth, as well as ways to break out of poverty traps. We explore two mechanisms of escape: one, through an influx of capital, and another through changing the percentage of GDP spent on healthcare. We find large influxes of capital is successful, but increasing health spending does not. Our results have important policy implications in the distribution of aid and within-country healthcare spending.

=== The Targeting and Timing of Treatment Influences the Emergence of Influenza Resistance in Structured Populations ===

Ben, Laurent, Oscar, Georg

Evolution of antiviral resistance in influenza carries large societal impacts through morbidity and mortality caused by treatment failure. Several previous studies put forth theory regarding the optimal timing, targeting and absolute level of treatment in populations. Few of these studies, however, have considered populations with explicit structure. Here we present a model of antiviral resistance on networks and explore the timing, targeting and levels of treatment. Interestingly, we find bistability as a result of treatment leading to the existence of an unstable manifold, above which successful treatment (i.e.: no resistance) is impossible. We find, contrary to previous results, that degree-targeted treatment is not optimal, and leads to higher levels of resistance than random treatment. Additionally, in accordance with previous results, we find an optimum level of treatment which is less than 100%. These findings findings have important consequences in guiding policy behind influenza treatment. The bistability indicates that caution should be taken when treating populations when the absolute numbers of infections are unknown. Positively, our results indicate that putting resources into targeted treatment is not necessary, random treatment is preferable.

=== Learning in Random Boolean Networks ===

Nick A., Keegan, Matteo, Vikram, Sarah, Mark

Inspired by biochemical networks which adapt on evolutionary timescales, neural networks that adapt during development and learning, and universal computation in cellular automata, we have implemented several models of learning in Random Boolean Networks (RBNs) in order to better understand the relationships between network structure, node interaction rules, and network output.

=== Enzyme Catalysis and the Outcome of Chemical Reactions ===
Piotr and Georg W.
Enzymes are catalysts that accelerate chemical reactions but do not affect their outcome. This traditional paradism was developed under artificail test tube conditions. Our project investigates the possibility that the presence of an enzyme can alter the course of a reaction if it takes place under more physiologic conditions.

=== How Does a Stochastic Environment affect Community Assembly? ===

Xue, Χλοε, Xiaoli

We are interested in how exogenous temporal variability in resource availability affects the community structure of organisms with different resource-use strategies. Organisms induce additional resource stress on each other through competition. This is an abstraction of an arid environment with unreliable rainfall; the organisms themselves have been abstracted to four unitless parameters that allocate their resources to different parts of their lifecycles. The system has memory, as the previous presence of an organism affects the resource transport mechanism (an abstraction of soil).

=== How Does a Network’s Structure Influence its Traceability? ===

Xin and Abby

We are interested in systematically studying the problem of finding the source of a contamination spread through a network. We model a contamination spreading through the food distribution network, which we represent by interconnections between farmers, distributors, and retailers, and construct an estimator for the outbreak source given only this structure. We show how the ability of the estimator to narrow down the source identification problem changes with the connectivity and the number of observations. We propose a measure for traceability, or the overall ability to identify the source of spreading given any set of outbreak observations, based on entropy. We show how this measure appropriately reflects the range of uncertainty in identifying the source. We believe this measure may be useful in the design of networks that are conducive to accurate identification of the source of contamination.

=== We Got the Skills to Pay the Bills===

Andrés, Charlie, Gareth, and Nick

Where does diversity in skills or occupations come from and why does it lead to more innovative cities?

Complex Systems Summer School 2012-Project Presentations

2012-06-27T02:37:04Z

CLewis: /* How Does a Stochastic Environment affect Community Assembly? */

{{Complex Systems Summer School 2012}}

Use this space to post project presentations and outlines. Include group members, a brief outline, and your slides.

=== Price-time Dynamics of Contracts Traded on Prediction Markets ===

Joanne, Vikram, Matteo, Sanith

Prediction markets have been shown to outperform traditional methods of polls and opinion surveys in forecasting future events. The futures contracts traded in these markets assess the expectation of occurrence of a variety of events spread across multiple domains (political, economic, entertainment, financial and weather). We explore the feasibility of 'predicting' the outcome of binary true/false prediction market contracts ahead of their expiry date using a neural-network based machine learning approach. In addition we focus on the characteristics of political-based contracts to establish whether they exhibit characteristic 'fundamental' properties.

=== How Complex Languages Replicate through Simple Brains ===

Katrien, Vanessa, Sandro, Cameron, Jasmeen

Through the use of an iterated learning experiment, we investigated the transmission of a "high entropy", randomised initial language through successive generations of participants. We want to see what features of the language replicated most easily, and what structure emerged by the end of the chain. Our hypothesis is that the language converges to a "low entropy" equilibrium state with a minimal number of words, morphemes, and form-meaning distinctions.

=== Collaboration in times of stress: an Agent Based Modelling approach ===

Fabio Cresto Aleina, Elena del Val, Tom Fennewald and Friederike Greb

We want to investigate the influence of exogenous stress on cooperative behaviour. We propose an agent based model in which the agents can be interpreted as farmers living in a water limited environment. With changes in precipitation patterns, the farmers undergo stress, and we observe how this impacts relationships among farmers and their properties.

=== Simple variation of the logistic map as a model to invoke questions on cellular protein trafficking ===
(Sepehr Ehsani, http://arxiv.org/abs/1206.5557)

Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown aspects of a biological system cannot provide more information about the set of biologically meaningful (e.g., 'hidden') states of the system than could be understood by the designer of the model ab initio. Here, the case is made for the utilization of such models to shift from a 'predictive' to a 'questioning' nature, and a simple natural-logarithm variation of the logistic polynomial map is presented that can invoke questions about protein trafficking in eukaryotic cells.

===Changes in Social Network Structure in Response to Crisis: Using Twitter data to Explore the Effect of the Tōhoku Earthquake.===

Christa Brelsford and Xin Lu

Abstract:
We use twitter data from 7 days before and after the Tōhoku Earthquake to explore how cooperation rates, social network structure and connectivity, and social network vulnerability changed in Japan in response to the disaster. An English language data set is collected for the same time period to use as a control. Data is collected for a period of 96 hours starting from March 4th 2011 2:46pm JST and for 96 hours beginning March 11th 2011 2:46 pm JST. The rate of cooperative behavior, measured by the occurrence of helping words in tweets increases slightly in the English dataset and by an order of magnitude in the Japanese dataset. A network analysis is also performed. Network edges are retweets and direct messages. In future work, we hope to explore whether problem solving capacity in a social system changes in response to crises, based on changes in the rate of cooperation and information transfer in a network.

=== The CSSS Network ===

Tom & Riccardo (with JP and others)

We will investigate the questions you are dying to know: What interesting interactions are revealed from the first 3 weeks of the Complex System Summer School survey? Have barriers between academic disciplines been broken down? Do power laws fit the data!? ...

Let us know if you have specific questions or if you would like to be involved in data analysis!

=== Is there a method in the madness? the dynamic structures of human language use ===

Priya and Riccardo

Psychiatric anecdotal reports point to the monotony, lack of emotion and sometimes intelligibility in many clinical populations. Linear measures of fluency and prosody, however, present only controversial differences between patients and healthy controls and only in unnatural phonations (i.e. say "aaaaa" for 30 secs).
We therefore go complex and chaotic on a set of more ecological recordings and transcriptions from 4 clinical populations (Asperger's, Schizophrenics, Depressed and Right Hemisphere Damage patients) as well as from healthy controls.
We then set a classifier-driven race: will non-linear analyses outcompete linear analyses in discriminating between pathologies?

=== Escaping the Poverty Trap: Modeling the Interplay Between Economic Growth and the Ecology of Infectious Disease ===

Georg, Ben, Laurent, Oscar

The dynamics of economies and infectious disease are inexorably linked: economic well-being influences health (sanitation, nutrition, etc) and health influences economic well-being (labor productivity lost to sickness and disease). Often societies are locked into "poverty traps" of poor health and poor economy. Here, we demonstrate poverty traps formed in models of infection and endogenous growth, as well as ways to break out of poverty traps. We explore two mechanisms of escape: one, through an influx of capital, and another through changing the percentage of GDP spent on healthcare. We find large influxes of capital is successful, but increasing health spending does not. Our results have important policy implications in the distribution of aid and within-country healthcare spending.

