Santa Fe Institute Events Wiki - User contributions [en]

Presentations 2014

2014-06-29T17:37:33Z

Pfenningers:

{{Complex Systems Summer School 2014}}

9:00 - 9:15: Introducing energy constraints into Neutral models of biodiversity 

9:15 - 9:30: Biological and Software Systems 

9:30 - 9:45: Information Theory of the Heart

9:45 - 10:00: Tradeoff between division of labor and robustness to perturbation

10:00 - 10:15: The architecture of an empirical genotype-phenotype mapping

10:15 - 10:30: BREAK

10:30 - 10:45: Cities Growth

10:45 - 11:00: Network Tolerance of Failure

11:00 - 11:15:

11:15 - 11:30: Interdisciplinary Research Networks

11:30 - 11:45:

12:00 - 1:00: LUNCH & GROUP PHOTO

1:00 - 1:15 

1:15 - 1:30:

1:30 - 1:45:

2:00 - 2:15:

2:15 - 2:30:

2:30 - 2:45:

2:45 - 3:00: BREAK

3:00 - 3:15: 

3:15 - 3:30: 

3:30 - 3:45: 

3:45-4:00: 

4:00 - 4:15 

4:15 - 4:30 

4:30 -

Complex Systems Summer School 2014-After Hours

2014-06-28T16:19:18Z

Pfenningers:

{{Complex Systems Summer School 2014}}

==Monday June 30: Swing Dancing Round 2==

Come swing dancing at Odd Fellow's Hall (1125 Cerillos Road) at 7pm Monday night! Lesson is at 7, free dancing begins at 8. Entry fee is $8 and $3 respectively.

Meet up '''in the parking circle after evening lecture (8:15ish)''' if you're interested. And sign up for a car below:

JP's car: 
1. JP 
2. Diana 
3. Anna 
4. Morgan 
5. Renske 

JP's other car: 
1. Sanja 
2. Nicolas 

==Sunday June 29: JP's BBQ==

Anyone interested in having a little barbecue at my family's farm on Sunday? I was thinking 4:00 - 9:00 or so. Beer, bonfire, burgers, brats. Maybe a wine tasting.

If you're interested, let me know!

That sounds awesome. If there's any possibility of a group of folks leaving early (by 6 or so) I'm in! - Diana 
Definitely in! - Diego 
Alberto 
Cecilia 
Anna 
Jose 
Nicolas 
Brais 
Claire 
Luis 
Michael 
Morgan 
George 

==Saturday June 28: Sunset hike up Atalaya mountain==

Meet: a couple minutes before 7:00pm at the lower parking circle -- we want to leave at 7:00pm

1. Stefan 

==Saturday June 28: Taos!==

Taos! Refuge of artists and hippies!

[[JP]] is going to take a bit of a tour of northern New Mexico on Saturday. We'll head up through Espanola, along the banks of the Rio Grande to Taos, and then down the High Road. Who knows, we might stop at a few of the wineries along the way to sample their goods.

Trip stops may include the Taos Gorge Bridge, Earthships, Taos Pueblo, historic mountain towns, a few wineries for tastings, and the Santuario de Chimayo.

JP's car 
1.JP 
2.Jose 
3 Nicolas 
4.Morgan 
5.Diego 

JP's 4runner 
1.Alberto 
2.Sanja 
3.Massimo 
4.Francesca 
5.Leto 
6.George 

Jenn's car 
1. Jenn 
2. Claire 
3. Ernest Liu 
4. Blaz 

Still needs a ride 
1. Cecilia 
2. Matt Ayres - happy to fit in the boot or in the back of a runner . . . . 

==JP's Adventures in Gastronomy==

St. John's College dining got you down? Realized that yesterday's baked potatoes are tomorrow's potatoes au gratin? Then you, my friend, need to get off campus.

On Wednesday, let's go off campus for drinks at Santa Fe Brewing Company after Geoffrey's evening lecture. Meet in the coffee shop at 8:00 to determine who wants to go. My car has limited seats, but maybe someone else can volunteer a car?

Thursday night, let's get out and go somewhere nice. I'm thinking either Epazote or Pink Adobe, but I reserve the right to go other places as decided. Add your name here and I'll set up some reservations. We'll leave at 6:30pm on Thursday.

 
'''Wednesday Santa Fe Brewing Company'''

JP's Car 
Sanja 
Luis 
Cole 
Leto 
Alberto (go DGT group!) 

JP's OTHER car 
1.Beth 
2.Massimo 
3.Francesca 
4.Emília 
5. Cecilia 

Still needs a ride 
Ana María 
Nicolas 
Diego 
Jose 
Sarah 
Claudius 

'''Thursday dinner'''

JP's Car 
1.JP 
2.Anna 
3. Diana 
4.Morgan 
5. Jose 

JP's OTHER car 
1.Jenn (driver) 
2.Catherine 
3. 
4. Renske 
5. Cole 
6. Ana Maria 

Still needs a ride - 1st Cab 
Diego 
George 
Sanja 

== Saturday June 28, 2014 9:00 am Santa Fe Botanical Garden ==

This month the feature is Origami in the Garden. The gardens are open 7 days a week 9-5. I plan to leave from the circle at 9 am. It's less than a mile walk to the gardens. Entrace fee is $7.

1. James 
2. Diana 
3. <strike>Anna</strike> Sorry, too much work to do today 
4. ... 

==Watch Orange is the New Black: Season Two, with Nix!==
One of my partners gave in and started watching it without me, so I need to catch up with her! After my lectures next week, of course. -Nix

Possibly Interested: 
1. Nix 
2. Cole 
==June 30, 5:30am - Sunrise hike to Atalaya mountain==

We'll meet at 5:30 am at the circle then hike as far as we can go to be back by 8:00 am.

Equipment:
- Walking sneakers or mountain boots
- Backpack
- Liquids: about 1.5 liters
- Different warm layers (it could be windy and chilly)

This is running every M, W, and F.

If you do not have something or you have any question just contact James Holdener

Participants:
1. James Holdener
2.

==June 26, 6:30am - Kung Fu Training==

For all of you who want to get seriously active before breakfast; we'll do an hour of kung fu training. Most of this will be general workout - running, pushups, etc. Then I will show you the most basic positions in kung fu, and their transitions in one of the basic forms. Disclaimer: I am not by any measure qualified to teach (only been doing it for 2 years). If you can take what I say with a grain of salt, if you know the limits of your own body and want to get active, feel free to join! If you cannot make it today, there will be opportunities next week too :). 

You'll need: 
- comfy clothes, layers you can throw off 
- flexible shoes (can also go barefoot, but the grass is wet and cold...) 
- water 

We'll meet at the parking circle closest to the dorms, and then walk down to the sports field. 

Participants: 
1. Renske 
2. Diana 
3. George (Please do not wait for me if I do not show up till 6.35. Thanks!) 

==June 27, 6:00-9:00pm Todd and the Fox==

See Juniper's brother's band [https://www.facebook.com/events/306176446198443/ Todd and the Fox] play on the Plaza at the Santa Fe Band Stand. For full line up of the Santa Fe Bandstand (June 23-August 28) visit [http://santafebandstand.org/ here]

1. Juniper

2. Matthew Ayres

3. Flavia Marquitti

4. Leto Peel

5. Morgan Edwards

6. Claire Lagesse

7. Leo

8. Ernest Yu Liu

9. Cecilia

10. Emília

11. Sanja

12. Renske

13. Nicolas Scholtes

14. José Aguilar-Rodríguez

15. Francesca

16. Marcus Levine

17. Diego

18. Sarah L

19. Alberto

20. George

==World Cup==
All times are Santa Fe (MST)
 
Thursday, June 12 
1) Brazil vs. Croatia - 1400 (MST) 
 
Friday, June 13 
1) Mexico vs. Cameroon - 1000 (MST) 
2) Spain vs. Netherlands - 1300 (MST) 
3) Chile vs. Australia - 1600 (MST) 
 
Saturday, June 14 
1) Colombia vs. Greece - 1000 (MST) 
2) Uruguay vs. Costa Rica - 1300 (MST) 
3) England vs. Italy - 1600 (MST) 
4) Côte d'Ivoire vs. Japan - 1900 (MST) 
 
Sunday, June 15 
1) Switzerland vs. Ecuador - 1000 (MST) 
2) France vs. Honduras - 1300 (MST) 
3) Argentina vs. Bosnia and Herzegovina - 1900 (MST) 

'''Sports Bars in Santa Fe: ''' 
[http://junctionsantafe.com/ Junction] 
[http://www.yelp.com/biz/el-paseo-bar-and-grill-santa-fe El Paseo Bar] 
[http://www.santafenewmexican.com/news/business/on-tap-craft-beers-from-around-state-at-downtown-s/article_de6b6182-fdcd-58ef-9f2e-6e9cc5bf5a85.html Santa Fe Tap Room] 
[http://www.cowgirlsantafe.com/ Cowgirl Cafe] 
[http://www.riochamasteakhouse.com/ Rio Chama Steak House] 

'''On campus viewing opportunities:''' Lower Campus Common's Room has a TV that can air the games, and on some occasions we can project the games after-hours in the Great Hall

==Santa Fe Railyard Events==

There are a ton of really fun and cool events happening all summer at the Santa Fe Railyard, check the calendar out [http://www.railyardsantafe.com/ here]

 
 
== '''PREVIOUS EVENTS'''==

==June 20, 6:30am - Kung Fu training==

For all of you who want to sleep a bit longer, but then get seriously active before breakfast, we'll do some kung fu training. Most of this will be general workout - running, pushups, etc.
Then I will show you the most basic positions in kung fu, and their transitions in one of the basic forms. Disclaimer: I am not by any measure qualified to teach (only been doing it for 2 years).
If you can take what I say with a grain of salt, if you know the limits of your own body and want to get active, feel free to join! If you cannot make it today, there will be opportunities next week too :).

You'll need: 
- comfy clothes, layers you can throw off 
- flexible shoes (can also go barefoot, but the grass is wet and cold...) 
- water 

We'll meet at the parking circle closest to the dorms, and then walk down to the sports field. 

Participants: 
1. Renske 
2. Diana (Renske - I have some legit physical limitations, but I can handle them, and I'd like to try!) 
3. James 
4. Cecilia 

==Sunday June 22, 6:00-9:00pm Santa Fe Fuego Baseball Game==

Come heckle and drink beer while watching some minor league baseball - [http://www.santafe.com/calendar/event/santa-fe-fuego-vs.-trinidad-triggers1 Fuego v. Trinidad Triggers]

1. Juniper

2. Mathew Ayres

3. Lin Li

4. Flavia Marquitti

5. Leto Peel

6. Claire Lagesse

7. Ernest Yu Liu

8. Alberto Antonioni

9. Diego Barneche

10. Nicolas Scholtes

11. Massimo Stella

==June 22, El Rancho de las Golondrinas==

[[JP]] is going to the lavender festival at Golondrinas Museum (www.golondrinas.org) on Sunday. Let's meet up at 12:30 in the cafeteria and then head out?

JP's Car 

1.JP 
2.Catherine 
3.Hiroshi 
4.Lin Li 
5.Sanja 

Still wants to go 
1. 
2. 
3. 
4. 

==June 22, 7:00am - Hike the mountain!==

Meet Diana in the parking lot near the dorms at 7am this Sunday to hike up to the top of the mountain before brunch!

==June 21, 10:00am - Bandelier Field Trip==

We're taking a trip to [http://www.nps.gov/band/index.htm Bandelier National Monument] on Saturday June 21th. Please visit the [[Bandelier 2014 | Bandelier Field Trip]] Page to sign up!

== The Game. ==
A few of us have talked about a game we would like to play during the summer school. Let me know via email (cole.mathis@asu.edu) by Wednesday (6/18) morning if you would like to play the game.

''The Rules:''

You will be randomly assigned the name of another player (your target) and an object (your weapon).

Your job is to get your target to accept your weapon from you.

If/when your target accepts your weapon from you, your target it out (you killed them), and you are now given his target and weapon.

You cannot tell anyone who your target is or what your weapon is.

For example, Suppose I (Cole) am assigned Leto as my target and a pen as my weapon. I need to somehow offer Leto a pen and he must accept it from me. When Leto accepts the weapon he is out, and I inherit his target and weapon, and the game continues.

To win the game you must be the last person left.

Once the game starts it will be constantly played, you can get killed at any time and you can kill at anytime until the game is over.

We will not publish a list of all participants.... Anyone may be playing. We will not publish a list of people who have been killed in the game although deaths may happen in public.

When you are out (killed) you should email me (cole.mathis@asu.edu) to let me know and forward your target and weapon to your murderer, please include the situation that led to your death (particularly if it was interesting, clever, or most importantly funny!

We think this would be a lot of fun and easy to play with this many people so please email me before wednesday if you are interested!

cole.mathis@asu.edu

DO NOT PUBLISH YOUR INTENT TO PLAY HERE!

==Jessica Birthday celebration! - June 16, some bar/restaurant downtown, leaving from Saint Johns at 7:30pm==

We are going to celebrate at Cowgirl (http://www.cowgirlsantafe.com/)

The map is here: http://goo.gl/maps/lEFxd

We can meet at the parking lot close to the dorms, 7:15pm. There are some people with their own cars. We can fit some people on these cars, and call taxis (or we can go walking, if you prefer).

 

==June 11, 6:30pm - Sunset hike to Atalaya mountain ('''pictures''')==

Pictures: https://picasaweb.google.com/104772005161459586991/AtalayaSantaFeNM11062014

Track: http://es.wikiloc.com/wikiloc/view.do?id=7069532

==June 12, 10:00pm Full Moon Walk==

It's FULL MOON!!! And Friday 13th! I think this deserves a FULL moon walk with a few drinks on the top of that hill near the campus and a FULL appreciation of the FULL moon. Maybe also a good opportunity to bring the banjo and whatever fits!!

Stock up on drinks and leave at 10pm outside of the Peterson Student Center after the others return from Tomasitas...

Joining: 
1. Leo 
2. Nicolas 
3. Leto 
4. Brais (maybe) 
5. Pooya 
6. Ana María 

==June 12, 6:00pm Tomasita's==

Come experience some down home New Mexican cooking at Tomasita's. Margaritas and enchiladas! Yum!

JP's car

1.JP 
2.Nix 
3.Sanja 
4.Catherine 
5. 

==June 11, 7:00pm Santa Fe Bite==

Green chile cheeseburger time. Meet at the parking circle in front of the coffee shop.

JP's car

1.JP 
2.Nix 
3.Ana Maria 
4.Diana L-G 
5.Morgan Edwards 

Juni's car

1. Juni 
2. Sanja 
3. Nicolas 
4. 
5. 

==June <strike> 10</strike>11, 5:00pm - Supplies Run==

JP is going down to buy the stuff everyone needs. He'll take you if you would like.

JP's GTI (5 seats)

1.JP 
2.Anna Olson 
3.Bernardo Furtado 
4.Ali Kharrazi 
5.Ana Maria Gomez Lopez 

Common Supplies:

What kinds of supplies can we all split? Make a list here and JP will buy a big box or two for everyone.

1). Laundry Soap 
2). Bottles of water (for the hikes) ? Otherwise, please buy a big one (or multiple small ones) for Renske :) 
3) 3 Flashlights and batteries for James 
4) Earplugs. If nobody needs them, please buy a pack for Pooya. Thanks! 
5) Beer (I second this request - ''Nicolas'') 

Individual Supplies:

1) Olive oil-- 1 liter bottle---Vipin 
2) Downy Dryer Sheet -- a small box enough for ~6-8 loads--- Nhat Nguyen
3) Please buy converter for power plug (Europe- US) for Sanja
4) Another converter for power plug (Europe-US), toothpaste, sun protection, Brais.