=== The Targeting and Timing of Treatment Influences the Emergence of Influenza Resistance in Structured Populations ===

Ben, Laurent, Oscar, Georg

Evolution of antiviral resistance in influenza carries large societal impacts through morbidity and mortality caused by treatment failure. Several previous studies put forth theory regarding the optimal timing, targeting and absolute level of treatment in populations. Few of these studies, however, have considered populations with explicit structure. Here we present a model of antiviral resistance on networks and explore the timing, targeting and levels of treatment. Interestingly, we find bistability as a result of treatment leading to the existence of an unstable manifold, above which successful treatment (i.e.: no resistance) is impossible. We find, contrary to previous results, that degree-targeted treatment is not optimal, and leads to higher levels of resistance than random treatment. Additionally, in accordance with previous results, we find an optimum level of treatment which is less than 100%. These findings findings have important consequences in guiding policy behind influenza treatment. The bistability indicates that caution should be taken when treating populations when the absolute numbers of infections are unknown. Positively, our results indicate that putting resources into targeted treatment is not necessary, random treatment is preferable.

=== Learning in Random Boolean Networks ===

Nick A., Keegan, Matteo, Vikram, Sarah, Mark

Inspired by biochemical networks which adapt on evolutionary timescales, neural networks that adapt during development and learning, and universal computation in cellular automata, we have implemented several models of learning in Random Boolean Networks (RBNs) in order to better understand the relationships between network structure, node interaction rules, and network output.

=== Enzyme Catalysis and the Outcome of Chemical Reactions ===
Piotr and Georg W.
Enzymes are catalysts that accelerate chemical reactions but do not affect their outcome. This traditional paradism was developed under artificail test tube conditions. Our project investigates the possibility that the presence of an enzyme can alter the course of a reaction if it takes place under more physiologic conditions.

=== How Does a Stochastic Environment affect Community Assembly? ===

We are interested in how exogenous temporal variability in resource availability affects the community structure of organisms with different resource-use strategies. Organisms induce additional resource stress on each other through competition. This is an abstraction of an arid environment with unreliable rainfall; the organisms themselves have been abstracted to four unitless parameters that allocate their resources to different parts of their lifecycles. The system has memory, as the previous presence of an organism affects the resource transport mechanism (an abstraction of soil).

=== How Does a Network’s Structure Influence its Traceability? ===

Xin and Abby

We are interested in systematically studying the problem of finding the source of a contamination spread through a network. We model a contamination spreading through the food distribution network, which we represent by interconnections between farmers, distributors, and retailers, and construct an estimator for the outbreak source given only this structure. We show how the ability of the estimator to narrow down the source identification problem changes with the connectivity and the number of observations. We propose a measure for traceability, or the overall ability to identify the source of spreading given any set of outbreak observations, based on entropy. We show how this measure appropriately reflects the range of uncertainty in identifying the source. We believe this measure may be useful in the design of networks that are conducive to accurate identification of the source of contamination.

=== We Got the Skills to Pay the Bills===

Andrés, Charlie, Gareth, and Nick

Where does diversity in skills or occupations come from and why does it lead to more innovative cities?

Complex Systems Summer School 2012-Project Presentations

2012-06-27T02:33:55Z

CLewis: /* How Does a Network’s Structure Influence its Traceability? */

{{Complex Systems Summer School 2012}}

Use this space to post project presentations and outlines. Include group members, a brief outline, and your slides.

=== Price-time Dynamics of Contracts Traded on Prediction Markets ===

Joanne, Vikram, Matteo, Sanith

Prediction markets have been shown to outperform traditional methods of polls and opinion surveys in forecasting future events. The futures contracts traded in these markets assess the expectation of occurrence of a variety of events spread across multiple domains (political, economic, entertainment, financial and weather). We explore the feasibility of 'predicting' the outcome of binary true/false prediction market contracts ahead of their expiry date using a neural-network based machine learning approach. In addition we focus on the characteristics of political-based contracts to establish whether they exhibit characteristic 'fundamental' properties.

=== How Complex Languages Replicate through Simple Brains ===

Katrien, Vanessa, Sandro, Cameron, Jasmeen

Through the use of an iterated learning experiment, we investigated the transmission of a "high entropy", randomised initial language through successive generations of participants. We want to see what features of the language replicated most easily, and what structure emerged by the end of the chain. Our hypothesis is that the language converges to a "low entropy" equilibrium state with a minimal number of words, morphemes, and form-meaning distinctions.

=== Collaboration in times of stress: an Agent Based Modelling approach ===

Fabio Cresto Aleina, Elena del Val, Tom Fennewald and Friederike Greb

We want to investigate the influence of exogenous stress on cooperative behaviour. We propose an agent based model in which the agents can be interpreted as farmers living in a water limited environment. With changes in precipitation patterns, the farmers undergo stress, and we observe how this impacts relationships among farmers and their properties.

=== Simple variation of the logistic map as a model to invoke questions on cellular protein trafficking ===
(Sepehr Ehsani, http://arxiv.org/abs/1206.5557)

Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown aspects of a biological system cannot provide more information about the set of biologically meaningful (e.g., 'hidden') states of the system than could be understood by the designer of the model ab initio. Here, the case is made for the utilization of such models to shift from a 'predictive' to a 'questioning' nature, and a simple natural-logarithm variation of the logistic polynomial map is presented that can invoke questions about protein trafficking in eukaryotic cells.

===Changes in Social Network Structure in Response to Crisis: Using Twitter data to Explore the Effect of the Tōhoku Earthquake.===

Christa Brelsford and Xin Lu

Abstract:
We use twitter data from 7 days before and after the Tōhoku Earthquake to explore how cooperation rates, social network structure and connectivity, and social network vulnerability changed in Japan in response to the disaster. An English language data set is collected for the same time period to use as a control. Data is collected for a period of 96 hours starting from March 4th 2011 2:46pm JST and for 96 hours beginning March 11th 2011 2:46 pm JST. The rate of cooperative behavior, measured by the occurrence of helping words in tweets increases slightly in the English dataset and by an order of magnitude in the Japanese dataset. A network analysis is also performed. Network edges are retweets and direct messages. In future work, we hope to explore whether problem solving capacity in a social system changes in response to crises, based on changes in the rate of cooperation and information transfer in a network.

=== The CSSS Network ===

Tom & Riccardo (with JP and others)

We will investigate the questions you are dying to know: What interesting interactions are revealed from the first 3 weeks of the Complex System Summer School survey? Have barriers between academic disciplines been broken down? Do power laws fit the data!? ...

Let us know if you have specific questions or if you would like to be involved in data analysis!

=== Is there a method in the madness? the dynamic structures of human language use ===

Priya and Riccardo

Psychiatric anecdotal reports point to the monotony, lack of emotion and sometimes intelligibility in many clinical populations. Linear measures of fluency and prosody, however, present only controversial differences between patients and healthy controls and only in unnatural phonations (i.e. say "aaaaa" for 30 secs).
We therefore go complex and chaotic on a set of more ecological recordings and transcriptions from 4 clinical populations (Asperger's, Schizophrenics, Depressed and Right Hemisphere Damage patients) as well as from healthy controls.
We then set a classifier-driven race: will non-linear analyses outcompete linear analyses in discriminating between pathologies?

=== Escaping the Poverty Trap: Modeling the Interplay Between Economic Growth and the Ecology of Infectious Disease ===

Georg, Ben, Laurent, Oscar

The dynamics of economies and infectious disease are inexorably linked: economic well-being influences health (sanitation, nutrition, etc) and health influences economic well-being (labor productivity lost to sickness and disease). Often societies are locked into "poverty traps" of poor health and poor economy. Here, we demonstrate poverty traps formed in models of infection and endogenous growth, as well as ways to break out of poverty traps. We explore two mechanisms of escape: one, through an influx of capital, and another through changing the percentage of GDP spent on healthcare. We find large influxes of capital is successful, but increasing health spending does not. Our results have important policy implications in the distribution of aid and within-country healthcare spending.

=== The Targeting and Timing of Treatment Influences the Emergence of Influenza Resistance in Structured Populations ===

Ben, Laurent, Oscar, Georg

Evolution of antiviral resistance in influenza carries large societal impacts through morbidity and mortality caused by treatment failure. Several previous studies put forth theory regarding the optimal timing, targeting and absolute level of treatment in populations. Few of these studies, however, have considered populations with explicit structure. Here we present a model of antiviral resistance on networks and explore the timing, targeting and levels of treatment. Interestingly, we find bistability as a result of treatment leading to the existence of an unstable manifold, above which successful treatment (i.e.: no resistance) is impossible. We find, contrary to previous results, that degree-targeted treatment is not optimal, and leads to higher levels of resistance than random treatment. Additionally, in accordance with previous results, we find an optimum level of treatment which is less than 100%. These findings findings have important consequences in guiding policy behind influenza treatment. The bistability indicates that caution should be taken when treating populations when the absolute numbers of infections are unknown. Positively, our results indicate that putting resources into targeted treatment is not necessary, random treatment is preferable.

=== Learning in Random Boolean Networks ===

Nick A., Keegan, Matteo, Vikram, Sarah, Mark

Inspired by biochemical networks which adapt on evolutionary timescales, neural networks that adapt during development and learning, and universal computation in cellular automata, we have implemented several models of learning in Random Boolean Networks (RBNs) in order to better understand the relationships between network structure, node interaction rules, and network output.

=== Enzyme Catalysis and the Outcome of Chemical Reactions ===
Piotr and Georg W.
Enzymes are catalysts that accelerate chemical reactions but do not affect their outcome. This traditional paradism was developed under artificail test tube conditions. Our project investigates the possibility that the presence of an enzyme can alter the course of a reaction if it takes place under more physiologic conditions.

=== How Does a Stochastic Environment affect Community Assembly? ===

We are interested in how exogenous temporal variability in resource availability affects the community structure of organisms with different resource-use strategies. Organisms induce additional resource stress on each other through competition, and affect the resource transport mechanisms. This is an abstraction of an arid environment with unreliable rainfall; the organisms themselves have been abstracted to four unitless parameters that allocate their resources to different parts of their lifecycles.

=== How Does a Network’s Structure Influence its Traceability? ===

Xin and Abby

We are interested in systematically studying the problem of finding the source of a contamination spread through a network. We model a contamination spreading through the food distribution network, which we represent by interconnections between farmers, distributors, and retailers, and construct an estimator for the outbreak source given only this structure. We show how the ability of the estimator to narrow down the source identification problem changes with the connectivity and the number of observations. We propose a measure for traceability, or the overall ability to identify the source of spreading given any set of outbreak observations, based on entropy. We show how this measure appropriately reflects the range of uncertainty in identifying the source. We believe this measure may be useful in the design of networks that are conducive to accurate identification of the source of contamination.

=== We Got the Skills to Pay the Bills===

Andrés, Charlie, Gareth, and Nick

Where does diversity in skills or occupations come from and why does it lead to more innovative cities?

Spatial-Stochastic

2012-06-20T17:57:47Z

CLewis: /* Papers: */

= Stochasticity and Space Project =

==Things we Need:==
* Explicit hypotheses
* links to papers,
* state variables
* definitions of agent traits w.r.t. space variables,
* forcing conditions
* sample code?

Looks like we can do anything on a square grid in NetLogo, and even import GIS data.

==Proposed: ==

===State variables:===

* Limiting resource (which can also be in excess)(E.g., water, nutrients)
* Patch/cell/region ability to conserve resource (E.g., soil organic matter)
* Patch connections (e.g., elevation -> horizontal flow)
* Connectivity (i.e. how well patches are connected)

===Agent characteristics:===

* Efficiency in capturing resource
* Efficiency in surviving low-resource conditions
* R-k strategy
* Spatial reach, for getting resource or spreading offspring
* Interactions? One kind of agent more efficient in the presence of another?
* Threshold responses to external inputs, or saturation
* What ecological processes does an agent do? (e.g. growth, water uptake, nutrient uptake, death, dispersal etc.)

===Forcing conditions:===
* Input of resource, variable in space or time
* Variance of input

===Hypotheses:===
* Variable resource input favors different agent traits than reliable inputs with the same mean value
* Agents develop spatial variability to gather sparse resources
* Unreliable resources favor cooperative strategies (Demetrius, e.g.)
* Hubler's hypotheses: with little noise, the system minimizes dissipation and is efficient; with much noise, the system maximizes dissipation and is robust.

===Papers:===
* [http://igitur-archive.library.uu.nl/milieu/2008-0111-200810/rietkerk-04-self%20organised.pdf Self-Organized Patchiness and Catastrophic Shifts in Ecosystems]
* [http://www.nature.com/nature/journal/v405/n6783/pdf/405228a0.pdf The diversity-stability debate]
* [[File: Reinterpreting Space, time lags, and functional response in ecological models.pdf]]
* [[File: Ecology of Tropical Dry Forest.pdf]]
* [[File: Mechanism of plant survival and mortality during drought.pdf]]
* [[File: Ecophysiology of trees of seasonally dry tropics.pdf]]
* [http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01404.x/abstract Field theory for biogeography]

==Contact: ==
maybe we need emails to facilitate communications.

* Xiaoli: xiaolidong2008@gmail.com
* Xue: xue.feng@duke.edu
* Χλοε: chlewis (at berkeley edu)

we are looking for the unknown X in Xeriscapes.

Complex Systems Summer School 2012-After Hours

2012-06-18T22:17:39Z

CLewis: /* Dancing */

{{Complex Systems Summer School 2012}}

Use this space to organize your own after hours activities.

==Some Banjo fun out on the town==

My brother will be having a concert this Saturday June 16 at the Second Street Brewery (original location) from 6-9p.m. I will be at the parking circle at 6p.m. For those who do not sign up for a car don't forget Friday and Saturday $5 cabs.

[http://www.secondstreetbrewery.com/2012/05/todd-the-fox-9/ Todd and the Fox Venue Details]

[http://www.toddandthefox.com/fr_home.cfm To hear their music]

If anyone would like to join:

Car 1: Juniper's Car 

1. Katrien (not sure if we'll be back from the lake trip by 6pm. Somebody can take my place if they want.) back up: Georg Weber

2. Marque

3. Sarah

4. Marco

==Dancing==

Swing dancing on Monday 18th June.
Lessons from 7 to 8 P.M.
Dancing from 8 on wards.
The cost is $8 including the lesson and dancing (or $3 for the dancing). Venue: Odd Fellows Hall, 1125 Cerrillos Road. We have not yet decided on transportation. We could either take a cab or walk -- Let's try to decide during dinner.
Sign up below if you are interested:

1.Vikram -- Slightly biased towards taking the lesson. 
2. Xue -- dancing, though not a strong preference. 
3. Mark - I could use a lesson, or twelve. Do we have transportation? 
4. Chloe -- would rather walk down with everyone than skip the lesson. 
5.

PS: If you are on the edge because you want to attend the session on "Introduction to Python". I would be happy to walk you through the basics of Python at a later time. -- Vikram

PPS: how about a Dancing Python lunch tomorrow? I can do intro tutoring too. --Chloe

Other varieties --

There's a contra on the 23rd; swing dancing most Mondays; this is supposed to be a great tango town, and the drop-in-friendly beginner class on Thursday PM was good ($20, though).

[http://www.santafenewmexican.com/Sidebar/Dance_fever_in_Santa_Fe swing, salsa, tango]

[http://www.folkmads.org/may_jun_calendar12.html contras, here and ABQ]

We've heard great Appalachian-style folk musicians here already, but I haven't found a ceili or hoedown locally.

--Chloe

==Trip to Taos==

JP and Tom are going to go to Taos on Saturday 6/16. Sights to see will include the High Road to Taos, Taos Pueblo, the Taos Gorge, Taos Earthships, and the plenty of Taos Hippies.
 
Car 1: JP's Camry 

1.[[JP]] 
2. 
3.Piotr 
4.Matteo 
5.Vikram 
 

Car 2: Tom's Car 
1 
2 Miguel 
3 Riccardo 
4 Priya 

From Andres: I'm sorry... I decided to stay tomorrow at St. John's. I'm very sorry to letting you know so late...! I want to rest, and there is some work I'd like to do...
From Nick: Same for me guys. I feel exhausted. Sorry for telling you so late. Enjoy!

==Trip to Abiquiu==

We are organizing a trip to lake Abiquiu this weekend. ATTENTION ATTENTION! Drivers (Christa, Fabio, John, Tom and David) will meet at 8:30 tomorrow morning (Saturday), and will go with Christa to town to rent 4 cars. We'll pick the others up at 9:30. Those in Christas car, meet at 9am. See you tomorrow!

Fabio

Friederike

Elena

Mikkel

John

Nona

Abby

Marco

Aleksandra

Jasmeen

Dan

Sandro

Ian (if there is any room)

Vanessa (ditto)

Christa (my car seats 5 including me, but I want to stop by Los Alamos to pick up my dog on the way. That adds ~30 min to the drive. "Christa's Honda has manual transmission. do we need a second driver on the car who can drive a stick shift car?" "Yes"- Christa

1. Christa

2. Xue (though I'm also willing to be a driver if necessary)

3. Katrien

4. Jianfeng Xu

5. Xin

Tom

Nick A

==Bandelier Field Trip==

Bandelier Field Trip
Trip to Bandelier National Monument on Sat. June 9.
We might string a visit to the Valles Caldera and Bradbury Science Museum/Los Alamos in as well. If another group would like to stay around Bandelier, we can split up.