==June 13, 5:30am - Sunrise hike to Atalaya mountain==

Update: I've modifed to be back a half hour earlier to an hour to frehen up and eat before taking the bus to SFI.

We'll meet at 5:30 am at the circle then hike as far as we can go to be back by 7:30 am.

Equipment: 
- Walking sneakers or mountain boots 
- Backpack 
- Liquids: at least 1.5 litres 
- Different warm layers (it could be windy and chilly) 

I have two flashlights but they weren't needed on Wednesday.

If you do not have something or you have any question just contact James Holdener

Participants: 
1. James Holdener 
2. 

==June 14, 10am- Farmer's Market==

We are going to walk down to Santa Fe to go to the Saturday morning farmers market, as well as explore Santa Fe. Meet at 10am in the circle by the dorms.

==June 15, 10am- Yoga class==

Yoga has been postponed, maybe later on today.

==June 15, 3pm - Playing soccer/futbol==

Meet at 3:00pm at the parking lot. If you're late, just come find us at the field. It's #48 on this map of St. John's campus: http://www.sjc.edu/files/3713/9568/3101/stjohns3D.pdf

==June 19 Rodeo de Santa Fe==

<strike>Wednesday</strike> Thursday, June 19!

Come on down for the 65th annual Rodeo de Santa Fe! Watch real-life cowboys get thrown off of various species of raging livestock for their competition and your entertainment. Starts at 7:00pm, we should leave SJC about 6:00. http://rodeodesantafe.org/

JP's GTI 
1. JP 
2. Alireza Goudarzi 
3.Matthew Ayres 
4.Nhat Nguyen 
5.Lin Li 

JP's 4runner 
1.Stefan Pfenninger 
2.Ali Kharrazi 
3.Leto Peel 
4.Morgan Edwards 
5.Claire Lagesse 

Juni's Car 
1.Alberto Antonioni 
2.Luis Martinez Vaquero 
3.Jennifer Hellmann 
4. Laurent 

Sander's Car 
1.José Aguilar-Rodríguez 
2.Ernest Yu Liu 
3.Pooya Rezaei 
4.Qiao Zhi (George) 

Jessica's Car 
1. Renske Vroomans 
2. Emília Garcia Casademont 
3. Degang Wu 
4. Sanja Selakovic 

 James G's Rental 
1. James G. 
2. Catherine 
3. Heath 
4. Massimo 
5. Nicolas K. Scholtes 

Josh Garland's Awesome Mobile 
1.Francesca Lipari 
2.Leo 
3.Nicolas Scholtes 
4.Cecilia 

Still Needs a Ride

Complex Systems Summer School 2014-Tutorials

2014-06-24T01:42:13Z

Pfenningers: /* Tutorial: Introduction to Python and its scientific programming ecosystem */

{{Complex Systems Summer School 2014}}

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

Also, please email juniper@santafe.edu to request a tutorial slot.

=='''Tutorial: Rotors, Spirals and Scroll Waves''' ==
'''Speaker:''' Hiroshi Ashikaga 
'''Date & Time:''' June 16 from 2:00-2:30pm 
'''Content:''' A short introduction to cardiac electrophysiology and basic mechanisms of arrhythmia. 
'''Motivation:''' To get more people interested in the heart as a complex system. 
'''Prerequisite:''' Whoever has a heart. 
'''References:''' This is a short list of reference papers for those interested in the topic. I am happy to review them and discuss with any of you if you are interested. 

1. Winfree [[File:1989_WinfreeA_JTB.pdf]] 
2. Gray ''et al.'' [[File:1998_GrayRA_Nat.pdf]] 
3. Garfinkel ''et al.'' [[File:2000_GarfinkelA_PNAS.pdf]] 
4. Qu ''et al.'' [[File:2000_QuZ_ABME.pdf]] 
5. Fenton et al. [[File:2002_FentonFH_Chaos.pdf]] 
6. Weiss ''et al.'' [[File:2005_WeissJ_Circ.pdf]] 
7. Schotten [[File:2011_Schotten_PR.pdf]] 
8. Pandit and Jalife [[File:2013_Pandit_CircRes.pdf]] 

=='''Tutorial: Browser-Based Data Visualization'''==
'''Speaker:''' James Gentile 
'''Date & Time:''' June 17 form 7:00-8:15pm 

Data visualization is essential for analysis and communication but complex data often need complex visualizations. Interactive browser-based visualizations are unique because they can be viewed using (almost) any web browser. This tutorial will introduce [http://d3js.org/ d3.js], the JavaScript library behind many of the web’s great data views.

No JavaScript experience is required. I’ll be introducing the language, concepts and we’ll build an interactive visualization for delayed-point embedding.

If you’re planning to attend, I recommend downloading [http://www.mozilla.org/en-US/firefox/new/ Firefox] and a syntax-highlighting editor: [http://www.barebones.com/products/textwrangler/ TextWrangler] for Macs or
[http://notepad-plus-plus.org/ Notepad++] for Windows. These will help you follow along.

== '''Tutorial: Parallel Programming - A Brief Introduction''' ==

'''Speaker:''' Fahad Khalid 
'''Date & Time:''' June 18 7:00-8:15pm 
'''Content:''' A language agnostic introduction to basic concepts in parallel programming. 
'''Motivation:''' Several of us here at the CSSS do compute intensive simulations. Since single cores are not getting faster anymore, the only way to speed up simulations is by utilizing multiple cores. So it's good to know how to design and code a simulation that can take advantage of multiple cores. 
'''Pre-requisites:''' Just a passing familiarity with programming. 
'''Slides:''' [[File:Fahad_CSSS-2014_ParProg.pdf]]
 
Please use the ''comments'' sections below to let me know what you'd like to hear, what are your expectations from this tutorial, etc. I'll try my best to tailor the talk accordingly. Many thanks to those who've already suggested content for the talk. I'd appreciate if you could repeat the comments here as well (the CSSS Wiki seems to be a lot more organized than my brain :-)). 
 
'''Comments:''' 
* Please cover race condition.
* Generalized strategies for how a problem should be parallelized.
** Identifying problems that cannot (or should not) be parallelized.
* GPU vs CPU parallelization (e.g., CUDA vs traditional compute cluster)
* parfor in Matlab

== '''Tutorial: Introduction to Agent-based Modeling with Python''' ==
'''Speaker:''' Vipin P. Veetil 
'''Date and Time:''' June 19 4:15-5:15pm 
'''Description:''' In this tutorial we will build a ABM of Rock-Papers-Scissors game. We will learn how to initialize agents, get them to play with each others, record payoffs and develop different strategies. We will also learn how to get agents to play games on network using NetworkX. 
'''What to do before tutorial''':
Download and install python and an editor.
This is one option: https://www.enthought.com/products/canopy/ 
Another option: A lot of the brain power at Enthought left and founded Continuum Analytics to create Anaconda (https://store.continuum.io/cshop/anaconda/), a better solution than Canopy, (in Glen's humble opinion). They also created another cool tool in Wakari (https://wakari.io/).

'''Motivation''' ''Why agents?'' (http://www.brookings.edu/es/dynamics/papers/agents/agents.pdf) 
For time-constraint people, here is a two-page pamphlet in the SFI tradition arguing for the importance of ABM in economics [[File:Foley09 Econ needs ABM.pdf]]. 

'''Game Tournament''': At the end of the tutorial I will introduce you to the "Non-prisoners dilemma" game. I'll be running a tournament between different strategies. You are invited to submit a strategy for the tournament. More details soon.

'''Code for tutorial''':

https://github.com/VipinVeetil/RPS

https://github.com/VipinVeetil/Networks

== '''Tutorial: Introduction to Python and its scientific programming ecosystem''' ==
'''Speaker:''' Stefan Pfenninger 
'''Date & Time:''' June 23 4:15-5:15pm 

'''Description:''' High-level introduction to what Python is, what the major components of the scientific Python ecosystem are, and what the easiest (in my opinion) way is to start using it productively. Some simple examples will be shown. Participants should walk away equipped with the knowledge necessary to further explore on their own. Depending on the outcome of this session, we might follow it up with a hands-on session later in the week.

'''Audience:''' Ideally have at least basic skills in another programming language, and be interested in getting a quick, structured intro to Python, with links to where to find further information.

'''Slides:''' [[File:Python intro.pdf]], and download the [https://www.dropbox.com/s/u5gnr8kh4ddmpbf/network_data.csv CSV file for the NetworkX example]

== '''Tutorial: Computing with Intrinsic Dynamics of Systems''' ==
'''Speaker:''' Alireza Goudarzi 
'''Date & Time:''' June 23 7:00-8:15pm 

== '''Tutorial: Claire Lagesse - Introduction to Geographic Information Systems (GIS)''' ==
'''Speaker:''' Claire Lagesse 
'''Date and Time:''' June 24 7:00-8:00pm 

If you are willing to attend... Please download : 

* QGIS [http://www.qgis.org/en/site/forusers/download.html here]

* some data with [http://download.geofabrik.de/north-america/us/new-mexico-latest.shp.zip this] link

== '''Tutorial: Mathematica''' ==
'''Speaker:''' Massimo Stella 
'''Date and Time:''' June 26 from 1:30-2:30pm

Complex Systems Summer School 2014-Tutorials

2014-06-24T01:25:38Z

Pfenningers: /* Tutorial: Introduction to Python and its scientific programming ecosystem */

{{Complex Systems Summer School 2014}}

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

Also, please email juniper@santafe.edu to request a tutorial slot.

=='''Tutorial: Rotors, Spirals and Scroll Waves''' ==
'''Speaker:''' Hiroshi Ashikaga 
'''Date & Time:''' June 16 from 2:00-2:30pm 
'''Content:''' A short introduction to cardiac electrophysiology and basic mechanisms of arrhythmia. 
'''Motivation:''' To get more people interested in the heart as a complex system. 
'''Prerequisite:''' Whoever has a heart. 
'''References:''' This is a short list of reference papers for those interested in the topic. I am happy to review them and discuss with any of you if you are interested. 

1. Winfree [[File:1989_WinfreeA_JTB.pdf]] 
2. Gray ''et al.'' [[File:1998_GrayRA_Nat.pdf]] 
3. Garfinkel ''et al.'' [[File:2000_GarfinkelA_PNAS.pdf]] 
4. Qu ''et al.'' [[File:2000_QuZ_ABME.pdf]] 
5. Fenton et al. [[File:2002_FentonFH_Chaos.pdf]] 
6. Weiss ''et al.'' [[File:2005_WeissJ_Circ.pdf]] 
7. Schotten [[File:2011_Schotten_PR.pdf]] 
8. Pandit and Jalife [[File:2013_Pandit_CircRes.pdf]] 

=='''Tutorial: Browser-Based Data Visualization'''==
'''Speaker:''' James Gentile 
'''Date & Time:''' June 17 form 7:00-8:15pm 

Data visualization is essential for analysis and communication but complex data often need complex visualizations. Interactive browser-based visualizations are unique because they can be viewed using (almost) any web browser. This tutorial will introduce [http://d3js.org/ d3.js], the JavaScript library behind many of the web’s great data views.

No JavaScript experience is required. I’ll be introducing the language, concepts and we’ll build an interactive visualization for delayed-point embedding.

If you’re planning to attend, I recommend downloading [http://www.mozilla.org/en-US/firefox/new/ Firefox] and a syntax-highlighting editor: [http://www.barebones.com/products/textwrangler/ TextWrangler] for Macs or
[http://notepad-plus-plus.org/ Notepad++] for Windows. These will help you follow along.

== '''Tutorial: Parallel Programming - A Brief Introduction''' ==

'''Speaker:''' Fahad Khalid 
'''Date & Time:''' June 18 7:00-8:15pm 
'''Content:''' A language agnostic introduction to basic concepts in parallel programming. 
'''Motivation:''' Several of us here at the CSSS do compute intensive simulations. Since single cores are not getting faster anymore, the only way to speed up simulations is by utilizing multiple cores. So it's good to know how to design and code a simulation that can take advantage of multiple cores. 
'''Pre-requisites:''' Just a passing familiarity with programming. 
'''Slides:''' [[File:Fahad_CSSS-2014_ParProg.pdf]]
 
Please use the ''comments'' sections below to let me know what you'd like to hear, what are your expectations from this tutorial, etc. I'll try my best to tailor the talk accordingly. Many thanks to those who've already suggested content for the talk. I'd appreciate if you could repeat the comments here as well (the CSSS Wiki seems to be a lot more organized than my brain :-)). 
 
'''Comments:''' 
* Please cover race condition.
* Generalized strategies for how a problem should be parallelized.
** Identifying problems that cannot (or should not) be parallelized.
* GPU vs CPU parallelization (e.g., CUDA vs traditional compute cluster)
* parfor in Matlab

== '''Tutorial: Introduction to Agent-based Modeling with Python''' ==
'''Speaker:''' Vipin P. Veetil 
'''Date and Time:''' June 19 4:15-5:15pm 
'''Description:''' In this tutorial we will build a ABM of Rock-Papers-Scissors game. We will learn how to initialize agents, get them to play with each others, record payoffs and develop different strategies. We will also learn how to get agents to play games on network using NetworkX. 
'''What to do before tutorial''':
Download and install python and an editor.
This is one option: https://www.enthought.com/products/canopy/ 
Another option: A lot of the brain power at Enthought left and founded Continuum Analytics to create Anaconda (https://store.continuum.io/cshop/anaconda/), a better solution than Canopy, (in Glen's humble opinion). They also created another cool tool in Wakari (https://wakari.io/).

'''Motivation''' ''Why agents?'' (http://www.brookings.edu/es/dynamics/papers/agents/agents.pdf) 
For time-constraint people, here is a two-page pamphlet in the SFI tradition arguing for the importance of ABM in economics [[File:Foley09 Econ needs ABM.pdf]]. 

'''Game Tournament''': At the end of the tutorial I will introduce you to the "Non-prisoners dilemma" game. I'll be running a tournament between different strategies. You are invited to submit a strategy for the tournament. More details soon.

'''Code for tutorial''':

https://github.com/VipinVeetil/RPS

https://github.com/VipinVeetil/Networks

== '''Tutorial: Introduction to Python and its scientific programming ecosystem''' ==
'''Speaker:''' Stefan Pfenninger 
'''Date & Time:''' June 23 4:15-5:15pm 

'''Description:''' High-level introduction to what Python is, what the major components of the scientific Python ecosystem are, and what the easiest (in my opinion) way is to start using it productively. Some simple examples will be shown. Participants should walk away equipped with the knowledge necessary to further explore on their own. Depending on the outcome of this session, we might follow it up with a hands-on session later in the week.

'''Audience:''' Ideally have at least basic skills in another programming language, and be interested in getting a quick, structured intro to Python, with links to where to find further information.

'''Slides:''' [[File:Python intro.pdf]], CSV file for the second (NetworkX) example: TBA

== '''Tutorial: Computing with Intrinsic Dynamics of Systems''' ==
'''Speaker:''' Alireza Goudarzi 
'''Date & Time:''' June 23 7:00-8:15pm 

== '''Tutorial: Claire Lagesse - Introduction to Geographic Information Systems (GIS)''' ==
'''Speaker:''' Claire Lagesse 
'''Date and Time:''' June 24 7:00-8:00pm 

If you are willing to attend... Please download : 

* QGIS [http://www.qgis.org/en/site/forusers/download.html here]

* some data with [http://download.geofabrik.de/north-america/us/new-mexico-latest.shp.zip this] link

== '''Tutorial: Mathematica''' ==
'''Speaker:''' Massimo Stella 
'''Date and Time:''' June 26 from 1:30-2:30pm

Complex Systems Summer School 2014-Tutorials

2014-06-24T01:25:12Z

Pfenningers: /* Tutorial: Introduction to Python and its scientific programming ecosystem */

{{Complex Systems Summer School 2014}}

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

Also, please email juniper@santafe.edu to request a tutorial slot.