Head over to the [[Bandelier Trip 2012 | Bandelier Trip]] Page to sign up!

==Mafia==

[[JP]] is a huge fan of Mafia/Werewolf. Let's play a game sometime in the lower commons.

Let's meet Saturday evening at 8:00 in the lower commons for our first game.

- [[Ryan_James|Ryan]] is down for this.

- Jasmeen is also a big fan of Mafia.

- Ian has never played, but is interested

- Vikram is interested in learning the game.

- Tom F. would like to join and can also teach "The Resistance" a very similar game

- Katrien wants to play too

==FOOTBALL!==

Anyone up for a friendly game of soccer? We can check out equipment from the gym.

[Team: Continuous!] 
1. [[Piotr Milanowski|Piotr]] 
2. [[Marco Duenas|Marco]] 
3.[[Oleksandr Ivanov|Alex]] 
4. 
5. 
[Team: Discrete!] 
1. [[Fabio Cresto Aleina|Fabio]] 
2. [[Matteo Chinazzi|Matteo]] 
3.[[JP]] 
4. 
5.

Complex Systems Summer School 2012-After Hours

2012-06-18T22:17:19Z

CLewis: /* Dancing */

{{Complex Systems Summer School 2012}}

Use this space to organize your own after hours activities.

==Some Banjo fun out on the town==

My brother will be having a concert this Saturday June 16 at the Second Street Brewery (original location) from 6-9p.m. I will be at the parking circle at 6p.m. For those who do not sign up for a car don't forget Friday and Saturday $5 cabs.

[http://www.secondstreetbrewery.com/2012/05/todd-the-fox-9/ Todd and the Fox Venue Details]

[http://www.toddandthefox.com/fr_home.cfm To hear their music]

If anyone would like to join:

Car 1: Juniper's Car 

1. Katrien (not sure if we'll be back from the lake trip by 6pm. Somebody can take my place if they want.) back up: Georg Weber

2. Marque

3. Sarah

4. Marco

==Dancing==

Swing dancing on Monday 18th June.
Lessons from 7 to 8 P.M.
Dancing from 8 on wards.
The cost is $8 including the lesson and dancing (or $3 for the dancing). Venue: Odd Fellows Hall, 1125 Cerrillos Road. We have not yet decided on transportation. We could either take a cab or walk -- Let's try to decide during dinner.
Sign up below if you are interested:

1.Vikram -- Slightly biased towards taking the lesson. 
2. Xue -- dancing, though not a strong preference. 
3. Mark - I could use a lesson, or twelve. Do we have transportation? 
4. Chloe -- would rather walk down with everyone than skip the lesson. 
5.

PS: If you are on the edge because you want to attend the session on "Introduction to Python". I would be happy to walk you through the basics of Python at a later time. -- Vikram

PPS: how about a Dancing Python lunch tomorrow? I can do intro tutoring too.

Other varieties --

There's a contra on the 23rd; swing dancing most Mondays; this is supposed to be a great tango town, and the drop-in-friendly beginner class on Thursday PM was good ($20, though).

[http://www.santafenewmexican.com/Sidebar/Dance_fever_in_Santa_Fe swing, salsa, tango]

[http://www.folkmads.org/may_jun_calendar12.html contras, here and ABQ]

We've heard great Appalachian-style folk musicians here already, but I haven't found a ceili or hoedown locally.

--Chloe

==Trip to Taos==

JP and Tom are going to go to Taos on Saturday 6/16. Sights to see will include the High Road to Taos, Taos Pueblo, the Taos Gorge, Taos Earthships, and the plenty of Taos Hippies.
 
Car 1: JP's Camry 

1.[[JP]] 
2. 
3.Piotr 
4.Matteo 
5.Vikram 
 

Car 2: Tom's Car 
1 
2 Miguel 
3 Riccardo 
4 Priya 

From Andres: I'm sorry... I decided to stay tomorrow at St. John's. I'm very sorry to letting you know so late...! I want to rest, and there is some work I'd like to do...
From Nick: Same for me guys. I feel exhausted. Sorry for telling you so late. Enjoy!

==Trip to Abiquiu==

We are organizing a trip to lake Abiquiu this weekend. ATTENTION ATTENTION! Drivers (Christa, Fabio, John, Tom and David) will meet at 8:30 tomorrow morning (Saturday), and will go with Christa to town to rent 4 cars. We'll pick the others up at 9:30. Those in Christas car, meet at 9am. See you tomorrow!

Fabio

Friederike

Elena

Mikkel

John

Nona

Abby

Marco

Aleksandra

Jasmeen

Dan

Sandro

Ian (if there is any room)

Vanessa (ditto)

Christa (my car seats 5 including me, but I want to stop by Los Alamos to pick up my dog on the way. That adds ~30 min to the drive. "Christa's Honda has manual transmission. do we need a second driver on the car who can drive a stick shift car?" "Yes"- Christa

1. Christa

2. Xue (though I'm also willing to be a driver if necessary)

3. Katrien

4. Jianfeng Xu

5. Xin

Tom

Nick A

==Bandelier Field Trip==

Bandelier Field Trip
Trip to Bandelier National Monument on Sat. June 9.
We might string a visit to the Valles Caldera and Bradbury Science Museum/Los Alamos in as well. If another group would like to stay around Bandelier, we can split up.

Head over to the [[Bandelier Trip 2012 | Bandelier Trip]] Page to sign up!

==Mafia==

[[JP]] is a huge fan of Mafia/Werewolf. Let's play a game sometime in the lower commons.

Let's meet Saturday evening at 8:00 in the lower commons for our first game.

- [[Ryan_James|Ryan]] is down for this.

- Jasmeen is also a big fan of Mafia.

- Ian has never played, but is interested

- Vikram is interested in learning the game.

- Tom F. would like to join and can also teach "The Resistance" a very similar game

- Katrien wants to play too

==FOOTBALL!==

Anyone up for a friendly game of soccer? We can check out equipment from the gym.

[Team: Continuous!] 
1. [[Piotr Milanowski|Piotr]] 
2. [[Marco Duenas|Marco]] 
3.[[Oleksandr Ivanov|Alex]] 
4. 
5. 
[Team: Discrete!] 
1. [[Fabio Cresto Aleina|Fabio]] 
2. [[Matteo Chinazzi|Matteo]] 
3.[[JP]] 
4. 
5.

Experiment sign-up

2012-06-17T20:44:45Z

CLewis: /* Monday June 18 */

Hi! Please sign up for one slot below. The experiment will be held in the Senior Common Room (JP's office) next to the great hall. Please arrive on time!

- Katrien, Vanessa, Sandro, Cameron & Jasmeen

==Monday June 18==

Morning Break:

9.30-9.40:

9.40-9.50:

9.50-10.00:

10.00-10.10:

10.10-10.20:

10.20-10.30:

10.30-10.40:

Lunch Break:

12.05-12.15: Chloe

12.15-12.25:

12.25-12.35:

12.35-12.45:

12.55-1.05:

1.05-1.15:

1.15-1.25:

Afternoon:

4.30-4.40:

4.40-4.50:

4.50-5.00:

5.00-5.10:

5.10-5.20:

5.20-5.30:

5.30-5.40:

5.40-5.50:

5.50-6.00:

6.00-6.10:

6.10-6.20:

6.20-6.30:

6.30-6.40:

6.40-6.50:

6.50-7.00:

Complex Systems Summer School 2012-Photos

2012-06-16T20:30:33Z

CLewis:

{{Complex Systems Summer School 2012}}

Feel free to share links to your photos here.

[http://www.flickr.com/photos/57132973@N07/7381727052/in/photostream/lightbox/ Tom tries to cut in]

[http://www.flickr.com/photos/57132973@N07/7381727234/in/photostream/lightbox/ Tom is rebuffed]

A photo of the transit of Venus across the Sun: [[Media:Venus-transit-2.jpg]]

[http://www.dropbox.com/gallery/1694302/1/CSSS2012?h=0d4e88 Some pictures]

[http://www.flickr.com/photos/sepehrehsani/7350419208/ Transit of Venus 2012]

[http://www.flickr.com/photos/sepehrehsani/7165200933/ Dr. Hübler's wave chaos experiment]

PHOTOS by Sanith

[https://plus.google.com/photos/115406882267732059257/albums/5754491294229358321?authkey=CNzp1fLU2o-B2gE SFI 06/08/12]

Complex Systems Summer School 2012-After Hours

2012-06-14T22:54:09Z

CLewis: /* Dancing */

{{Complex Systems Summer School 2012}}

Use this space to organize your own after hours activities.

==Dancing at the Rouge Cat==

Some of us will be going dancing on Friday night at the [http://rougecat.com/ Rouge Cat] they have a downstairs disco floor and it's a whole lot of fun. JP and I will be leaving SJC parking circle around 10:00p.m. to head over there.

Car 1: Juniper's Car 

1.

2.

3.

4.

Car 2: JP's Car 

1.

2.

3.

4.

==Some Banjo fun out on the town==

My brother will be having a concert this Saturday June 16 at the Second Street Brewery (original location) from 6-9p.m. I will be at the parking circle at 6p.m.

[http://www.secondstreetbrewery.com/2012/05/todd-the-fox-9/ Todd and the Fox Venue Details]

[http://www.toddandthefox.com/fr_home.cfm To hear their music]

If anyone would like to join:

Car 1: Juniper's Car 

1. Katrien

2. Marque

3. Sarah

4. Marco

==Dancing==
The beginner tango classes tonight (Thursday, 14th June) are open to drop-ins, especially if we have lead-follow parity, but they're expensive for intro dance classes: $20 from 7:30 to 9. 
1. Chloe 
2. Vikram 
3. Aleksandra 

We'll share a cab from in front of the dining hall, leaving 7PM.

Other varieties --

There's a contra on the 23rd; swing dancing most Mondays; this is supposed to be a great tango town, and I'm looking for drop-in-friendly beginner classes...

[http://www.santafenewmexican.com/Sidebar/Dance_fever_in_Santa_Fe swing, salsa, tango]

[http://www.folkmads.org/may_jun_calendar12.html contras, here and ABQ]

We've heard great Appalachian-style folk musicians here already, but I haven't found a ceili or hoedown locally.

--Chloe

==Trip to Taos==

JP and Tom are going to go to Taos on Saturday 6/16. Sights to see will include the High Road to Taos, Taos Pueblo, the Taos Gorge, Taos Earthships, and the plenty of Taos Hippies.
 
Car 1: JP's Camry 

1.[[JP]] 
2.Nick G 
3.Piotr 
4.Matteo 
5.Vikram 
 

Car 2: Tom's Car 
1 Andres G. 
2 Miguel 
3 Riccardo 
4 Priya 

==Trip to Abiquiu==

We are organizing a trip to lake Abiquiu this weekend. Google maps says it should take about 1:10 hour driving from Santa Fe. Who's interested? We'll have to rent cars to go there.

Fabio

Friederike

Elena

Mikkel

John

Nona

Abby

Marco

Aleksandra

Jasmeen

Dan

Christa (my car seats 5 including me, but I want to stop by Los Alamos to pick up my dog on the way. That adds ~30 min to the drive. "Christa's Honda has manual transmission. do we need a second driver on the car who can drive a stick shift car?"

1. Christa

2. Xue (though I'm also willing to be a driver if necessary)

3. Katrien

4. Jianfeng Xu

5.

==Bandelier Field Trip==

Bandelier Field Trip
Trip to Bandelier National Monument on Sat. June 9.
We might string a visit to the Valles Caldera and Bradbury Science Museum/Los Alamos in as well. If another group would like to stay around Bandelier, we can split up.

Head over to the [[Bandelier Trip 2012 | Bandelier Trip]] Page to sign up!

==Mafia==

[[JP]] is a huge fan of Mafia/Werewolf. Let's play a game sometime in the lower commons.

Let's meet Saturday evening at 8:00 in the lower commons for our first game.

- [[Ryan_James|Ryan]] is down for this.

- Jasmeen is also a big fan of Mafia.

- Ian has never played, but is interested

- Vikram is interested in learning the game.

- Tom F. would like to join and can also teach "The Resistance" a very similar game

- Katrien wants to play too

==FOOTBALL!==

Anyone up for a friendly game of soccer? We can check out equipment from the gym.

[Team: Continuous!] 
1. [[Piotr Milanowski|Piotr]] 
2. [[Marco Duenas|Marco]] 
3.[[Oleksandr Ivanov|Alex]] 
4. 
5. 
[Team: Discrete!] 
1. [[Fabio Cresto Aleina|Fabio]] 
2. [[Matteo Chinazzi|Matteo]] 
3.[[JP]] 
4. 
5.

Complex Systems Summer School 2012-After Hours

2012-06-13T18:42:59Z

CLewis: /* Dancing */

{{Complex Systems Summer School 2012}}

Use this space to organize your own after hours activities.

==Dancing==
Of particular varieties --

There's a contra on the 23rd; swing dancing most Mondays; this is supposed to be a great tango town, and I'm looking for drop-in-friendly beginner classes...

[http://www.santafenewmexican.com/Sidebar/Dance_fever_in_Santa_Fe swing, salsa, tango]

[http://www.folkmads.org/may_jun_calendar12.html contras, here and ABQ]

We've heard great Appalachian-style folk musicians here already, but I haven't found a ceili or hoedown locally.

--Chloe

==Trip to Abiquiu==

We are organizing a trip to lake Abiquiu this weekend. Google maps says it should take about 1:10 hour driving from Santa Fe. Who's interested? We'll have to rent cars to go there.

Fabio

Friederike

Elena

Mikkel

John

==Saturday Football==

Who is up for a quick match tomorrow at 8am before the Bandelier trip? Let's make it a relaxed, just-for-fun match. Sign up below:

- [[Miguel Lurgi|Miguel]]

==Bandelier Field Trip==

Bandelier Field Trip
Trip to Bandelier National Monument on Sat. June 9.
We might string a visit to the Valles Caldera and Bradbury Science Museum/Los Alamos in as well. If another group would like to stay around Bandelier, we can split up.

Head over to the [[Bandelier Trip 2012 | Bandelier Trip]] Page to sign up!

==Mafia==

[[JP]] is a huge fan of Mafia/Werewolf. Let's play a game sometime in the lower commons.

Let's meet Saturday evening at 8:00 in the lower commons for our first game.

- [[Ryan_James|Ryan]] is down for this.

- Jasmeen is also a big fan of Mafia.

- Ian has never played, but is interested

- Vikram is interested in learning the game.

- Tom F. would like to join and can also teach "The Resistance" a very similar game

- Katrien wants to play too

==FOOTBALL!==

Anyone up for a friendly game of soccer? We can check out equipment from the gym.

[Team: Continuous!] 
1. [[Piotr Milanowski|Piotr]] 
2. [[Marco Duenas|Marco]] 
3.[[Oleksandr Ivanov|Alex]] 
4. 
5. 
[Team: Discrete!] 
1. [[Fabio Cresto Aleina|Fabio]] 
2. [[Matteo Chinazzi|Matteo]] 
3.[[JP]] 
4. 
5.

Complex Systems Summer School 2012-After Hours

2012-06-13T18:40:26Z

CLewis: /* Trip to Abiquiu */

{{Complex Systems Summer School 2012}}

Use this space to organize your own after hours activities.

==Dancing==
Of particular varieties --

There's a contra on the 23rd; swing dancing most Mondays; this is supposed to be a great tango town, and I'm looking for drop-in-friendly beginner classes...

[[http://www.santafenewmexican.com/Sidebar/Dance_fever_in_Santa_Fe][swing, salsa, tango]]

[[http://www.folkmads.org/may_jun_calendar12.html][contras, here and ABQ]]

We've heard great Appalachian-style folk musicians here already, but I haven't found a ceili or hoedown locally.

--Chloe

==Trip to Abiquiu==

We are organizing a trip to lake Abiquiu this weekend. Google maps says it should take about 1:10 hour driving from Santa Fe. Who's interested? We'll have to rent cars to go there.

Fabio

Friederike

Elena

Mikkel

John

==Saturday Football==

Who is up for a quick match tomorrow at 8am before the Bandelier trip? Let's make it a relaxed, just-for-fun match. Sign up below:

- [[Miguel Lurgi|Miguel]]

==Bandelier Field Trip==

Bandelier Field Trip
Trip to Bandelier National Monument on Sat. June 9.
We might string a visit to the Valles Caldera and Bradbury Science Museum/Los Alamos in as well. If another group would like to stay around Bandelier, we can split up.

Head over to the [[Bandelier Trip 2012 | Bandelier Trip]] Page to sign up!

==Mafia==

[[JP]] is a huge fan of Mafia/Werewolf. Let's play a game sometime in the lower commons.

Let's meet Saturday evening at 8:00 in the lower commons for our first game.