=='''Tutorial: Rotors, Spirals and Scroll Waves''' ==
'''Speaker:''' Hiroshi Ashikaga 
'''Date & Time:''' June 16 from 2:00-2:30pm 
'''Content:''' A short introduction to cardiac electrophysiology and basic mechanisms of arrhythmia. 
'''Motivation:''' To get more people interested in the heart as a complex system. 
'''Prerequisite:''' Whoever has a heart. 
'''References:''' This is a short list of reference papers for those interested in the topic. I am happy to review them and discuss with any of you if you are interested. 

1. Winfree [[File:1989_WinfreeA_JTB.pdf]] 
2. Gray ''et al.'' [[File:1998_GrayRA_Nat.pdf]] 
3. Garfinkel ''et al.'' [[File:2000_GarfinkelA_PNAS.pdf]] 
4. Qu ''et al.'' [[File:2000_QuZ_ABME.pdf]] 
5. Fenton et al. [[File:2002_FentonFH_Chaos.pdf]] 
6. Weiss ''et al.'' [[File:2005_WeissJ_Circ.pdf]] 
7. Schotten [[File:2011_Schotten_PR.pdf]] 
8. Pandit and Jalife [[File:2013_Pandit_CircRes.pdf]] 

=='''Tutorial: Browser-Based Data Visualization'''==
'''Speaker:''' James Gentile 
'''Date & Time:''' June 17 form 7:00-8:15pm 

Data visualization is essential for analysis and communication but complex data often need complex visualizations. Interactive browser-based visualizations are unique because they can be viewed using (almost) any web browser. This tutorial will introduce [http://d3js.org/ d3.js], the JavaScript library behind many of the web’s great data views.

No JavaScript experience is required. I’ll be introducing the language, concepts and we’ll build an interactive visualization for delayed-point embedding.

If you’re planning to attend, I recommend downloading [http://www.mozilla.org/en-US/firefox/new/ Firefox] and a syntax-highlighting editor: [http://www.barebones.com/products/textwrangler/ TextWrangler] for Macs or
[http://notepad-plus-plus.org/ Notepad++] for Windows. These will help you follow along.

== '''Tutorial: Parallel Programming - A Brief Introduction''' ==

'''Speaker:''' Fahad Khalid 
'''Date & Time:''' June 18 7:00-8:15pm 
'''Content:''' A language agnostic introduction to basic concepts in parallel programming. 
'''Motivation:''' Several of us here at the CSSS do compute intensive simulations. Since single cores are not getting faster anymore, the only way to speed up simulations is by utilizing multiple cores. So it's good to know how to design and code a simulation that can take advantage of multiple cores. 
'''Pre-requisites:''' Just a passing familiarity with programming. 
'''Slides:''' [[File:Fahad_CSSS-2014_ParProg.pdf]]
 
Please use the ''comments'' sections below to let me know what you'd like to hear, what are your expectations from this tutorial, etc. I'll try my best to tailor the talk accordingly. Many thanks to those who've already suggested content for the talk. I'd appreciate if you could repeat the comments here as well (the CSSS Wiki seems to be a lot more organized than my brain :-)). 
 
'''Comments:''' 
* Please cover race condition.
* Generalized strategies for how a problem should be parallelized.
** Identifying problems that cannot (or should not) be parallelized.
* GPU vs CPU parallelization (e.g., CUDA vs traditional compute cluster)
* parfor in Matlab

== '''Tutorial: Introduction to Agent-based Modeling with Python''' ==
'''Speaker:''' Vipin P. Veetil 
'''Date and Time:''' June 19 4:15-5:15pm 
'''Description:''' In this tutorial we will build a ABM of Rock-Papers-Scissors game. We will learn how to initialize agents, get them to play with each others, record payoffs and develop different strategies. We will also learn how to get agents to play games on network using NetworkX. 
'''What to do before tutorial''':
Download and install python and an editor.
This is one option: https://www.enthought.com/products/canopy/ 
Another option: A lot of the brain power at Enthought left and founded Continuum Analytics to create Anaconda (https://store.continuum.io/cshop/anaconda/), a better solution than Canopy, (in Glen's humble opinion). They also created another cool tool in Wakari (https://wakari.io/).

'''Motivation''' ''Why agents?'' (http://www.brookings.edu/es/dynamics/papers/agents/agents.pdf) 
For time-constraint people, here is a two-page pamphlet in the SFI tradition arguing for the importance of ABM in economics [[File:Foley09 Econ needs ABM.pdf]]. 

'''Game Tournament''': At the end of the tutorial I will introduce you to the "Non-prisoners dilemma" game. I'll be running a tournament between different strategies. You are invited to submit a strategy for the tournament. More details soon.

'''Code for tutorial''':

https://github.com/VipinVeetil/RPS

https://github.com/VipinVeetil/Networks

== '''Tutorial: Introduction to Python and its scientific programming ecosystem''' ==
'''Speaker:''' Stefan Pfenninger 
'''Date & Time:''' June 23 4:15-5:15pm 

'''Description:''' High-level introduction to what Python is, what the major components of the scientific Python ecosystem are, and what the easiest (in my opinion) way is to start using it productively. Some simple examples will be shown. Participants should walk away equipped with the knowledge necessary to further explore on their own. Depending on the outcome of this session, we might follow it up with a hands-on session later in the week.

'''Audience:''' Ideally have at least basic skills in another programming language, and be interested in getting a quick, structured intro to Python, with links to where to find further information.

'''Slides: [[File:Python intro.pdf]]''', CSV file for the second (NetworkX) example: TBA

== '''Tutorial: Computing with Intrinsic Dynamics of Systems''' ==
'''Speaker:''' Alireza Goudarzi 
'''Date & Time:''' June 23 7:00-8:15pm 

== '''Tutorial: Claire Lagesse - Introduction to Geographic Information Systems (GIS)''' ==
'''Speaker:''' Claire Lagesse 
'''Date and Time:''' June 24 7:00-8:00pm 

If you are willing to attend... Please download : 

* QGIS [http://www.qgis.org/en/site/forusers/download.html here]

* some data with [http://download.geofabrik.de/north-america/us/new-mexico-latest.shp.zip this] link

== '''Tutorial: Mathematica''' ==
'''Speaker:''' Massimo Stella 
'''Date and Time:''' June 26 from 1:30-2:30pm

File:Python intro.pdf

2014-06-24T01:22:34Z

Pfenningers:

Complex Systems Summer School 2014-Schedule

2014-06-22T20:46:45Z

Pfenningers: /* Monday, June 23 */

{{Complex Systems Summer School 2014}}

'''Please do not change the schedule without asking for Permission'''

To access a mobile app of the schedule, logistics, and faculty list please use your mobile device to visit: http://my.yapp.us/ESQ5T2

Please plan to arrive June 8 and depart on July 4, 2014

The program lectures will be held from June 9 to July 3, 2014

Please note that dormitories will only be available from June 8 to July 4, 2014

'''For a list of local happenings in Santa Fe visit: http://www.santafe.com/'''
 

==Physics Lab==
'''[[Physics Lab 2014 | Alfred Hübler's Physics Lab Signup]]'''



{| border="1" cellpadding="2"
! scope="col"width="100" align="center | Time
! scope="col"width="700" align="center | Activity

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 8
|-
|
|All events at St. John's College Unless Otherwise Noted
|-
|width="15%" | 11:00 a.m. - 5:00 p.m.
|Registration and check-in at [http://conferenceservices.sjcsf.edu/map.htm St. John's College in the Peterson Student Center.]
|-
|5:30 p.m. - 8:30 p.m.
|Welcome Reception & Dinner in [http://conferenceservices.sjcsf.edu/map.htm Peterson Student Center (upstairs) in Junior Commons Room]

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 9

|-
|width="15%" |9:00 a.m. - 9:30 a.m.
|Welcome and Introduction by CSSS Director [http://santafe.edu/about/people/profile/Sander%20(F.A.)%20Bais Sander Bais]
|-
|9:30 a.m. - 10:45 a.m.
|[http://santafe.edu/about/people/profile/Melanie%20Mitchell Melanie Mitchell] - [[Introduction to Complexity and Agent Based Modeling]]
|-
|10:45 - 11:00 a.m.
|Break
|-
| 11:00 am - 12:15 pm
|[http://santafe.edu/about/people/profile/Melanie%20Mitchell Melanie Mitchell] - [[Introduction to Complexity and Agent Based Modeling]]
|-
|12:15 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Elizabeth%20Bradley Liz Bradley] - Dynamics I
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/Elizabeth%20Bradley Liz Bradley] - Dynamics II
|-
|4:15 p.m. - 5:00 p.m.
|Navigating the Complex Systems Summer School - [http://tuvalu.santafe.edu/events/workshops/index.php/John_Paul_Gonzales JP Gonzales]
|-
|5:00 - 6:30 p.m.
|Dinner
|-
|7:00 - 8:30 p.m.
|Evening Lecture -[http://santafe.edu/about/people/profile/Sander%20(F.A.)%20Bais Sander Bais], [[Symmetry Breaking & Introduction]]
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 10
|-
|9:00 a.m - 10:15 a.m.
|[http://csel.cs.colorado.edu/~garlanjt/ Joshua Garland], Computer Lab I: Maps & Flows
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Elizabeth%20Bradley Liz Bradley] - Dynamics III
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset], [http://tuvalu.santafe.edu/events/workshops/index.php/Networks_and_Human_Social_Dynamics_and_Online_Competition Networks I]
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://www.santafe.com/blogs/andrew-lovato Andrew Lovato], Introduction to Santa Fe
|-
|4:15 p.m. - 5:00 p.m.
|Thinking about Project Ideas and student introductions
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|[http://csel.cs.colorado.edu/~garlanjt/ Joshua Garland] - Data Analysis Lab
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 11
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Elizabeth%20Bradley Liz Bradley] - Dynamics IV
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset], [http://tuvalu.santafe.edu/events/workshops/index.php/Networks_and_Human_Social_Dynamics_and_Online_Competition Networks II]
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset], [http://tuvalu.santafe.edu/events/workshops/index.php/Networks_and_Human_Social_Dynamics_and_Online_Competition Networks III]
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. -5:00p.m.
|Introduction to Student Projects - [http://www.santafe.edu/about/people/profile/Miguel%20Fuentes Miguel Fuentes] and [http://csel.cs.colorado.edu/~garlanjt/ Joshua Garland]
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 12
|-
|9:00 a.m - 10:15 a.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset] - [http://tuvalu.santafe.edu/events/workshops/index.php/Networks_and_Human_Social_Dynamics_and_Online_Competition Networks IV]
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Andreas%20Wagner Andreas Wagner], [[Evolution and Genotype Networks]]
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Alfred%20H%C3%BCbler Alfred Hubler] - Physics Lab Introduction
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/Alfred%20H%C3%BCbler Alfred Hubler] - Physics Lab Introduction
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 9:00 p.m.
|[[Physics Lab 2014 | Physics Lab Section I ]]
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 13 at '''Santa Fe Institute'''
|-
|8:30 a.m
|Shuttle leaves St. John's to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Andreas%20Wagner Andreas Wagner] -[[Evolution and Genotype Networks]]
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Andreas%20Wagner Andreas Wagner] - [[Evolution and Genotype Networks]]
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset] - [http://tuvalu.santafe.edu/events/workshops/index.php/Networks_and_Human_Social_Dynamics_and_Online_Competition Networks V]
|-
|2:45 p.m. - 3:30 p.m.
|Break
|-
|3:30 p.m. - 4:45 p.m.
|[http://www.redfish.com/stephen.htm Steve Guerin] - Sand Tables
|-
|5:00 p.m. - 7:30 p.m.
|BBQ at SFI
|-
|7:30 p.m.
|Shuttle leaves SFI and goes back to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 14

|-
|7:00 p.m. - 9:00 p.m.
|[[Physics Lab 2014 | Physics Lab Section II ]]
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 15
|-
|7:00 p.m. - 9:00 p.m.
|[[Physics Lab 2014 | Physics Lab Section III]]
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 16 

|-
|9:00 a.m - 10:15 a.m.
|[http://www.santafe.edu/about/people/profile/Scott%20Ortman Scott Ortman] - [[Urban Scaling and Social Complexity]]
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| [http://www.santafe.edu/about/people/profile/Sam%20Scarpino Sam Scarpino] - [[The Evolution of Antiviral Resistance]]
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:00 p.m.
|Introduction to the SFI Omidyar Fellowship - Ginger Richardson
|-
|2:00 p.m. - 2:30 p.m.
|Participant Tutorial: '''Rotors, Spirals and Scroll Waves''' - Hiroshi Ashikaga
|-
|2:30 p.m. - 4:15 p.m.
|Work on Projects - Groups touch base with Miguel and Josh
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects Groups touch base with Miguel and Josh
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 9:00 p.m.
|[[Physics Lab 2014 | Physics Lab Section IV]]
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 17 

|-
|9:00 a.m - 10:15 a.m.
|[http://www.santafe.edu/about/people/profile/Eric%20Libby Eric Libby] - Evolution of Biological Complexity
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Work on Projects
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://www.santafe.edu/about/people/profile/Ben%20Althouse Ben Althouse] - [[Using Modeling to Understand Infectious Disease Dynamics]]
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Work on Projects Groups touch base with Miguel and Josh
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects Groups touch base with Miguel and Josh
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:15 p.m.
|Participant Tutorial: [http://tuvalu.santafe.edu/events/workshops/index.php/Complex_Systems_Summer_School_2014-Tutorials#Tutorial:_Browser-Based_Data_Visualization James Gentile - Browser Based Data Visualization]
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 18 - day to work on projects

|-
|9:00 a.m. - 5:00 p.m.
|Time to work on projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:15 p.m.
|Participant Tutorial: Fahad Khalid - Parallel Programming in C/C++
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 19 - Vote on Tshirts

|-
|9:00 a.m - 10:30 a.m.
|[http://csc.ucdavis.edu/~rgjames/ Ryan Gregory James] - [[Complexity]]
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/John%20Harte John Harte] - [[The maximum entropy method of inference and its application to ecology]]
|-
|12:00 p.m. - 12:10 p.m.
|Vote on TShirts
|-
|12:10 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|[http://complextropy.com/cv.html Nix Barnett] - Complexity Lab I: Information in Stochastic Processes
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/John%20Harte John Harte] - [[The maximum entropy method of inference and its application to ecology]]
|-
|4:15 p.m. - 5:15 p.m.
|Participant Tutorial: Vipin P. Veetil - Introduction to Agent-based Modeling with Python
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 20 at '''Santa Fe Institute'''

|-
|8:30 a.m
|Shuttle leaves St. John's to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|[http://www.santafe.edu/about/people/profile/Ruben%20Andrist Ruben Andrist]
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://csc.ucdavis.edu/~rgjames/ Ryan Gregory James] - Complexity
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://csc.ucdavis.edu/~rgjames/ Ryan Gregory James] - Complexity
|-
|3:00 p.m. - 4:15p.m.
|[http://complextropy.com/cv.html Nix Barnett] - Complexity Lab II: Models and Complexity of Stochastic Processes
|-
|5:00 p.m.
|Shuttle back to St. John's College
|-
|5:30 p.m. - 6:00 p.m.
|Dinner at St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 21