- [[Ryan_James|Ryan]] is down for this.

- Jasmeen is also a big fan of Mafia.

- Ian has never played, but is interested

- Vikram is interested in learning the game.

- Tom F. would like to join and can also teach "The Resistance" a very similar game

- Katrien wants to play too

==FOOTBALL!==

Anyone up for a friendly game of soccer? We can check out equipment from the gym.

[Team: Continuous!] 
1. [[Piotr Milanowski|Piotr]] 
2. [[Marco Duenas|Marco]] 
3.[[Oleksandr Ivanov|Alex]] 
4. 
5. 
[Team: Discrete!] 
1. [[Fabio Cresto Aleina|Fabio]] 
2. [[Matteo Chinazzi|Matteo]] 
3.[[JP]] 
4. 
5.

Complex Systems Summer School 2012-Tutorials

2012-06-13T17:28:34Z

CLewis: /* Computational Mechanics */

{{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.

==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.

===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 

===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 

==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-TShirts

2012-06-12T22:00:13Z

CLewis: /* 2012 CSSS T-Shirt Design Submissions */

{{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

(Maybe orange and pine-green trajectories in the mountains, orange for the sun? -Chloe)

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

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).

I'd like a front breast-pocket style image of the SFI logo plus the complex systems summer school and year...

Could use some fine-tuning! Maybe grayscale, maybe a higher res snail shell... -- Sarah Tweedt

----

One more idea...a very messy doodle that would obviously need to be redone, but just putting it up since I haven't had time to make a nicer version yet. It's supposed to be the view from St. John's, made up of some sort of petroglyph-like complex system with the SFI logo as the sun.

[[File:smaller.jpg]]

-Jasmeen

Spatial-Stochastic

2012-06-12T01:44:28Z

CLewis: /* Contact: */

= Stochasticity and Space Project =

==Things we Need:==
* Explicit hypotheses
* links to papers,
* state variables
* definitions of agent traits w.r.t. space variables,
* forcing conditions
* sample code?

Looks like we can do anything on a square grid in NetLogo, and even import GIS data.

==Proposed: ==

===State variables:===

* Limiting resource (which can also be in excess)(E.g., water)
* Patch/cell/region ability to conserve resource (E.g., soil organic matter)
* Patch connections (e.g., elevation -> horizontal flow)

===Agent characteristics:===

* Efficiency in capturing resource
* Efficiency in surviving low-resource conditions
* R-k strategy
* Spatial reach, for getting resource or spreading offspring
* Interactions? One kind of agent more efficient in the presence of another?
* Threshold responses to external inputs, or saturation

===Forcing conditions:===
* Input of resource, variable in space or time
* Variance of input

===Hypotheses:===
* Variable resource input favors different agent traits than reliable inputs with the same mean value
* Agents develop spatial variability to gather sparse resources
* Unreliable resources favor cooperative strategies (Demetrius, e.g.)
* Hubler's hypotheses: with little noise, the system minimizes dissipation and is efficient; with much noise, the system maximizes dissipation and is robust.

===Papers:===
* [http://igitur-archive.library.uu.nl/milieu/2008-0111-200810/rietkerk-04-self%20organised.pdf Self-Organized Patchiness and Catastrophic Shifts in Ecosystems]
* [http://www.nature.com/nature/journal/v405/n6783/pdf/405228a0.pdf The diversity-stability debate]
* [[File: Reinterpreting Space, time lags, and functional response in ecological models.pdf]]
* [[File: Ecology of Tropical Dry Forest.pdf]]
* [[File: Mechanism of plant survival and mortality during drought.pdf]]
* [[File: Ecophysiology of trees of seasonally dry tropics.pdf]]

==Contact: ==
maybe we need emails to facilitate communications.

* Xiaoli: xiaolidong2008@gmail.com
* Xue: xue.feng@duke.edu
* Χλοε: chlewis (at berkeley edu)

we are looking for the unknown X in Xeriscapes.

Spatial-Stochastic

2012-06-12T01:41:07Z

CLewis: /* Contact: */

= Stochasticity and Space Project =

==Things we Need:==
* Explicit hypotheses
* links to papers,
* state variables
* definitions of agent traits w.r.t. space variables,
* forcing conditions
* sample code?

Looks like we can do anything on a square grid in NetLogo, and even import GIS data.

==Proposed: ==

===State variables:===

* Limiting resource (which can also be in excess)(E.g., water)
* Patch/cell/region ability to conserve resource (E.g., soil organic matter)
* Patch connections (e.g., elevation -> horizontal flow)

===Agent characteristics:===

* Efficiency in capturing resource
* Efficiency in surviving low-resource conditions
* R-k strategy
* Spatial reach, for getting resource or spreading offspring
* Interactions? One kind of agent more efficient in the presence of another?
* Threshold responses to external inputs, or saturation

===Forcing conditions:===
* Input of resource, variable in space or time
* Variance of input

===Hypotheses:===
* Variable resource input favors different agent traits than reliable inputs with the same mean value
* Agents develop spatial variability to gather sparse resources
* Unreliable resources favor cooperative strategies (Demetrius, e.g.)
* Hubler's hypotheses: with little noise, the system minimizes dissipation and is efficient; with much noise, the system maximizes dissipation and is robust.

===Papers:===
* [http://igitur-archive.library.uu.nl/milieu/2008-0111-200810/rietkerk-04-self%20organised.pdf Self-Organized Patchiness and Catastrophic Shifts in Ecosystems]
* [http://www.nature.com/nature/journal/v405/n6783/pdf/405228a0.pdf The diversity-stability debate]
* [[File: Reinterpreting Space, time lags, and functional response in ecological models.pdf]]
* [[File: Ecology of Tropical Dry Forest.pdf]]
* [[File: Mechanism of plant survival and mortality during drought.pdf]]
* [[File: Ecophysiology of trees of seasonally dry tropics.pdf]]

==Contact: ==
maybe we need emails to facilitate communications.

* Xiaoli: xiaolidong2008@gmail.com
* Xue: xue.feng@duke.edu
* Χλοε: chlewis (at berkeley edu)

Complex Systems Summer School 2012-Blog

2012-06-11T19:41:08Z

CLewis: /* Schooling interactions with non-square boundary */

{{Complex Systems Summer School 2012}}

Use this page as an informal forum to share your opinion and discuss anything at CSSS'12.

Students are encouraged to share their observations, insights, and opinions about daily lecture content as well as extracurricular activities.

Post your own links to notes, interesting articles, and anything else you think might contribute to the program.

== Can one get a chaotic map with two disco balls? ==

And, if so, isn't it practically our duty to do so?

(There's a disco ball in the lecture hall.)

== Schooling interactions with non-square boundary ==
The Monterey Bay Aquarium has an [http://www.youtube.com/watch?v=xZKxfvi9h0c [anchovy tank]] shaped like two nested sections of cones (you stand inside it). Boid-like behavior is pretty easy to see in the fish, particularly because the shape of the tank interferes with the school. I couldn't decide if the tank was actually inducing turbulence in the fish.

== Dynamical Systems: R and Python ==
I wrote some Python code for simulating deterministic dynamical systems and used it to play around with the Logistic map from yesterday's lectures. The Python class I wrote for simulating generic dynamical systems (admittedly only those with a single state variable!) can be found [https://sites.google.com/site/beyondmicrofoundationscoderepo/home/python/dynamics here] (I would have posted to the code to the wiki directly but apparently one cannot upload .py files). I have also written a [http://beyondmicrofoundations.blogspot.com/2012/06/monday-4-june-2012-at-2012-csss.html blog] post demonstrating some of the functionality of the Python code.

Also, there are several R packages that seem to implement the algorithms from the TISEAN program that we were introduced to yesterday. The packages are [http://cran.r-project.org/web/packages/RTisean/index.html RTisean], [http://cran.r-project.org/web/packages/tseriesChaos/index.html tseriesChaos], and [http://cran.r-project.org/web/packages/tsDyn/index.html tsDyn] and can be found on CRAN.

Enjoy,

D. Pugh

PS: I am very much a newbie to Python, and any suggestions on improving my coding are much appreciated!

I have written another blog [http://beyondmicrofoundations.blogspot.com/2012/06/5-6-june-2012-at-2012-csss.html post] and some more Python code for implementing parts of the TISEAN labs that we have been assigned. Code can be found here [https://sites.google.com/site/beyondmicrofoundationscoderepo/home/python/dynamics here]. Eventually, the code will contain solutions to the all of the labs and homework.

== Python wrapper for TISEAN ==

Thanks for sharing your python code David.

Incidentally there is also a Python wrapper for TISEAN available
[http://www.stud.fernuni-hagen.de/q4576411/andreas_2/computer/projekte/tisean.html here]. Not sure how good it is, but might be worth checking out.

Sanith

Bandelier Trip 2012

2012-06-06T23:10:51Z

CLewis: /* John Paul's Camry: 4 (maybe 5) seats */

{{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.

==Cars:==

===Tom's Sedan: 4 seats===
1. [[Nicholas Allgaier]] 

2. Vikram Vijayaraghavan 

3. Katrien Beuls 

4. Riccardo Fusaroli 

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

1. [[John Paul]] 

2. [[Matteo Chinazzi]] 

3. [[Chloe Lewis]] 

4.

5.

===Juniper's Car: 4 (maybe 5) seats===

1.

2.

3.

4.

5.

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

1.

2.

3.

4.

5(middle seat in a 2 door civic).

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

2.

3.

Complex Systems Summer School 2012-Blog

2012-06-06T22:05:48Z

CLewis: /* Dynamical Systems: R and Python */

{{Complex Systems Summer School 2012}}

Use this page as an informal forum to share your opinion and discuss anything at CSSS'12.

Students are encouraged to share their observations, insights, and opinions about daily lecture content as well as extracurricular activities.

Post your own links to notes, interesting articles, and anything else you think might contribute to the program.

== Schooling interactions with non-square boundary ==
The Monterey Bay Aquarium has an [http://www.youtube.com/watch?v=xZKxfvi9h0c [anchovy tank]] shaped like two nested sections of cones (you stand inside it). Boid-like behavior is pretty easy to see in the fish, particularly because the shape of the tank interferes with the school. I couldn't decide if the tank was actually inducing turbulence in the fish.

== Dynamical Systems: R and Python ==
I wrote some Python code for simulating deterministic dynamical systems and used it to play around with the Logistic map from yesterday's lectures. The Python class I wrote for simulating generic dynamical systems (admittedly only those with a single state variable!) can be found [https://sites.google.com/site/beyondmicrofoundationscoderepo/home/python/dynamics here] (I would have posted to the code to the wiki directly but apparently one cannot upload .py files). I have also written a [http://beyondmicrofoundations.blogspot.com/2012/06/monday-4-june-2012-at-2012-csss.html blog] post demonstrating some of the functionality of the Python code.

Also, there are several R packages that seem to implement the algorithms from the TISEAN program that we were introduced to yesterday. The packages are [http://cran.r-project.org/web/packages/RTisean/index.html RTisean], [http://cran.r-project.org/web/packages/tseriesChaos/index.html tseriesChaos], and [http://cran.r-project.org/web/packages/tsDyn/index.html tsDyn] and can be found on CRAN.

Enjoy,

D. Pugh

PS: I am very much a newbie to Python, and any suggestions on improving my coding are much appreciated!

== Python wrapper for TISEAN ==

Thanks for sharing your python code David.

Incidentally there is also a Python wrapper for TISEAN available
[http://www.stud.fernuni-hagen.de/q4576411/andreas_2/computer/projekte/tisean.html here]. Not sure how good it is, but might be worth checking out.

Sanith

Spatial-Stochastic

2012-06-06T21:59:40Z

CLewis:

Spatial-Stochastic

2012-06-06T04:15:21Z

CLewis: Ideas for Stochasticity and Space

= Stochasticity and Space Project =

I (Chloe) remember Stochasticity and Space as the minimal set of what today's pre-dinner discussion decided to concentrate on, and as I recall it we agreed to write up what we were thinking about as explicitly as possible so that we could see exactly what we we have to weld into a project. Explicit hypotheses, links to papers, definitions of what state variables are tracked, definitions of traits w.r.t. space variables, sample code?

I have a square-grid cellular automaton with agents running in Python that I can share, with the skeleton of an experimental `runner' (load an initial condition, specify the algorithms for the updates of /n/ state variables, run for specified time, save result).

Complex Systems Summer School 2012-Projects & Working Groups

2012-06-06T04:06:27Z

CLewis: /* Space, Stochasticity, Stability; Speciation? */

{{Complex Systems Summer School 2012}}

==Project proposals==

=== Nonequilibrium game theory ===
My hope is to adapt some SFI-based models, by people like Crutchfield and Farmer, so that they will quantitatively or qualitatively reproduce features of real human data. Of course, that is very specific, and I'm up for all kinds of ideas in the areas of game learning, game dynamics, small group collective behavior, cognitive science, nonlinear time series, non-eq time series, etc., etc.

Meet me, Seth Frey, at dinner on Thursday and Friday.

=== Enzyme kinetics – Do enzymes just accelerate equilibrium or play an active role in chemical reactions? ===
Enzyme networks (e.g. glycolysis) and catalysts in complex mixtures (e.g. Belusov-Zhabotinski reaction) can profoundly influence the outcome of a chemical reaction system. What about a single enzyme? Biochemistry textbooks uniformly say that an enzyme accelerates a reaction without altering its outcome. Yet, the set of differential equations that generically describes enzyme catalysis has remarkable resemblance to the Roessler equations (a textbook example of a non-linear, complex system). With a fixed substrate input or a steady substrate flow, a single enzyme probably cannot affect the reaction outcome. However, sinusoidal or pulsating substrate input, substrate activation or product inhibition, coupling of two enzymes could turn the reaction pattern non-linear. For this project, the sets of equations to study are quite well established – they need to be analyzed. In contrast to some of the more ambitious ideas circulated, this task is exhaustively doable in less than four weeks.

I am Georg Weber. If you are interested in studying this problem, please find me on Tuesday over lunch or dinner (or talk to me at any other unstructured time).
=== Traffic pattern analysis - Can we estimate car velocity by only observing car counts? ===
==== Problem statement ====
Imagine you have a monitored highway section with a start and end point. At both points you count the number of cars that pass by. The question I'd like to answer / simulate / estimate is: can we make some inference about the velocity of cars although we only have their counts? This would be very useful from an engineering / economic perspective because it's much easier / cheaper to count cars instead of actually tracking them from A to B.
==== Ideas on how to approach this ====
I have some intuition about how to go about this, but these are purely statistical (think of it as birth and death process; or as particles in a system that have a certain lifetime - cars in the highway section are like particles in a system, and their velocity is just inverse proportional to their lifetime in this highway section). I would like to see if using explicit physical modeling of motion and agent-based modeling of traffic flow could shed more light on this problem.

'''Update 06/05/12:''' Just today we saw ''Takens theorem'' about how we can infer a systems structure from only observing a subset of variables. Well, it seems like that's exactly what this project is about.

If you are interested to see more about this check out the [[Georg_M_Goerg#SFI_Project:_Traffic_pattern_analysis_-_Can_we_estimate_car_velocity_by_only_observing_car_counts.3F_.3D|SFI Project]] subsection on [[Georg_M_Goerg|Georg M. Goerg]] or email me to my_3_initials_in_lowercase@stat.cmu.edu. Let's say we meet on Wednesday for lunch (or just ask me any other time you see me around).

=== Cultural Evolution - General Meet-up ===
Attention anyone who is interested in cultural evolution or applying your models/methodologies to this fabulous topic!

Let's meet at 4:15 (June 5th) in the cafe during the first "Time to work on Projects" slot. A bunch of us coalesced there tonight and figured we should all properly meet up and then bud off into different projects. Please post your potential buds below:

=== Cultural Evolution - things that look like drift but aren't ===
Lots of cultural evolution looks like drift (Bently et al 2004 'Random drift and culture change"). But what social transmission or cognitive learning mechanisms are isomorphic to random sampling with replacement from cultural inputs? In biological evolution, drift serves as a null model of sorts - one that should be ruled out before you can claim that anything more interesting is happening. However, it's not clear what the "uninteresting" type of change is for things that replicate by passing through human cognition and human social systems - like culture does. Is there even a reasonable equivalent of drift in cultural transmission? How should we go about conceptualizing and modeling the evolutionary forces at play in culture?

One candidate for a drifty-lookin' human behavior is probability matching: when people reproduce similar distributions of variation to that which they've learned from. And probability matching is rampant in human behavior (from language learning, to decision making, and even at the neural level). But I think this is a clearly different process than drift, however it still may qualify under Bentley's vague criteria - we can test that out. And there have got to be more drift-esque processes, anyone have any ideas?

If you're interested in these issues or modeling evolution (of any type of system), please give me a shout!