|-
|10:00 a.m - 5:00 p.m.
|Unofficial trip to [http://www.nps.gov/band/index.htm Bandelier National Monument]
|-
|7:00 p.m - 8:00 ap.m.
|Mariachi Band by the Koi Pond
|-
|8:00 p.m - 12:00 a.m.
|2013 CSSS Dance with Breadloaf workshop in St. John's College Coffee Shop
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 22
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 23
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Jennifer%20A.%20Dunne Jennifer Dunne] - [http://tuvalu.santafe.edu/events/workshops/index.php/Ecological_Networks Ecological Network Structure]
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Work on Projects
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|Time to work on Projects
|-
|3:00 p.m. - 4:15 p.m.
| [http://tuvalu.santafe.edu/~simon/ Simon DeDeo] - Other Minds
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects / Participant Tutorial: Stefan Pfenninger - Python intro
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:15 p.m.
|Participant Tutorial: Alireza Goudarzi - Computing with Intrinsic Dynamics of Systems
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 24
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Jennifer%20A.%20Dunne Jennifer Dunne] - [http://tuvalu.santafe.edu/events/workshops/index.php/Ecological_Networks Ecological Network Dynamics]
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 pm
|[http://tuvalu.santafe.edu/~simon/ Simon DeDeo] - Group Minds
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|Time to Work on Projects
|-
|3:00 p.m. - 4:15 p.m.
| Jure Leskovec - Machine Learning
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:00 p.m.
|Participant Tutorial: Claire Lagesse: GIS Tutorial
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 25

|-
|9:00 a.m - 10:15 a.m.
|[http://cs.stanford.edu/people/jure/ Jure Leskovec] - Machine Learning
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Sidney Redner- Complex Networks
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Sidney Redner- Complex Networks
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://www.santafe.edu/about/people/profile/Anne%20Kandler Anne Kandler] - Matching Models with Data
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|[http://santafe.edu/about/people/profile/Geoffrey%20West Geoffrey West] - Cities
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 26
|-
|9:00 a.m - 10:15 a.m.
|Project Time
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://www.santafe.edu/about/people/profile/Luis%20Bettencourt Luis Bettencourt] - Cities Project
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:30 p.m.
| Participant Tutorial: Mathematica - Massimo Stella
|-
|2:30 p.m. - 4:15 p.m.
|Time to work on Projects
|-
|4:15 p.m. - 5:00 p.m.
|Time to Work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 27 at '''Santa Fe Institute'''

|-
|8:30 a.m
|Shuttles leave St. John's College to go to SFI
|-
|9:00 a.m - 10:15 a.m.
| [http://santafe.edu/about/people/profile/Marcus%20J%20Hamilton Marcus Hamilton] - Cities Project
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://www.santafe.edu/about/people/profile/Luis%20Bettencourt Luis Bettencourt] - Cities Project
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|Time to Work on Projects
|-
|3:00 p.m. - 4:15 p.m.
|Panel Discussion with: W. Brian Arthur, Luis Bettencourt, Simon DeDeo, Jennifer Dunnem, and Cosma Shalizi
|-
|5:00 p.m.
|Shuttle back to St. John's
|-
|5:30 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 28
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 29
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 30
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] - Algorithms and Landscapes
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] - NP-Completeness and the P vs. NP Question
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] - Monte Carlo Algorithms and Phase Transitions
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://tuvalu.santafe.edu/~wbarthur/ W. Brian Arthur] - [[Complexity Economics: A Different Framework for Economic Thought]]
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture - Pablo Marquet
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, July 1
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] - The Power of Randomness
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://tuvalu.santafe.edu/~jdf/About%20Me.html J. Doyne Farmer] - Economics
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 5:00 p.m.
|[http://www.santafe.edu/about/people/profile/Evandro%20Ferrada Evandro Ferrada] - Evolution
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, July 2
|-
|9:00 a.m - 10:15 a.m.
|[http://tuvalu.santafe.edu/~jdf/About%20Me.html J. Doyne Farmer] - Economics
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|TBA
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] , Quantum Computation
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|TBA
|-
|4:15 p.m. - 5:00 p.m.
|Work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Miguel Fuentes Evening Lecture
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, July 3 at '''Santa Fe Institute'''
|-
|8:30 a.m
|Shuttle leaves St. John's College for SFI
|-
|9:00 a.m - 10:15 a.m.
|Presentations
|-
|10:15 - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Presentations
|-
|12:00 p.m. - 12:15 p.m.
|Group Photo
|-
|12:15 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|Presentations
|-
|3:00 p.m. - 3:30 p.m.
|Break
|-
|3:30 p.m. - 5:00 p.m.
|Presentations and Closing Remarks
|-
|5:00 p.m. - 7:00 p.m.
|Farewell BBQ at SFI
|-
|7:30 p.m.
|Shuttles go back to St. John's
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, July 4
|-
|10:00 a.m.
|Check-out and departure (don't forget to return your keys!)
|-

Complex Systems Summer School 2014-Tutorials

2014-06-20T13:38:17Z

Pfenningers: added python intro

{{Complex Systems Summer School 2014}}

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

Also, please email juniper@santafe.edu to request a tutorial slot.

=='''Tutorial: Rotors, Spirals and Scroll Waves''' ==
'''Speaker:''' Hiroshi Ashikaga 
'''Date & Time:''' June 16 from 2:00-2:30pm 
'''Content:''' A short introduction to cardiac electrophysiology and basic mechanisms of arrhythmia. 
'''Motivation:''' To get more people interested in the heart as a complex system. 
'''Prerequisite:''' Whoever has a heart. 
'''References:''' This is a short list of reference papers for those interested in the topic. I am happy to review them and discuss with any of you if you are interested. 

1. Winfree [[File:1989_WinfreeA_JTB.pdf]] 
2. Gray ''et al.'' [[File:1998_GrayRA_Nat.pdf]] 
3. Garfinkel ''et al.'' [[File:2000_GarfinkelA_PNAS.pdf]] 
4. Qu ''et al.'' [[File:2000_QuZ_ABME.pdf]] 
5. Fenton et al. [[File:2002_FentonFH_Chaos.pdf]] 
6. Weiss ''et al.'' [[File:2005_WeissJ_Circ.pdf]] 
7. Schotten [[File:2011_Schotten_PR.pdf]] 
8. Pandit and Jalife [[File:2013_Pandit_CircRes.pdf]] 

=='''Tutorial: Browser-Based Data Visualization'''==
'''Speaker:''' James Gentile 
'''Date & Time:''' June 17 form 7:00-8:15pm 

Data visualization is essential for analysis and communication but complex data often need complex visualizations. Interactive browser-based visualizations are unique because they can be viewed using (almost) any web browser. This tutorial will introduce [http://d3js.org/ d3.js], the JavaScript library behind many of the web’s great data views.

No JavaScript experience is required. I’ll be introducing the language, concepts and we’ll build an interactive visualization for delayed-point embedding.

If you’re planning to attend, I recommend downloading [http://www.mozilla.org/en-US/firefox/new/ Firefox] and a syntax-highlighting editor: [http://www.barebones.com/products/textwrangler/ TextWrangler] for Macs or
[http://notepad-plus-plus.org/ Notepad++] for Windows. These will help you follow along.

== '''Tutorial: Parallel Programming - A Brief Introduction''' ==

'''Speaker:''' Fahad Khalid 
'''Date & Time:''' June 18 7:00-8:15pm 
'''Content:''' A language agnostic introduction to basic concepts in parallel programming. 
'''Motivation:''' Several of us here at the CSSS do compute intensive simulations. Since single cores are not getting faster anymore, the only way to speed up simulations is by utilizing multiple cores. So it's good to know how to design and code a simulation that can take advantage of multiple cores. 
'''Pre-requisites:''' Just a passing familiarity with programming. 
'''Slides:''' [[File:Fahad_CSSS-2014_ParProg.pdf]]
 
Please use the ''comments'' sections below to let me know what you'd like to hear, what are your expectations from this tutorial, etc. I'll try my best to tailor the talk accordingly. Many thanks to those who've already suggested content for the talk. I'd appreciate if you could repeat the comments here as well (the CSSS Wiki seems to be a lot more organized than my brain :-)). 
 
'''Comments:''' 
* Please cover race condition.
* Generalized strategies for how a problem should be parallelized.
** Identifying problems that cannot (or should not) be parallelized.
* GPU vs CPU parallelization (e.g., CUDA vs traditional compute cluster)
* parfor in Matlab

== '''Tutorial: Introduction to Agent-based Modeling with Python''' ==
'''Speaker:''' Vipin P. Veetil 
'''Date and Time:''' June 19 4:15-5:15pm 
'''Description:''' In this tutorial we will build a ABM of Rock-Papers-Scissors game. We will learn how to initialize agents, get them to play with each others, record payoffs and develop different strategies. We will also learn how to get agents to play games on network using NetworkX. 
'''What to do before tutorial''':
Download and install python and an editor.
This is one option: https://www.enthought.com/products/canopy/ 
Another option: A lot of the brain power at Enthought left and founded Continuum Analytics to create Anaconda (https://store.continuum.io/cshop/anaconda/), a better solution than Canopy, (in Glen's humble opinion). They also created another cool tool in Wakari (https://wakari.io/).

'''Motivation''' ''Why agents?'' (http://www.brookings.edu/es/dynamics/papers/agents/agents.pdf) 
For time-constraint people, here is a two-page pamphlet in the SFI tradition arguing for the importance of ABM in economics [[File:Foley09 Econ needs ABM.pdf]]. 

'''Game Tournament''': At the end of the tutorial I will introduce you to the "Non-prisoners dilemma" game. I'll be running a tournament between different strategies. You are invited to submit a strategy for the tournament. More details soon.

'''Code for tutorial''':

https://github.com/VipinVeetil/RPS

https://github.com/VipinVeetil/Networks

== '''Tutorial: Introduction to Python and its scientific programming ecosystem''' ==
'''Speaker:''' Stefan Pfenninger 
'''Date & Time:''' June 23 4:15-5:15pm 

'''Description:''' High-level introduction to what Python is, what the major components of the scientific Python ecosystem are, and what the easiest (in my opinion) way is to start using it productively. Some simple examples will be shown. Participants should walk away equipped with the knowledge necessary to further explore on their own. Depending on the outcome of this session, we might follow it up with a hands-on session later in the week.

'''Audience:''' Ideally have at least basic skills in another programming language, and be interested in getting a quick, structured intro to Python, with links to where to find further information.

== '''Tutorial: Computing with Intrinsic Dynamics of Systems''' ==
'''Speaker:''' Alireza Goudarzi 
'''Date & Time:''' June 23 7:00-8:15pm 

== '''Tutorial: Claire Lagesse - GIS Tutorial''' ==
'''Speaker:''' Claire Lagesse 
'''Date and Time:''' June 24 7:00-8:00pm 

== '''Tutorial: Mathematica''' ==
'''Speaker:''' Massimo Stella 
'''Date and Time:''' June 26 from 1:30-2:30pm

Emergence of Consciousness Page

2014-06-17T02:42:56Z

Pfenningers: /* Perspective Summaries */

I created this page to share and discuss our models for the emergence of consciousness from matter. Please share your models and add discussion so we can all see and think about it. We will use this page in the end to write up a summary and hopefully compare and contrast the models and discuss what properties of consciousness can be explained by what model.

Thanks,
Alireza

=Working Ideas=

== (1) Consciousness as Hyper Attractors of Brain (Alireza)==
In this schema states of our mind/consciousness as attractors of the dynamics that arise from our brain. We receive sensory information that act as perturbations pushing the trajectory out of a basin of attractor and into a new basin.

[[File:photo.png | 500px|center]]

== (2) Reference! Tegmark - The fourth state of matter =
This can be an interesting starting point... at least one perspective on the topic http://arxiv.org/pdf/1401.1219v2.pdf Sarah

=Perspective Summaries=
 
==Consciousness Table==
I thought that it might be useful to attempt to organize our understandings of consciousness in a table—perhaps to make clear where and whether a consensus emerges on the nature of the phenomena that we are investigating.

I offer here an idiosyncratic table that I find useful to organize my thoughts on this topic. Feel free to add/reorganize categories and qualify entries in the notes below.
Or better yet...can we come up with a simpler table that captures the typical properties that consciousness is thought to have or not have.
 --john balwit

<table>

<tr><td> </td><td>Property</td> <td>Yes</td><td>No</td> <td>NA </td></tr>
<tr><td>1.</td> <td>Requires matter</td> <td> x</td> <td> </td> <td> </td></tr>
<tr><td>2.</td> <td>Exclusive property of biological systems</td> <td> x</td> <td> </td> <td> </td></tr>
<tr><td>3.</td> <td> Has parts <td> x</td> <td> </td> <td></td></tr>
<tr><td>4.</td> <td>Admits of gradations or degree (continuous or discrete)
<td> x</td> <td> </td> <td></td></tr>
<tr><td>5.</td> <td>Likely to be artificial created in the AI lab <td> x</td> <td> </td> <td></td></tr>
<tr><td>6.</td> <td>Intrinsically paradoxical research area.
(involves strange loopy-ness Gödel, Turing) <td> ?</td> <td> </td> <td></td></tr>
<tr><td>7.</td> <td>Requires interaction with external environment (perception?) <td> x</td> <td> </td> <td></td></tr>
<tr><td>8.</td> <td>Requires interaction with internal environment (reflection?) <td> </td> <td> x </td> <td></td></tr>
<tr><td>9.</td> <td>Necessarily Embodied (result of sensor interactions, hormonal environment etc.) <td> x</td> <td> </td> <td></td></tr>
<tr><td>10.</td> <td>Necessarily Embedded (result of large scale system interactions) <td> x</td> <td> </td> <td></td></tr>
<tr><td>11.</td> <td>Deterministic system with stochastic inputs. <td> x</td> <td> </td> <td></td></tr>
<tr><td>12.</td> <td>Relies on quantum things that I do/do not understand <td> </td> <td> </td> <td>?</td></tr>
<tr><td>13.</td><td> Defined by its ineffability, will always recede from scientific apprehension. <td> ?</td> <td> </td> <td></td></tr>
<tr><td>14.</td><td> Encodes history (requires memory, genes) <td> x</td> <td> </td> <td></td></tr>
</table>

 Notes: 
 

==Sean Hayes==

[http://www.imprint.co.uk/chalmers.html The Hard Problem of Consciousness]
:This paper makes the important distinction between the 'easy' and 'hard' problems of consciousness in relative terms. I think it would be useful to use this framework to focus the precise problems we're investigating around consciousness. 
My definition for consciousness at it's simplest form is just having subjective experience. While some of the discussion this afternoon touched on integrative brain problems (which falls under 'easy' problems of consciousness in the above, as a way to describe issues of cognition), my question is whether this property of consciousness is an emergent phenomenon. While this is difficult to address objectively, I think it can be approached from our perspectives by comparing consciousness with other emergent phenomena. 

The big question that I've been trying to resolve myself along this line of thinking is related to the 'binding problem' ([http://tuvalu.santafe.edu/events/workshops/images/8/8d/Revonsuo_and_Newman_1999_-_Binding_and_Consciousness.pdf 1],[http://tuvalu.santafe.edu/events/workshops/images/3/37/Revonsuo_1999_-_Binding_and_the_Phenomenal_Unity_of_Consciousness.pdf 2]). I'm probably bastardizing the definition a bit, but essentially the issue is conscious experience is not a distributed phenomenon but rather that experience is inherently singular - to me this is entirely distinct from emergence, which is inherently a distributed feature of a complex system. Moreover, our conscious experience not only receives input from the complex, distributed network of our brain, but itself can cause changes in brain behavior and function. Is this actually an emergent phenomenon, or the concentration of information into a centralized control (our subjective experience)? Are there characteristics of subjective experience which do act the way we expect emergent phenomena to behave?

==Cole Mathis==
I think that consciousness is an Emergent property of the electro-chemical interactions occurring in my brain. The difficulty in understanding the dynamics and/or the origin of consciousness is (in my opinion) the hard problem in emergence: how can macroscopic features of the system have causal control of the microscopic degrees of freedom? One of the canonical examples of emergent phenomena is the emergence of thermodynamics from statistical mechanics. Here the behavior of a system with many degrees of freedom (an ideal gas) can be effectively represented using bulk (emergent) variables (temperature, pressure, volume, etc.) This example is great but it says nothing about the flow of information in the system or the casual direction. For example consider a box of an ideal gas, if I hold the volume constant and heat this box, the pressure will go up. An increase in pressure on the macro scale corresponds to an increase in the average speed of the particles on the microscopic scale, however we do not say that the increased pressure caused the increase in the average speed (although we might say that the increase of the average translational kinetic energy caused the increase in pressure). In this system the causal arrow points only from the micro-scale to the macro-scale. With consciousness we have exactly the opposite situation. If the state of my neurons are the microscopic state variables and my conscious thoughts are the macroscopic variables, then when I think about typing, the macroscopic variables configure the microscopic variables in just the right way to send signals down to fingers, my fingers didn’t start typing and then cause my brain to think about typing (I hope.) So here the causal direction is reversed. How did this reversal/ asymmetry arise and how can we generalize this notion?
[http://www.pnas.org/content/early/2013/11/12/1314922110.full.pdf Quantifying Casual Emergence shows macro can beat micro]

==Claire Lagesse==

Here are some ideas about my personal experiment of what consciousness could be...
There is no reference but just some thinking from what I learned. I don't deal with consciousness in my every day work but as a conscious human being I experiment it every day ! :)
I'm really sorry for my french-english !

What is consciousness ? Where does it starts ? Where does it ends ? Are we conscious of the sun on our skin, of the wind, of our breathe, of our position, of the temperature, of all the elements surrounding us ? Does the consciousness start with a 'me' ? A dissociation of the external world from our body ? Then, what are the limits of our body ? Is the hair just fallen a part of 'me' ? What about my legs ? They are a part of my body, but if one is cut of it won't be 'me' any more. So maybe we could define our 'me' as the living part of our body. So, for people with a Locked Inside Syndrome their 'me' can be the minimal part of their body alive : their brain. That's maybe why the analogy is often made between the brain and consciousness : it is considered as the minimal part of our body which has to be alive for a 'me' still existing. Even our heart can be replace by a machine.

If we define consciousness with a 'me' apart from the surrounding world, it could be problematic for some persons with mental disease. What about autism ? In some cases, persons with a major autistic trouble cannot make the difference between their own body and the world surrounding them. Can we say they are not conscious ? That sounds a little extreme.

Could we extend consciousness to each living organism ? Is a plant conscious ? Plants are moving all day long, but at a different time scale than ours. They are moving with the sun, with the wind... Does it means they are conscious of them or could we just see it as a action / reaction mechanism ? It goes the same way for some animals. Is the jellyfish conscious of its moves with waves ? Is the shell conscious ? Is the frog conscious ? Each animal is responding to its physiological needs : feed, security and reproduction. Feed goes with a body, security goes with a surrounding (potentially dangerous) and reproduction goes with finding and interacting with another animal of my own specie.

Could we consider those behaviors as conscious ? What are the limits of this hypothesis ? It is possible to program a robot to find food, make itself secure and make sure to reproduce the sooner it can. But it won't be conscious those behaviors are for its own survival and its specie one. But can we say that animals are conscious of it ?

Thinking about artificial intelligence, one could say that consciousness begin with feelings, and a computer is not able to feel anything. Happiness, sadness, love, hate, if we look closely they all have a chemical reaction as an origin. The mystery could be what produce this chemical reaction.

Ants or bees have great collective behavior. They form a fascinating system with some extremely complex emerging properties. But it is not sure that each ant, each bee, is conscious it is taking part in a complex system. It is more about a robust collective intelligence than about consciousness. However, in an anthill 20% of ants are not doing anything. What is this 'useless' time for ? Are the ants conscious of this free time ? Is this demonstrating something about a system we are judging as hyper efficient ?

A third idea could be the knowledge that our consciousness is limited in the time. As human beings, we are conscious that we will die some day. So we develop some cults and funeral rite. Could it be a 'proof' of consciousness ? This way of thinking may exclude a lot of animals of consciousness.

One could ask the difference between consciousness and intelligence. Can an artificial intelligence be conscious ? Is consciousness recognizable by feelings, non efficient time or the simple fact to name it ? Could we say that consciousness is the amount of things linked to our body that we are not able to scientifically explain ? Does the consciousness define the 'me' out of my body limits ? And so what about all the unconscious things I do every day ? Breathe, blink, dream... Is it about the will of doing something more than in the fact of doing it ? Are we defined by our body, our will or our acts ? Is the consciousness the fact to ask ourselves about consciousness ?

==John Balwit ==

Definitions matter. Definitions create boundaries around elements of a system that we attempt to model and understand. Definitions also create a background of implicit assumptions that are necessarily less well examined. Definitions of consciousness are perhaps inherent circular, the definitions “import” themselves into their own definition. For example, let’s start to build a definition of consciousness It makes sense to reflect for a moment on the ever present phenomena of consciousness and begin with “I feel the warm sun on my cheek. … etc. “ Already we have made assumptions which may prove to be missteps. There is clearly some connection between consciousness and the personal pronouns that we use to label our identity—the locus of our perception. This may be one of the key things that we hope to understand as we attempt to understand consciousness. In this respect, It appears that even Descartes choose a starting point that was well down the road—got ahead of himself. “I think therefore I am” is no philosophical atom. * A second problem in the “reflective” exercise above is the implicit assumption that “pausing to reflect” give clearer access to the phenomena of consciousness. It might be the case (and I happen to believe that it is the case) that this particular kind of introspection obscures a more general apprehension of the phenomena that we are interested in understanding.

Disciplines matter too. Our understandings are necessarily informed by our experience. Our disciplines provide us with tools and models of various systems that build our intuitions in different ways. I study evolutionary biology, systems, models and have affinities for the philosophical position in cognitive science called Embodied Embedded Cognition (EEC). The ECC theoretical position is critical of the classical cognitivist approach which relies on a mechanistic “internal representation”.

My definition of consciousness is something like this:

Some (perhaps all) evolved systems perceive and respond to an environment. This is a property of matter, energy, and the properties of the systems as they are arranged in space. Slowly driven systems far from equilibrium (biological systems, perhaps others) have an opportunity to create “perceptual, modeling subsystems” that generate models of the world that may “run faster” than the physical system in which they are embedded and therefore serve adaptive, predictive functions. The chemical systems of plants have these property, language systems used by humans also have this property. My discipline suggests that the models that these subsystems generate are instances of consciousness.

Now consider the parts of these models? These models are not strictly localized within the modeling subsystem, rather they involve relationships between the environment and the modeling subsystem and can be thought to “hover” immaterially between the subsystem. Practitioners of various meditation practices frequently observe this “untethered” property of consciousness. In the philosophical literature there are colorful “brain in a vat” and “philosophical zombie” thought experiments which make a compelling case that consciousness is property of not just the matter in our modeling subsystems but of all matter that participates in those relationships. This “embedded” aspect of consciousness holds that the interplay between the world and the modeling system introduce important constraints that influence the content or character of consciousness-i.e. there is no general consciousness.

The “embodied” aspect of consciousness refers to the observation that modeling subsystems have an “internal milieu” which deeply “colors” the behavior or characteristics of consciousness

My discipline (and my temperament) value precision and rigor. There are established ways to bring rigor to various domains of study. However, it is not immediately clear to me how to make falsifiable claims; to generate testable hypotheses in the area of consciousness. I would like to be able to do this. Using AI and a generative science is an interesting but not, I would say, promising approach. As we create ever more sensitive, and responsive technology we will almost certainly encounter more cases that we are likely to consider as “marginal cases” of consciousness In the event that we do create the “paradigm case” of consciousness – an AI like to one in the movie “Her”-- it is still not clear that we will gain understanding into the nature of consciousness from this system. Our success will ironically be revealed in the inaccessibility of the states that the AI will claim to have.

Finally, a few words on mystery and the ineffable: Part of the motivation for research in the area of consciousness lies in the surprising observation that electro-chemical systems like ourselves give rise to the beautiful, vivid, textured, emotionally-tinged, riddled-with-longing, plagued-with-ambition, haunted-by-death and, oh yes, “is that sunshine on my cheek” kind of experiences that characterize one’s own experience.
There is a striking incongruity between the processes that we imagine are taking place at the “lowest levels”. My intuitive reaction to this is that we just don’t understand physics and chemical reactions very well. Our theories and our mathematics are cartoon sketches. We are justifiably impressed with ourselves for the progress made but the notion that “all is known” stands now, as always, as the principle barrier to greater understanding. For most of human history animism has been taken for granted. The Greeks, the Judeo-Christian tradition and the western scientific world view that these modes of thought gave rise to (and in which we happily participate) changed all that by creating zero order approximations that made certain things evident but obscured others. I am persuaded by some of Stuart Kaufmann’s work in this area and feel that as our understanding of the properties that are inherent in matter, energy and the long histories that are encoded in their arrangement in time and space –as our understanding of these things grow we will increasing come to feel “at home in the universe.”

*Cogito ergo sum seems to work for many folks, but, personally, I rarely think. I spend most of my time reacting and as much time as possible mountain biking. Furthermore, I also participate in many relationships with family, with my colleagues and with my larger community that make it unclear were my “locus of self” or “locus of control” resides. Maybe it is just “me”. I don’t think so.

==Matthew Ayres ==

Defining Consciousness

What is it to be conscious? The debate has been running for a long time and is fundamentally tied to our existence, search for order, search for self-understanding and the wider connection to the universe in which we find ourselves.

1. Questions to consider
• Are their differing types or forms of consciousness?
• Does consciousness evolve over time?
• Is consciousness actually definable?
• Can consciousness be deconstructed?
• Can consciousness be observed or measured?

I’m sure there are many more questions and by asking these questions, I’m developing a set of assumptions I’m making in order to offer some form of draft view of consciousness.

2. Assumptions
At this stage and by default, to define consciousness, one must believe it is definable and measurable. Ill start with this assumption. Secondly, I will assume there is a universal consciousness, that may be bespoke or have a series of elements in which it comes into being. The time dimension is rather hard so for this stage, ill remain neutral until the work is further developed.

3. What may be elements of consciousness?
• Awareness – the understanding of self as an entity
• Intelligence - the ability to make highly complex decisions
• Self-determination - the ability to make choices that may or many not be self-interested
• Thought – the conceptual development of framing that helps interpret life
• Feelings – the rich experiences that inform, influence and integrate with rational thought
• Emergence – the ability to learn and create new thought based on both experience as well as non-learned unique thought.
Clearly this list is too short!

4. What is consciousness ‘not’?
In asking this question, I’m attempting to reduce the overall size of the problem by restricting its scope. While this is best used at a collective group level, I’ll offer some initial thoughts:

Rocks; passive / unaware
Computer software; follows predefined instructions
Plants; limited / [no?] self determinism

5. Definition V1.0
Based on the initial thoughts above, a draft definition has been attempted.

“Consciousness is an adaptive self-awareness that self-determines thoughts and actions in an evolving environment.”

It already seems clumsy, however is thrown on the cutting room floor for discussion.

==Beth Lusczek ==

I've had some interesting discussions with folks in this group about what could be termed altered states of consciousness. This might be as simple as looking at the world through "baby eyes", as being in a meditative state, or having flashes of ego death. These experiences could be described as feeling more connected to the world, feeling able to access more information, to integrate thought and emotion, and to see connections instead of walls and divisions. Sometimes this involves altered senses of space and time. These "altered states" are fleeting and can be difficult to recreate in memory. Are these states some inherent property of consciousness? Do they serve a purpose or are they merely part of the human experience? What functional structures are engaged in these states? Are there different signaling patterns? fMRI studies on Buddhist monks can address these last questions.

==Stefan Pfenninger==

I have just three thoughts.

First, I'm interested in whether consciousness is uniquely human or not. To what extent is it linked to a sense of self? There is lots of evidence that a whole range of animals have a sense of self. We also know that some primates use tools. But there seems to be evidence that some primates come eerily close to "being human", for example in that they have some sort of understanding of mortality (e.g. see the book, The Bonobo and the Atheist by Frans de Waal [1]). Also worth reading, Michael Pollan has a recent piece in the New Yorker that explores whether plants could be considered intelligent or even conscious [2].

Second, although it may not help arriving at a fundamental explanation of consciousness, examining how meditation alters consciousness is interesting to me because it is something we can investigate ourselves without needing a lab (although of course you can also try to peak into meditators brains using modern brain imaging).

Finally, I probably consider myself a materialist, but I wonder whether it will ever be possible to explain consciousness as an emergent property of matter. Even assuming that this is possible in theory, my guess is that we are a very long way from understanding the physical universe well enough to actually do so. Hypotheses like this guy Penrose claiming that quantum vibrations inside neurons have something to do with consciousness [3] don't seem anywhere close to being testable at the moment, but I admit I have no idea what quantum vibrations in neurons mean in the first place (and would be very happy to let somebody explain this to me).

[1] http://www.amazon.com/The-Bonobo-Atheist-Humanism-Primates/dp/0393347796/

[2] http://www.newyorker.com/reporting/2013/12/23/131223fa_fact_pollan?currentPage=all

[3] http://dx.doi.org/10.1016/j.plrev.2013.08.002

Complex Systems Summer School 2014-Project Group Meeting Schedule

2014-06-16T21:37:57Z

Pfenningers: /* Tuesday, June 17 */

{{Complex Systems Summer School 2014}}

'''Please use this space to list the times and locations of project group meetings, in the following format:''' 
'''12:30pm Name of Project (meeting place)''' 
 

==Saturday, June 14==
14:00 : The pollination problem from a game theory approach (Class room)

==Sunday, June 15==
10:00am : Division of Labor/Network Stability Tradeoff 
10:00am : Network Warping via Chaotic Dynamics (Cafeteria) 
11:00am : Information Theory of the Heart (ARIEL) [http://tuvalu.santafe.edu/events/workshops/index.php/Information_Theory_of_the_Heart_Page] 
12:00pm : Emergence of Consciousness (Cafeteria) 
12:00pm : Multiplex networks 
6:00pm : Cells and Software (Koi pond) 
6:30pm : Co-evolution of Anti-vaccination Sentiment and Flu Infections (cafeteria) 
7:00pm : Research Field Evolution (cafeteria) 
7:15pm : Dynamics and stability of food webs with parasites (cafeteria) 
9:00pm : Biodiversity (Lecture Hall/Cafeteria) 

==Monday, June 16==

2:30pm : Cities Growth (meeting until 4:00) (Lecture Hall) 
2:30pm : Information Theory of the Heart (Lecture Hall) 
3:15-4:15pm : Pollination and Game Theory (Lecture Hall) 
4:00pm : Network topology and quarantine (Lecture Hall) 
4-5:30pm : Genotype-Phenotype Mapping (Ariel) 
4:15pm : Failure Tolerance in Networks (Lecture Hall) 
4:15pm : Coupling of Networks (Evans Science lab, room 2.15) 

==Tuesday, June 17==

10:30AM-11:30AM: Evolution of interdisciplinary research (lecture hall) 
10:45AM-12PM: Division of labor vs. stability tradeoff - Model Development Meeting (lecture hall) 
10:45AM-12PM: Multiplex Networks, modeling (tentative) 
3:00PM-4:15PM: Bitcoin group (lecture hall) 

==Wednesday, June 18==

==Thursday, June 19==

==Friday, June 20==

==Saturday, June 21==

==Sunday, June 22==

10-11AM: Division of labor vs. stability tradeoff - General Meeting - (second floor of student center) 