Vanessa

vanferdi [at] gmail.com

==="Small Steps and Big Ideas" Group===

[http://tuvalu.santafe.edu/events/workshops/index.php/Christa_Brelsford Christa] [http://tuvalu.santafe.edu/events/workshops/index.php/Daniel_Wu Dan] [http://tuvalu.santafe.edu/events/workshops/index.php/Xin_Lu Xin] and Tom spent a while talking after dinner about a bunch of big ideas. Some things we thought about were *big data type network problems, *integrating qualitative social information with models of physical systems, *using games to understand cooperation and decision making.

We'll meet at dinner at 5:30 today (Tuesday, June 5th) in the cafeteria.

=== 107 Proteins in 10-15 cubic meters ===
Cells rely on proteins to perform vital metabolic and signaling functions; however, it is unclear how proteins are successfully directed to their necessary cellular location(s) in a densely-packed macromolecular environment within the cytoplasm and on the cellular membrane in a short timescale (see for example [http://www.pnas.org/content/108/16/6438.full Weigel et al., PNAS 2011]). Using the cell as a manipulatable model of complexity, one could begin to define the parameters and questions, as they pertain to prokaryotic and eukaryotic cells. If interested, please drop me a line: Sepehr Ehsani; sepehr.ehsani[at]utoronto.ca.

=== Innovation and Technological Progress ===

I noticed that a number of people mentioned that they were interested in some way in relation to innovation. I was wondering if anyone was interested in a project looking at how particular technologies progress over time and whether charting the form of successful (and/or unsuccessful) previous technologies such as the transistor, fission reactor, mobile phone, etc. in terms of either price, efficiency, or some other variable may be useful in predicting whether a current technology such as solar PV, fuel cell, or something else is following a similar trajectory. Other possible ideas might be to look at using patent, publication, or collaboration network data to reveal certain features of innovation that are not captured by other statistics, particularly for technologies that have yet to reach the market. SFI Professor Doyne Farmer has looked at some of this already in 'The Role of Design Complexity in Technology Improvement', see link: http://adsabs.harvard.edu/abs/2009arXiv0907.0036M

This could be a jumping off point for some ideas on data, methods, models etc. Just throwing the idea out there and it's welcome to completely change but if you're interested, message me (Gareth Haslam) haslam@ias.unu.edu or find me in class.

=== Space, Stochasticity, Stability; Speciation? ===

[http://tuvalu.santafe.edu/events/workshops/index.php/Xue_Feng Xue], [http://tuvalu.santafe.edu/events/workshops/index.php/Chloe_Lewis Chloe] and [http://tuvalu.santafe.edu/events/workshops/index.php/Xiaoli_Dong Xiaoli]are all working in ecosystems that experience_ a lot of unpredictability in a limiting ecosystem variables (water and/or nutrients); we see patchiness in space and time in how organisms are arranged; and we have some ideas about how the stochasticity may cause the spatial arrangements. [http://tuvalu.santafe.edu/events/workshops/index.php/Si_Tang Si] is working on the stability and robustness of ecosystems.

With enough time, this is likely to involve speciation either to express different strategies, or as a result of spatial separation.

The [[Spatial-Stochastic]] group is writing up their ideas to share here and look for overlap and coupling.

=== Plasticity in Neural Networks ===
I've done some modeling which shows that the amount of genetic variation that accumulates at any particular metabolic gene (enzyme) in a population at any given time is a function of the network topology in which the gene is embedded, as well as the distance of the network output from an optimum. So, for instance, in a linear metabolic network, enzymes at the beginning of a pathway will tend to be more constrained (show less variation in the population) than at the end of the pathway. This makes sense given that any changes in those first genes would ripple through the system and have a greater relative effect than mutations in later genes. However, this is only true when a population is already close to an optimum. When far from an optimum, we see the exact opposite trend with more variation in the front of the pathway. This also makes sense - when far from a goal, taking bigger steps gives individuals a better chance of achieving higher fitness. The system as a whole then uses the different relative step sizes according to pathway position to "fine tune" its output.
I think these findings are quite general - at least the model we used was simple enough that it could apply to many different types of directional developmental processes. We can conceptualize these "genes" more generally as sequential steps in a developmental process with some arbitrary goal. These could be steps in a factory assembly line, major product revisions versus minor releases, or (and this is my favorite), neurons learning about their environment. I'm curious what would happen if we took a similar approach to model neural networks. Genetic variation is the raw material for evolution while neural plasticity is the raw material for learning. The question we would be trying to answer is where, within a neural network, would we expect the most plasticity given a particular network topology and distance form a learning goal.
Please contact me (Mark Longo) if this sounds interesting. I'll be available during unstructured time, or you can email mlongo@stanford.edu.
[http://tuvalu.santafe.edu/events/workshops/index.php/Mark_D._Longo]

=== Robustness of complex networks ===
[[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 ====
* [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://www.barabasilab.com/pubs/CCNR-ALB_Publications/200007-27_Nature-ErrorAttack/200007-27_Nature-ErrorAttack.pdf Error and attack tollerance of complex networks]
* [http://www.cis.upenn.edu/~mkearns/teaching/NetworkedLife/hierarchical.pdf Hierarchical organization in complex networks]
* [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://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]
* Add a relevant paper...

=== Systemic Risk in Financial Networks and/or an ABM of money/liquidity===

'''Systemic Risk in Financial Networks:''' Hypothesis: the motive to diversify risk at the level of the individual agent (i.e., for an agent to increase its connectivity) will increase systemic risk (by systemic risk I mean vulnerability of the system to widespread collapse). Point of departure is the [http://en.wikipedia.org/wiki/Forest-fire_model Forest Fire] model from statistical physics.

Key difference(s) between the physics version of the Forest Fire model, and the "economics" version of the Forest Fire model I have in mind are:
* Tree growth probability (which determines network structure) must be endogenous. Agents must be able to choose which other agents to link with.
* Probability of lightning strikes (i.e., defaults on specific loans) must also be endogenous.

I think that financial networks might exhibit self-organizing criticality in the sense that diversification will reduce the probability of lightning strikes (i.e., defaults), however over time systemic risk builds up as a result of the diversification which means that eventually a small number of lightning strikes might be enough to bring the entire system down.

'''ABM of the emergence of Money:'''
Basically, I would be interested in building an ABM of the emergence of money based around the following economic models of money developed by Nobu Kiyotaki and John Moore:
* [www.princeton.edu/~kiyotaki/papers/Evilistherootofallmoney.pdf Evil is the Root of all Money]
* [www.princeton.edu/~kiyotaki/papers/Financial-Deepening.pdf Financial Deepening]

These models take a broad view of money: "money" is any asset which is widely accepted as a medium of exchange. In these models agents manage projects which require capital investment now in order to generate a return at some point in the future and agents must trade financial promises (think debt contracts) in order to obtain the needed investment. Two key parameters of is these models (which are assumed COMMON to all agents in the above models in order to maintain analytical tractibility) are 0 < theta < 1 and 0 < phi < 1. Theta is the fraction of the future return from the project that an agent can promise to repay in the future in exchange for investment now. Phi is the fraction of the face value of a debt contract (which by construction is a contract between two agents) that can be re-sold to a third agent.

Hypothesis: In an ABM where agents differ in terms of both theta and phi, the promises of only a small number of agents will be widely traded (i.e., will serve as money).

If anyone might be interested in working on these projects, send me and email: drobert.pugh at gmail dot com

=== Price-time dynamics of contracts traded on prediction markets===
Prediction markets have been shown to outperform traditional methods of polls and opinion surveys in forecasting future events. I am interested in exploring the price-time dynamics of contracts traded on prediction markets to better understand how they are able to aggregate individual opinion to establish collective insight.

Several questions that I’m curious to probe further:
* How do ‘information shocks’ generated by news sources influence price-time trajectories?
* Can features of the underlying dynamics be characterized using a simple model?
* What is the minimum number of traders required for an accurate prediction?
On a separate note, I invite you to share your opinion regards whether “China will win the most medals at the 2012 London Olympics”, by logging into the following [https://csss12.inklingmarkets.com/user/login site] (please send me your email address and I will send you the login details).

If you haven't used a prediction market before don't worry -just follow the instructions provided in the site to 'buy' and 'sell' contracts according to your expectation.

If you are interested in the discussing any of the above questions or have other ideas related to prediction markets please get in touch with me at: sanith at mitre dot org

Complex Systems Summer School 2012-Projects & Working Groups

2012-06-05T04:51:44Z

CLewis: /* Project proposals */

Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-05T04:19:39Z

CLewis:

{{Complex Systems Summer School 2012}}

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

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

==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. 
7. 
8. 
9. 
10. 
11. 
12. 
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. 
9. 
10. 
11. 
12. 
13. 
14. 
15.