==Monday, June 23==

==Tuesday, June 24==

==Wednesday, June 25==

==Thursday, June 26==

==Friday, June 27==

==Saturday, June 28==

==Sunday, June 29==

==Monday, June 30==

==Tuesday, July 1==

==Wednesday, July 2==

Complex Systems Summer School 2014-Project Group Meeting Schedule

2014-06-16T00:34:17Z

Pfenningers: /* Tuesday, June 17 */

{{Complex Systems Summer School 2014}}

'''Please use this space to list the times and locations of project group meetings, in the following format:''' 
'''12:30pm Name of Project (meeting place)''' 
 

==Saturday, June 14==
14:00 : The pollination problem from a game theory approach (Class room)

==Sunday, June 15==
10:00am : Division of Labor/Network Stability Tradeoff 
10:00am : Network Warping via Chaotic Dynamics (Cafeteria) 
11:00am : Information Theory of the Heart (ARIEL) [http://tuvalu.santafe.edu/events/workshops/index.php/Information_Theory_of_the_Heart_Page] 
12:00 : Emergence of Consciousness (Cafeteria) 
12:00: Multiplex networks 
6:00pm : Cells and Software (Coy pond) 
7:00pm : Research Field Evolution (cafeteria) 
7:15pm : Dynamics and stability of food webs with parasites (cafeteria) 
9:00pm : Biodiversity (Lecture Hall/Cafeteria) 

==Monday, June 16==

2:30pm : Cities Growth (meeting until 4:00) (Lecture Hall) 
2:30pm : Information Theory of the Heart (Lecture Hall) 
3:15-4:15pm : Pollination and Game Theory (Lecture Hall) 
4-5:30pm : Genotype-Phenotype Mapping (Ariel) 
4:15pm : Failure Tolerance in Networks (Lecture Hall) 
4:15pm : Coupling of Networks (Evans Science lab, room 2.15) 

==Tuesday, June 17==

10:45AM-12PM: Division of labor vs. stability tradeoff - Model Development Meeting (lecture hall) 
3:00PM-4:15PM: Bitcoin group (lecture hall) 

==Wednesday, June 18==

==Thursday, June 19==

==Friday, June 20==

==Saturday, June 21==

==Sunday, June 22==

10-11AM: Division of labor vs. stability tradeoff - General Meeting - (second floor of student center) 

==Monday, June 23==

==Tuesday, June 24==

==Wednesday, June 25==

==Thursday, June 26==

==Friday, June 27==

==Saturday, June 28==

==Sunday, June 29==

==Monday, June 30==

==Tuesday, July 1==

==Wednesday, July 2==

Complex Systems Summer School 2014-Project Group Meeting Schedule

2014-06-16T00:33:52Z

Pfenningers: /* Tuesday, June 17 */

{{Complex Systems Summer School 2014}}

'''Please use this space to list the times and locations of project group meetings, in the following format:''' 
'''12:30pm Name of Project (meeting place)''' 
 

==Saturday, June 14==
14:00 : The pollination problem from a game theory approach (Class room)

==Sunday, June 15==
10:00am : Division of Labor/Network Stability Tradeoff 
10:00am : Network Warping via Chaotic Dynamics (Cafeteria) 
11:00am : Information Theory of the Heart (ARIEL) [http://tuvalu.santafe.edu/events/workshops/index.php/Information_Theory_of_the_Heart_Page] 
12:00 : Emergence of Consciousness (Cafeteria) 
12:00: Multiplex networks 
6:00pm : Cells and Software (Coy pond) 
7:00pm : Research Field Evolution (cafeteria) 
7:15pm : Dynamics and stability of food webs with parasites (cafeteria) 
9:00pm : Biodiversity (Lecture Hall/Cafeteria) 

==Monday, June 16==

2:30pm : Cities Growth (meeting until 4:00) (Lecture Hall) 
2:30pm : Information Theory of the Heart (Lecture Hall) 
3:15-4:15pm : Pollination and Game Theory (Lecture Hall) 
4-5:30pm : Genotype-Phenotype Mapping (Ariel) 
4:15pm : Failure Tolerance in Networks (Lecture Hall) 
4:15pm : Coupling of Networks (Evans Science lab, room 2.15) 

==Tuesday, June 17==

10:45AM-12PM: Division of labor vs. stability tradeoff - Model Development Meeting (lecture hall)
3:00PM-4:15PM: Bitcoin group (lecture hall)

==Wednesday, June 18==

==Thursday, June 19==

==Friday, June 20==

==Saturday, June 21==

==Sunday, June 22==

10-11AM: Division of labor vs. stability tradeoff - General Meeting - (second floor of student center) 

==Monday, June 23==

==Tuesday, June 24==

==Wednesday, June 25==

==Thursday, June 26==

==Friday, June 27==

==Saturday, June 28==

==Sunday, June 29==

==Monday, June 30==

==Tuesday, July 1==

==Wednesday, July 2==

Complex Systems Summer School 2014-Sign Up Sheet for Meetings with Miguel and Josh

2014-06-16T00:31:47Z

Pfenningers:

{{Complex Systems Summer School 2014}}

{| border="1" cellpadding="2"
! scope="col"width="100" align="center | Time
! scope="col"width="700" align="center | Activity

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 16 
|-
|2:30 p.m. - 2:40 p.m.
|Miguel: Cells and Software - Is Evolution a Software Engineer?
|-
|2:45 p.m. - 2:55 p.m.
|Miguel: Josh: Unified Theory of Biodiversity
|-
|3:00 p.m. - 3:10 p.m.
|Miguel: Tradeoff between system efficiency and robustness Josh: Fractal-like structures in economic data
|-
|3:15 p.m. - 3:25 p.m.
|Miguel: Josh:
|-
|3:30 p.m. - 3:40 p.m.
|Miguel: Josh:
|-
|3:45 p.m. - 3:55 p.m.
|Miguel: Josh:
|-
|4:00 p.m. - 4:10 p.m.
|Break
|-
|4:15 p.m. - 4:25 p.m.
|Miguel: Josh:
|-
|4:15 p.m. - 4:25 p.m.
|Miguel: Josh:
|-
|4:30 p.m. - 4:40 p.m.
|Miguel: Pollination Group Josh:
|-
|4:45 p.m. - 4:55 p.m.
|Miguel: Josh: Economic inequality, kinship networks, and political transitions
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 17 

|-
|2:45 p.m. - 2:55 p.m.
|Miguel: The architecture of an empirical genotype-phenotype mapping Josh: Failure Tolerance in Networks
|-
|3:00 p.m. - 3:10 p.m.
|Miguel: Josh: Chaotic Graphs
|-
|3:15 p.m. - 3:25 p.m.
|Miguel: Josh: Network topology and quarantine
|-
|3:30 p.m. - 3:40 p.m.
|Miguel: Josh:
|-
|3:45 p.m. - 3:55 p.m.
|Miguel: Josh:
|-
|4:00 p.m. - 4:10 p.m.
|Break
|-
|4:15 p.m. - 4:25 p.m.
|Miguel: Bitcoin Josh: Growth of Cities Group
|-
|4:15 p.m. - 4:25 p.m.
|Miguel: Josh:
|-
|4:30 p.m. - 4:40 p.m.
|Miguel: Josh:
|-
|4:45 p.m. - 4:55 p.m.
|Miguel: Josh:
|-

Complex Systems Summer School 2014-Projects & Working Groups

2014-06-13T03:16:51Z

Pfenningers: /* Bitcoin */

{{Complex Systems Summer School 2014}}

==Bitcoin==

[[Bitcoin | Bitcoin Page]]

Bitcoin is an online peer-to-peer currency which has gained popularity in recent years. With increased general interest and now more and more companies accepting transactions in Bitcoin, so to has its value and is currently priced at $633 for 1 Bitcoin!

'''So what is Bitcoin?'''

The idea behind Bitcoin was to remove the need for a centralised banking system. The way this works is to have all transactions made public and then have the Bitcoin community validate transactions by donating computational power (and rewarded in Bitcoins). For further details see this blog:

http://www.michaelnielsen.org/ddi/how-the-bitcoin-protocol-actually-works/

'''So why is it interesting?'''

Usually companies and individuals keep all of their financial records private, but ALL transaction in Bitcoin are publicly available, so this provides a unique opportunity to study financial transactions. While the transactions are public, the owners of Bitcoin remain (relatively) anonymous, and so this has led to associations with criminal activities (e.g. on the silk road) from illegal drugs to hired hit-men. In addition to illegal activities using the currency, there have also been a number of illegal activities against the currency, such as high valued heists of the order of $100 million.

''Oh, and of course its a big temporally evolving network.''

If you're interested in working on this then add your name below. If there is interest, then we can have a "Bitcoin, beers and blackboard" session to throw some ideas around.

Interested:

Leto 
Shai 
Flavia (flamarquitti@gmail.com) 
Jessica Santana jsant@stanford.edu 
Stefan 
Ana María 
Brais (brais.alvarez@eui.eu) 
James (jholdener@mitre.org) 
George(qiaozhi827@gmail.com) 
Sean Hayes (shaye004@ucr.edu) 
Alberto (alberto.antonioni@unil.ch) 
Matthew Ayres (matthew.ayres@growthandinnovation.com.au) 

Meeting today (Jun 12) 6pm in the main conference room.

Resources: https://bitcoin.org/en/resources 
http://blockchain.info/charts 
http://blockexplorer.com/ 
http://bitcoincharts.com/ 
Web of trust: http://bitcoin-otc.com/trust.php 

==MITRE Data Sets==

To access the data please contact Juniper she has it on a hard drive. Here is a PDF that explains the datasets and gives some sample challenge questions.
[[Media:mitredata.pdf |MITRE DATA PDF]] If you have any specific questions about the data you can contact Matt Koehler at mkoehler@mitre.org

==Death in physical, biological and social systems==

Firms, nation states, human beings and stars all die. Do the causes of "death" in physical, biological and social systems have something in common? If yes, what is it?

''Interested''

Ana María 
Vipin (vipin.veetil at gmail dot com) 
Emilia 
Luis Martínez (fnxabraxas@gmail.com) 

==Fractal-like structures in economic data==

In the 1960-70s Mandelbrot showed that some economic time series have fractal-like structures, i.e. they look the same at many time scales. The existence of these structures has been debated since. Do economic time series like S&P 500 index have fractal-like structures? If yes, how fractal-like are they?

''Interested'' 

Vipin (vipin.veetil at gmail dot com) 
Blaz 
Qiao Zhi 

==Microbial Community Data Sets==

The Earth Microbiome Project [http://www.earthmicrobiome.org/ EMP] is a massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. All data sets are processed in the same way (DNA extraction, PCR primers, sequencing, bioinformatics), making them inter-comparable. You can explore these data sets (including some time series, and a bunch of spatial samplings) at the following link [http://microbio.me/emp EMP Data] (no need to create a login ID, just scroll down to 'Download Public Data'). If you have questions, please contact Sean Gibbons (sgibbons at uchicago dot edu).

==Does Larger Memory Capacity Brings about Evolutionary Advantage?==

Evolutionary game theory modeling. Agents/players on lattice or networks. A player with n-step memory has responses to all 4^n past game outcomes. Intuitively, a player with longer memory can have more sophisticated strategy, which might be used to exploit player with smaller memory capacity. Yet according to the Prisoner's Dilemma tournament organized by Axelrod, Tit-for-Tat, which can be modeled using only one-step memory, fares better than a number of sophisticated strategies invented by experts in the field of game theory. From the game theory perspective, does smaller memory capacity actually have evolutionary benefits?

''Interested:'' 
Degang Wu (dwuab@ust.hk) 
Blaz 
Brian 
Flavia (flamarquitti@gmail.com) 
Cole Mathis (cole.mathis@asu.edu) 
Claudius 
Luis Martinez ((fnxabraxas@gmail.com) 

==North American Breeding Birds Survey and tropical trees==

This dataset contains ~4500 sites where populations of birds (~600 species overall, ~60 species on average in every site) were sampled over the past 44 years. This gives numerous time series of both population sizes and the overall number of species. Some problems with this dataset include large observational errors. A dataset of tropical trees with the exact diameter, identity (from among 300 species) and location of ~250000 trees over 6 censuses is also available. Please contact Michael Kalyuzhny for these.

==The Multiplex Networks==

[[Multiplex Networks | Multiplex Networks Page]]

How does the structure of social networks affect the emergence and persistence of norms? Why are some norms (like fashion styles) less persistent than others (like religious beliefs)? Is this because different kinds of norms live on different social networks (with same individual participating in different networks)? If yes, how do these social networks interact?

And finally, what do the answers to the above questions tell us about policy interventions? Can certain critical properties of network structures be exploited to change norms, like going to the moon without much fuel? If two networks interact, say religious belief and fashion styles, can interventions in one be used to bring about changes in another?

PS: Here [https://www.dropbox.com/s/bpjf9mc1qhknkee/ResearchReview.pdf link 1] is a short review of multiplexes that I put up together. It is not exhaustive but the references can give us an idea of the field. If you find any error please let me know (Massimo).

''Interested''

Vipin (vipin.veetil at gmail do com) 
Sarah L 
Alberto (alberto.antonioni@unil.ch) 
Francesca 
Nhat (nhattdnguyen@gmail.com) 
Sanja (sanjakojasanja@gmail.com) 
Massimo 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Cecilia (ci.andreazzi@gmail.com) 
Sean Hayes (shaye004@ucr.edu) 
Claudius 
Luis Martínez (fnxabraxas@gmail.com) 
Brais (brais.alvarez@eui.eu) 
Matthew Ayres (matthew.ayres@growthandinnovation.com.au) 

==Network Tolerance of Failure==

How might a network endure non-catastrophic failure without isolating the failing components? Most network failure models consider resilience against failure as a result of isolating failing components. In contrast, is it possible for the network to be robust through "tolerance" of failure? Perhaps, for example, a symbiotic relationship sustains a weakened node until it has recovered its prior performance. Or perhaps a transmitting network retains a connection to an offline node to reduce an anticipated memory load of re-establishing the connection when it comes back online. What are some of the ways in which networks are able to maintain connection to a failing node without failing themselves in the process - how is the cascade halted without isolation? This is meant to be a broad question to generate more specific ideas. Importantly, this question refers to "tolerance of" failure in contrast to "resilience against" failure.
 Contact: Jessica Santana jsant@stanford.edu

=> It may be interesting to at least discuss (if not merge) this with the project we're proposing (not yet on here but it involves the optimal design of the isolation approach as a function of a measure comprising the network topology, node properties, node-saving attributes of a regulator etc.). There's also the last project on this page dealing with topology and resilience which could also be incorporated. - ''Nicolas''

Interested:

James Holdener (jholdener@mitre.org) 
Junjian Qi 
Ells Campbell 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Sean Hayes(shaye004@ucr.edu) 
Ali Kharrazi 
Nicolas K. Scholtes 
Cecilia (ci.andreazzi@gmail.com) 

*For those interested in this project, we will be meeting at 1 pm in the cafeteria with a related project to determine how to split up the groups. Cheers, Jessica* 

==Influence of different types of parasites and pathogens in networks on dynamics and stability of food webs==

In nature there is a number of infectious agents which have different evolutionary approaches in way how they influence their hosts. We want to built artificial ecological network and to compare how these evolutionary solutions affect stability of food webs.
 Contact: sanjakojasanja@gmail.com

Interested:

Stojan (stojand@mpib-berlin.mpg.de) 
Nhat (nhattdnguyen@gmail.com) 
Sanja (sanjakojasanja@gmail.com) 
Cecilia (ci.andreazzi@gmail.com) 
Hey people can you please update your e-mails so we can be easier in contact?

==Growth of Cities==

Do foraging animals and growing cities utilize resources in the same way? We're interested in building an agent-based model which generates a road network on a map of varying resources by following a set of simple, probabilistic rules. How do the properties of this network evolve through time? How much of city growth can be explained by resource constraints? Do simple rules of growth parallel simple rules of animal foraging behavior? This project will explore agent-based modeling, but will also present opportunities to examine the limits of modeling. Contacts: Diana LaScala-Gruenewald (dianalg11 at gmail.com) and Claire Lagesse (lagesse.claire at gmail.com).

Interested: 
Morgan Edwards 
Rohan Mehta (rsmehta at stanford dot edu) 
Alberto Antonioni (alberto.antonioni@unil.ch) 
Ernest Liu (yu.liu@math.uu.se) 
Michael Kalyuzhny (michael.kalyuzhny at mail.huji.ac.il) 
Hiroshi Ashikaga (hashika1@jhmi.edu) 
Bernardo Furtado bernardo.furtado at ipea.gov.br 
Luis Martínez (fnxabraxas@gmail.com) 
Alex Brummer 
James Holdener (jholdener@mitre.org) 

* "Cities" group
Claire

* "Foraging" group

>>> Next Meeting : Monday, 2:30 p.m. (?)

==Towards a Unified Theory of Biodiversity==

The idea is to build on the Unified Neutral Theory of Biodiversity and create a realistic unified theory that incorporates important scaling phenomena following power laws, energetic constraints, and stochasticity that have been previously neglected. Basically, we want to modify the unrealistic assumptions that birth, death, speciation rates are stochastic uniform functions across all species within a given meta-community. In fact, these processes have recently been shown to scale with body size following power laws of the form Y= C * M^alpha, where C is a constant independent of body mass, M, and alpha is the scaling exponent. These constraints will also dictate how much energy is required at different trophic levels and body sizes, ultimately constraining abundance of organisms in natural systems. Stochasticity will still play a role, but it should be first bounded by energetic constraints. We also plan to incorporate environmental noise, that is to say, incorporate in the model the realistic assumption that the environment changes through time and therefore so will the fitness of different species in the meta-community.
The ultimate goal is to provide a Unified Theory that can make clear predictions about size-abundance-distributions in natural systems, and, perhaps, also make predictions about speciation-extinction dynamics. We currently hold data to test predictions on an 'ecological' time scale. At this point we are uncertain on whether we could obtain good fossil/contemporary data to calibrate/test models.

Interested: 
Diego Barneche Rosado (diego.barneche@mq.edu.au) 
Cornelia Metzig (cornelia.metzig@hotmail.com) 
Michael Kalyuzhny (michael.kalyuzhny at mail.huji.ac.il) 
Ana María 

==Coupling of different types of networks==

We want to develop a concept of how to work with networks of qualitatively different types of relationships or interactions that can influence each other (eg. natural and social). Sign up and come to brainstorm with us :) Contact: sanjakojasanja@gmail.com

For example, people's beliefs about the health benefits/risks of vaccination can be influenced by their social network, and may be studied using belief propagation models. Simultaneously, diseases may spread through a population, which can be studied using diffusion or other epidemiological models. Furthermore, people's beliefs about vaccination may affect their probability of getting infected by a disease, and in turn, getting infected may cause them to re-evaluate their beliefs.

Another example could involve an ecological network expressing predation and competition among species coupled with an environmental network.

Interested: 
Sanja 
Fahad 
Brian 
Nhat (nhattdnguyen@gmail.com) 
Beth Lusczek 
Glen Otero 

Please fill the doodle 
http://doodle.com/m99hkws4k46icx8b

==Co-evolution of Anti-vaccination Sentiment and Flu Infections==

People's beliefs about the health benefits/risks of vaccination can be influenced by their social network, and may be studied using belief propagation models. Simultaneously, diseases may spread through a population, which can be studied using diffusion or other epidemiological models. Furthermore, people's beliefs about vaccination may affect their probability of getting infected by a disease, and in turn, getting infected may cause them to re-evaluate their beliefs.

Previous work has separately studied (1) how beliefs propagate and change over time, (2) how diseases spread through a population over time, and (3) the (static) correlation between beliefs about vaccination and infection rates; but possibly not all three simultaneously.

This project has some similarities to the project on "Coupling Different Types of Networks," and it may make sense for the two groups to be in communication with each other, or even to merge the two projects. This can be discussed later as the projects develop.

Interested: 
Ells 
Nhat 
Glen 
Andy 
Brian 
Alberto (alberto.antonioni@unil.ch) 
Cecilia (ci.andreazzi@gmail.com) 

== Consciousness as an emergent state of matter – what do you think?==

You’re conscious right now, reading this. How does subjective experience emerge out of the bundles of particles that we all are? 

Scholars of many fields have been deconstructing the mind/body dualism for a while, but consciousness remains a big, hard question. I’m no expert and by proposing this as a topic I’m not expecting that any of us will solve it, but I would be very interested in exchanging on the issue with the smart individuals that you are, grounded in so many backgrounds and unafraid of complex problems. 

So... physicians and physicists, social scientists, biologists, mathematicians, philosophers, computer scientists and others… what do you think? Don’t hold back – if beer is necessary for you to address this issue, it can be arranged. 

Contact Sarah L (laborde.7@osu.edu) 

Interested: 
Alireza (alireza.goudarzi at gmail.com)[totally agree with writing down something to figure out what are plausible ways to think about and study this] 
Fahad (fahad.khalid@hpi.uni-potsdam.de) [love the topic ... I'm glad someone brought it up ... I might have some ideas to contribute] 
Claire (lagesse.claire at gmail.com) [it sounds fascinating... :) ] 
Stefan (s.pfenninger12@imperial.ac.uk) 
Hiroshi (hashika1@jhmi.edu) [Happy to contribute from a medical and personal point of view] 
Sean Hayes(shaye004@ucr.edu) 
Cole Mathis (cole.mathis@asu.edu) [The origin and consciousness and the origin of life (my main research interest) have a lot in common, I'm always down to talk about consciousness with some beers, if something novel emerges that's great.] 
Emília [happy to contribute from various points of view, but I advance that, to me, it has a lot to do with memory] 
Ana María (anamaria.gomezlopez@yale.edu) 
Brian (bthompso8784@gmail.com) 
Sean Gibbons (sgibbons at uchicago dot edu) [Definitely interested in joining the conversation] 
Matthew Ayres (matthew.ayres@growthandinnovation.com.au) 
Luis Martínez (fnxabraxas@gmail.com) 
Beth Lusczek (lusc0006@umn.edu) 
Stojan (stojand@mpib-berlin.mpg.de) (sounds perfect for a beer discussion) 
José Aguilar-Rodríguez (jose.aguilar@ieu.uzh.ch) 
Bernardo Furtado (bernardo.furtado@ipea.gov.br)(Happy to learn. Consciously on subconsciously.) 
Nicolas K. Scholtes (nicolas dot scholtes at unamur dot be) [The science fiction aficionado in me is jumping up and down in his chair!] 
Renske Vroomans (R.M.A.Vroomans@uu.nl) [I'd love to join the conversation, I love big topics!]

Note: this doesn’t have to become a formal project, although it could. Let me know if you’re interested in a chat, writing an interdisciplinary dialogue piece, or anything related to this question. 

*An after hour catch-up on Friday evening or this week-end? Here's a basic doodle poll to work out times: http://doodle.com/yi5wp3brbd2z8u5n 

There is a published paper written by a MIT researcher "Consciousness as a State of Matter", just in case if you do not know this... Ernest

==Tradeoffs between division of labor and stability in networks==

The Black Queen Hypothesis [http://mbio.asm.org/content/3/2/e00036-12.abstract BQH] describes the evolution of functional dependencies in microbial ecosystems. This process results in a subset of a community providing necessary services for the rest of the community (see link). Organisms that can outsource essential functions escape the cost performing these functions and have more resources for growth and reproduction. However, this process makes the ecosystem more delicate, as the destruction of key species can eliminate their crucial service(s) and lead to system collapse. Thus, there is a tradeoff between the stability of a network (in the face of perturbations), and the degree of cooperation (how many tasks can be outsourced). As a result of this tradeoff, we could expect different community types to arise in stable vs. variable environments. There is likely some critical range between these two modes (high vs. low environmental variability), where some mixed strategy is optimal. 

This process may have an analogue in the development of multicellular life (vs. free-living single-celled organisms), where each cell type expresses a subset of the genome and provide a specific set of services to the whole (division of labor). This might also be reflected in social or economic networks (higher stability = more cooperative?). A connection could potentially be made to life-history tradeoffs for individual organisms (r vs. k selection - oligotrophs vs. copiotrophs), or in dissipative chemical systems (e.g. [http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.4818538 Stat-Mech of Self Replication]). 

Definitely a work in progress, please add your thoughts if you are interested! Also, please include your contact info alongside your name. 

'''NEXT MEETING: TBA - Rohan will send out an poll to decide on a time''' 

*Thoughts:

Vipin: I believe that this mechanism may have much to do with why "business cycle" occur.

Luis: Maybe this could be also related with the structure and complexity of institutions and its stability. Successful societies increase their size and develop more complex institutions (with higher level of bureaucracy for example) and that can make them less "flexible" and susceptible to get destroyed under not predicted crisis. I think this is related with "social entropy"...

Ali: This paper might be of interest: http://people.biology.ufl.edu/ulan/pubs/Zorach.pdf They use Shannon's entropy to calculate "number of roles" or division of labor in a network. It is related to trade-off of division of labor and robustness.

*Interested: 
Sean Gibbons (sgibbons at uchicago dot edu) 
Rohan Mehta (rsmehta at stanford dot edu) 
Stojan (stojand@mpib-berlin.mpib.de) 
Emília (emilia.garcia.casademont at gmail dot com) 
Ali Kharrazi ali[at}pp dot u-tokyo dot ac dot jp 
Vipin (vipin.veetil at gmail dot com) 
Luis Martínez (fnxabraxas@gmail.com) 
Ernest Liu (yu.liu@math.uu.se) 
Cole Mathis (cole.mathis@asu.edu) 
José Aguilar-Rodríguez (jose.aguilar@ieu.uzh.ch) 
Renske Vroomans (R.M.A.Vroomans@gmail.com) 

==How can evolutionary game theory be applied to electricity trading==

The interest of this project is the following: how can evolutionary game theory be used to find optimal strategies for consumers and/or producers that bid in the electricity market. Also some real data can be considered. 
Contact Blaz 

Interested: 
Degang Wu 
Alberto

== Information Theory of the Heart ==

The heart is a complex system with simple rules of operation and minimal central control. Under normal conditions, it orchestrates a self-organized, emergent behavior of 2 to 3 billion heart cells to perform sophisticated, well-timed pumping of the blood. Under abnormal conditions, it can lead to sudden cardiac death due to cardiac arrhythmias, which are also emergent, collective behaviors of a large number of heart cells, where each heart cell doesn't necessarily need to be abnormal. 

Each heart cell is a dynamic information processing system, which transmits digital information (0 – resting, 1 – excited) in the form of electrical wave. We aim to establish a theoretical basis to quantify information transmission within the heart using information theory and network theory. Our hypothesis is that arrhythmias following heart attack result from an adaptive mechanism to optimize information transmission in abnormal hearts. 

If you want to discuss more please contact Hiroshi (hashika1@jhmi.edu). 

''Interested:'' 
Hiroshi 
Flavia (flamarquitti@gmail.com) 
Brian 
Bernardo Furtado 
José Aguilar-Rodríguez (jose.aguilar@ieu.uzh.ch) 

== Cells and Software: Is Evolution a Software Engineer? ==

There appear to be striking similarities between how we design software, and how evolution designed cells. Some of the analogies are: 
- The concept of "Encapsulation". In object oriented programs, data inside an object is protected by an interface of functions. Similarly, processes within a cell (intra-cellular signaling cascades) are protected from the extra-cellular messaging activities through membrane-bound receptors acting as the interface. 
- Apoptosis (programmed cell death) is similar to proper memory deallocation in programs, while Necrosis is similar to dangling pointers and memory corruption. 
- Proteolysis (breaking down of proteins into constituent amino acids) is similar to automatic garbage collection. 

There are certain constraints (perhaps physical constraints) on the available solutions in biology. Solutions within this constrained solution space eventually result in the emergence of complex behavior. This emergent behavior has enabled humans to engineer solutions to everyday problems. These artificially engineered solutions are very similar in principal to the solutions that already exist in biological systems. 

Are our creative processes ultimately bound by the physical constraints that underlie molecular mechanisms? Or, do we just tend to interpret the phenomena at the molecular level according to our own understanding, which is limited by our senses and neurological processes? Is it all about optimization, and everything else is just a side effect?
Can/do “Patterns” transcend disciplines? 

Motifs (biological systems) – Patterns (software). Patterns/motifs transcending biological and software systems could perhaps, fill gaps in our knowledge of biological systems, and help us design better software systems. Deterministic patterns could perhaps indicate what is required for high level functions to emerge from molecular interactions. And perhaps these similarities occur at the interface between low level interaction and emergent phenomena.

So let's further explore biological and software systems, and try to find answers to these questions.

For more information, please contact Fahad (fahad.khalid@hpi.uni-potsdam.de). 

''Interested:'' 
Fahad 
Ernest (yu.liu@math.uu.se) 
Diana 
Degang (dwuab@ust.hk) 
Stojan 
Ana María 
Brian 
George (qiaozhi827@gmail.com) 
Glen Otero 
Renske 

==Susceptibility of Fields of Research to Interdisciplinary Influences (network perspective) ==

Fields of Research are more often than not isolated from one another in terms of their community, jargon, perspective, research programme (in the sense of Lakatos) and their journals and lots more.

This isolation stands in the way of a fruitful merging and interaction of fields. One needs to understand the obstructions. Hence an analysis of the determining factors for 'community inbreeding' is sought after. Eventually also a quantitative measure for the susceptibility of a research field could be formulated.

A clear-cut project could be based on data together with a network type analysis of a precise question around the determining factors.
We could look at citation data or journal based data or maybe there is a chance to get hold of data from Jessica's collegues, who works on the diffusion of knowledge.

It would be great also to discuss and gather our ideas and experiences.

Meeting: June 12, 4:20, balcony outside Great Hall.

''Interested'' 
Leo (horstmey@mis.mpg.de ) 
Jennifer Hellmann 
Anna Olson 
Lin Li 
Stefan Pfenninger [other angles include: citation networks/academic generations and how they change through time (Diego's idea); citations between subfields to quantify interdisciplinarity and how it changes over time] 
Catherine Bale

==Simple case for studying about “from single-cell to multi-cell / species collaboration”==

QUESTION: how single-cell evolves to multi-cell, even they do not have so-called “intelligence”?

How to do:
Let’s imagine that there is a land where resources A, B, C are located, and a kind of creature which need all of these resources to survive (imagine many creatures live in this land). 
One surviving strategy is that every creature gathers A, B and C and eat them on its own. But maybe under some condition, specialization would automatically happen (e.g. one creature gather A and another gather B, and then they share). 
The goal is to find the necessary condition if possible (we could think out of many sufficient conditions, but finding necessary conditions seems not so easy).

Interested: 
Ernest Liu (yu.liu@math.uu.se) 

comment: are you familiar with holland's "echo" stuff ..stojan 

COMBINED with project 17 "Tradeoffs between division of labor and stability in networks".

==An Analysis of the Hierarchies Present in Modern Economic Theory ==

The idea of this project is to provide a comprehensive survey of the hierarchical structure of economics (macro -> microeconomics) following the reductionist = constructionist + emergence framework of Anderson (N.B. This equation is my own interpretation of Anderson's paper and is open for discussion). Ideally, we would first investigate the microfoundations literature of macroeconomics and the possibility for ABM to rectify some of the redundancies therein after which we would reverse the direction and see how, given some 'fundamental' laws of economic behaviour, we could couple these with emergent phenomena (whatever they may be) to reconstruct the economy at the macro-level.

''Interested'' 
Nicolas ( nicolas dot scholtes at unamur dot be) 
Claudius

== The Topological Modeling of Infrastructure Networks ==

There is some disagreement on the topology of power networks in the literature. There are preferential attachment, small-world and random graph models proposed to explain the topology of power networks. There are caveats associated with each of these generative models. For instance, there is the cost of building new transmission lines that may question the validity of preferential models.

'''The broad question that we attempt to answer here is:''' 

-Can these previous network models create real-world power networks? 
-Can we come up with a better model that can replicate a power network or at least one with similar characteristics? 
-What about other infrastructure networks, e.g., natural gas network, water piping networks, etc? 

Interested:
Pooya Rezaei 
Tom McAndrew 
James Holdener (jholdener@mitre.org) 

== Functional Networks and their evolution ==

We are interested in researching (possibly hierarchical) networks that have a function which can be quantified. We are interested in understanding how such networks evolve and may continue to deliver all or part of their function when they are damaged. As of now, we do not have a clear conceptualization of these ideas in formal network language, and our immediate task is to think of the formal network structure we wish to explore (e.g. b-partite, multileveled). Possible concrete cases to apply this formal characterization to are trees (i.e. plants), power grids, or financial networks.

Interested (please contact us to join the debate):

Alex Brummer (brummera@email.arizona.edu) 
Shai Gorsky (shai.gorsky@utah.edu) 
Beth Lusczek (lusc0006@umn.edu) 
Stefan Pfenninger (s.pfenninger12@imperial.ac.uk) 
Jessica Santana (jsant@stanford.edu) 
Anna Olson (olsona at cs dot uchicago dot edu) 
Nicolas K. Scholtes (nicolas dot scholtes at unamur dot be 
Ali Kharrazi 
Renske Vroomans (R.M.A.Vroomans@uu.nl) 

== Multi-scalar approaches to understand regime shifts in a socio-ecological system ==

Field-based research, be it qualitative or quantitative, often yields fragmentary and limited data sets when collected in settings with political instability, economic disparity, and rapidly changing environmental conditions. Using the Logone river floodplain in Cameroon as a case study, this project aims to carry out multi-scalar analysis of fragmentary data sets to understand larger social dynamics and ecological regime shifts in this region. Our goal is to address the challenges of network analysis, agent-based modeling, and game theory in this context by examining multiple units of analysis at different scales. 
 
Some of the possible issues to study are: common pool resources problems, influence of (corrupt) institutions, influence of the internal structure of these societies, etc. 
 
We will attempt to meet at '''6:30pm today Thursday''' in the lecture room. 
 

Sarah L 
Ana María 
Claudius 
Luis Martínez (fnxabraxas@gmail.com) 
Ali Kharrazi 
Francesca Lipari 

== The architecture of an empirical genotype-phenotype mapping ==

One of the central open questions in biology is to understand how genotypes map onto phenotypes. While system and developmental biologists are
interested in the physical, biochemical and physiological basis of genotype-phenotype maps, evolutionary biologists try to comprehend their evolutionary causes
and consequences. Our current knowledge on this question comes from computational models that allow us to rapidly map genotypes to phenotypes for some biological
systems, facilitating the systematic exploration of their vast genotype spaces. These models have shown that many genotypes usually map onto the same phenotype.
These genotypes form genotype networks, or neutral networks, that spread into genotype space. These networks contain as vertices all the genotypes that share a
same phenotype, where genotypes are connected by edges if they differ by a single mutation. 
 
Thanks to several computational models, the formalism of genotype networks has been very successful at providing new insights about the evolution of systems as
diverse as RNA, proteins, regulatory networks and metabolism. Payne & Wagner have recently pioneered the application of this formalism to transcription factor (TF)
binding sites. TFs are DNA-binding proteins that regulate gene expression by binding to short sequences on DNA — TF binding sites — that
are in close physical proximity to the genes’ coding sequence, thus inducing or repressing gene transcription. The set of DNA sites bound by a particular TF
can be viewed as a genotype network. This mapping from TF binding sites onto their cognate TFs constitutes the first exhaustive genotype-phenotype map entirely
based on experimental data. 
 
Research questions that can be asked in this system: 
1. What is the geometry of empirical genotype networks in genotype space and how that geometry affects evolutionary exploration? 
2. What is the community structure of these empirical genotype networks? Is this structure determined by the biophysics of TF-DNA binding? 
3. How accesible is one phenotype from any other phenotype in this system and how that accessibility defines phenotype space as a topological space? 
 
If you are interested please contact José (jose.aguilar@ieu.uzh.ch). 
 
References: 
1. Stadler, B.M., Stadler, P.F., Wagner, G.P., and Fontana, W. (2001). The topology of the possible: formal spaces underlying patterns of evolutionary change. J. Theor. Biol. 213, 241–74. 
2. Payne, J.L., and Wagner, A. (2014). The robustness and evolvability of transcription factor binding sites. Science 343, 875–7. 
 
Interested: 
Cole 
Glen 
José 
Leto 
Massimo 
Renske 

==Network warping via Chaotic Dynamics==

There has been an explosion of research in temporal networks, and in Chaos Theory separately. Why not combined them? The idea is this: Generate different network structures (Erdos-Renyi etc.) whos probability of connections depends on a Chaotic attractor. 

Are there topological invariants on these networks?

Interested:
Tom McAndrew 
Sean G. (sgibbons at uchicago dot edu) 
Anna Olson (olsona at cs dot uchicago dot edu) 

==Network robustness as a function of nodes' resilience==

Are there characteristics of a network's nodes that make the network more or less robust to failure? Perhaps degree assortativity, or nodes' positions relative to the demands made on them? Given that network failure can affect every node in a network, nodes might, as it were, gain an advantage from being positioned far away from nodes that could catastrophically fail.

Interested: 
Anna Olson (olsona at cs.uchicago.edu) 
Jenn Hellmann 
Leo Horstmeyer 

==Optimal Quarantine Strategies in Financial Networks==
We are interested in borrowing and adapting concepts from epidemiology to provide policy guidelines that minimize the damage to the global financial system when defaults cascade between financial institutions.

From a network perspective, we would like to identify optimal quarantine strategies (selective edge pruning, node isolation, community isolation, etc) by simulating default cascades of variable intensity on an idealized financial network. A key component of this analysis would focus on the temporal delay between the identification of a cascade threat and implementation of a control measure.

1. Brais

Complex Systems Summer School 2014-Projects & Working Groups

2014-06-12T13:29:36Z

Pfenningers: /* Bitcoin */

{{Complex Systems Summer School 2014}}

==Bitcoin==

Bitcoin is an online peer-to-peer currency which has gained popularity in recent years. With increased general interest and now more and more companies accepting transactions in Bitcoin, so to has its value and is currently priced at $633 for 1 Bitcoin!

'''So what is Bitcoin?'''

The idea behind Bitcoin was to remove the need for a centralised banking system. The way this works is to have all transactions made public and then have the Bitcoin community validate transactions by donating computational power (and rewarded in Bitcoins). For further details see this blog:

http://www.michaelnielsen.org/ddi/how-the-bitcoin-protocol-actually-works/

'''So why is it interesting?'''

Usually companies and individuals keep all of their financial records private, but ALL transaction in Bitcoin are publicly available, so this provides a unique opportunity to study financial transactions. While the transactions are public, the owners of Bitcoin remain (relatively) anonymous, and so this has led to associations with criminal activities (e.g. on the silk road) from illegal drugs to hired hit-men. In addition to illegal activities using the currency, there have also been a number of illegal activities against the currency, such as high valued heists of the order of $100 million.

''Oh, and of course its a big temporally evolving network.''

If you're interested in working on this then add your name below. If there is interest, then we can have a "Bitcoin, beers and blackboard" session to throw some ideas around.

Interested:

Leto 
Shai 
Flavia 
Jessica Santana jsant@stanford.edu 
Stefan 

==MITRE Data Sets==

To access the data please contact Juniper she has it on a hard drive. Here is a PDF that explains the datasets and gives some sample challenge questions.
[[Media:mitredata.pdf |MITRE DATA PDF]] If you have any specific questions about the data you can contact Matt Koehler at mkoehler@mitre.org

==Death in physical, biological and social systems==

Firms, nation states, human beings and stars all die. Do the causes of "death" in physical, biological and social systems have something in common? If yes, what is it?

''Interested''

Vipin 
Ana María (I really find this topic interesting) 

==Fractal-like structures in economic data==

In the 1960-70s Mandelbrot showed that some economic time series have fractal-like structures, i.e. they look the same at many time scales. The existence of these structures has been debated since. Do economic time series like S&P 500 index have fractal-like structures? If yes, how fractal-like are they?

''Interested'' 

Vipin 
Blaz 
Qiao Zhi 

==Microbial Community Data Sets==

The Earth Microbiome Project [http://www.earthmicrobiome.org/ EMP] is a massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. All data sets are processed in the same way (DNA extraction, PCR primers, sequencing, bioinformatics), making them inter-comparable. You can explore these data sets (including some time series, and a bunch of spatial samplings) at the following link [http://microbio.me/emp EMP Data] (no need to create a login ID, just scroll down to 'Download Public Data'). If you have questions, please contact Sean Gibbons (sgibbons at uchicago dot edu).

==Does Larger Memory Capacity Brings about Evolutionary Advantage?==

Evolutionary game theory modeling. Agents/players on lattice or networks. A player with n-step memory has responses to all 4^n past game outcomes. Intuitively, a player with longer memory can have more sophisticated strategy, which might be used to exploit player with smaller memory capacity. Yet according to the Prisoner's Dilemma tournament organized by Axelrod, Tit-for-Tat, which can be modeled using only one-step memory, fares better than a number of sophisticated strategies invented by experts in the field of game theory. From the game theory perspective, does smaller memory capacity actually have evolutionary benefits?
Please contact Degang Wu (dwuab@ust.hk).

''Interested:'' 
Blaz 
Brian 
Flavia 
Cole Mathis (cole.mathis@asu.edu) 
Claudius

==North American Breeding Birds Survey and tropical trees==

This dataset contains ~4500 sites where populations of birds (~600 species overall, ~60 species on average in every site) were sampled over the past 44 years. This gives numerous time series of both population sizes and the overall number of species. Some problems with this dataset include large observational errors. A dataset of tropical trees with the exact diameter, identity (from among 300 species) and location of ~250000 trees over 6 censuses is also available. Please contact Michael Kalyuzhny for these.

==Santa Fe tournament of time series analysis!==

Do fluctuations in timeseries arise from nonlinear dynamics or from stochasticity? Specifically, there are several examples of ecological time series where chaos/complex periodicity were found (and published in Science and other leading journals). But usually such analyses didn't examine alternative models of stochastic dynamics. I propose making some meta-analysis and trying to compare the predictive power of both kinds of models. This can also be done in other fields were such timeseries are available. If you want to talk about this - contact Michael Kalyuzhny

Interested:
Michael Kalyuzhny 
Degang Wu 

==The Multiplex Networks==

How does the structure of social networks affect the emergence and persistence of norms? Why are some norms (like fashion styles) less persistent than others (like religious beliefs)? Is this because different kinds of norms live on different social networks (with same individual participating in different networks)? If yes, how do these social networks interact?

And finally, what do the answers to the above questions tell us about policy interventions? Can certain critical properties of network structures be exploited to change norms, like going to the moon without much fuel? If two networks interact, say religious belief and fashion styles, can interventions in one be used to bring about changes in another?

''Interested''

Vipin 
Sarah L 
Alberto 
Francesca 
Nhat (nhattdnguyen@gmail.com) 
Sanja 
Massimo 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Cecilia 
Sean Hayes (shaye004@ucr.edu) 
Claudius

==Network Tolerance of Failure==

How might a network endure non-catastrophic failure without isolating the failing components? Most network failure models consider resilience against failure as a result of isolating failing components. In contrast, is it possible for the network to be robust through "tolerance" of failure? Perhaps, for example, a symbiotic relationship sustains a weakened node until it has recovered its prior performance. Or perhaps a transmitting network retains a connection to an offline node to reduce an anticipated memory load of re-establishing the connection when it comes back online. What are some of the ways in which networks are able to maintain connection to a failing node without failing themselves in the process - how is the cascade halted without isolation? This is meant to be a broad question to generate more specific ideas. Importantly, this question refers to "tolerance of" failure in contrast to "resilience against" failure.
 Contact: Jessica Santana jsant@stanford.edu

Interested:

James Holdener 
Junjian Qi 
Ells Campbell 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Sean Hayes(shaye004@ucr.edu)

==Influence of different types of parasites and pathogens in networks on dynamics and stability of food webs==

In nature there is a number of infectious agents which have different evolutionary approaches in way how they influence their hosts. We want to built artificial ecological network and to compare how these evolutionary solutions affect stability of food webs.
 Contact: sanjakojasanja@gmail.com

Interested:

Stojan 
Nhat (nhattdnguyen@gmail.com) 
Sanja 
Cecilia: Are we going to discuss today at 9? No probably, but tomorrow, today is a free day! Relax!:D

==Growth of Cities==

Do foraging animals and growing cities utilize resources in the same way? We're interested in building an agent-based model which generates a road network on a map of varying resources by following a set of simple, probabilistic rules. How do the properties of this network evolve through time? How much of city growth can be explained by resource constraints? Do simple rules of growth parallel simple rules of animal foraging behavior? This project will explore agent-based modeling, but will also present opportunities to examine the limits of modeling. Contacts: Diana LaScala-Gruenewald (dianalg11 at gmail.com) and Claire Lagesse (lagesse.claire at gmail.com).

Interested: 
Morgan Edwards 
Rohan Mehta 
Alberto Antonioni 
Ernest Liu 
Michael Kalyuzhny 
Hiroshi Ashikaga (hashika1@jhmi.edu) 

==Towards a Unified Theory of Biodiversity==

The idea is to build on the Unified Neutral Theory of Biodiversity and create a realistic unified theory that incorporates important scaling phenomena following power laws, energetic constraints, and stochasticity that have been previously neglected. Basically, we want to modify the unrealistic assumptions that birth, death, speciation rates are stochastic uniform functions across all species within a given meta-community. In fact, these processes have recently been shown to scale with body size following power laws of the form Y= C * M^alpha, where C is a constant independent of body mass, M, and alpha is the scaling exponent. These constraints will also dictate how much energy is required at different trophic levels and body sizes, ultimately constraining abundance of organisms in natural systems. Stochasticity will still play a role, but it should be first bounded by energetic constraints. We also plan to incorporate environmental noise, that is to say, incorporate in the model the realistic assumption that the environment changes through time and therefore so will the fitness of different species in the meta-community.
The ultimate goal is to provide a Unified Theory that can make clear predictions about size-abundance-distributions in natural systems, and, perhaps, also make predictions about speciation-extinction dynamics. We currently hold data to test predictions on an 'ecological' time scale. At this point we are uncertain on whether we could obtain good fossil/contemporary data to calibrate/test models.

Interested: 
Diego Barneche Rosado 
Cornelia Metzig 
Michael Kalyuzhny 

==Coupling of different types of networks==

We want to develop a concept of how to work with networks of qualitatively different types of relationships or interactions that can influence each other (eg. natural and social). Sign up and come to brainstorm with us :) Contact: sanjakojasanja@gmail.com

For example, people's beliefs about the health benefits/risks of vaccination can be influenced by their social network, and may be studied using belief propagation models. Simultaneously, diseases may spread through a population, which can be studied using diffusion or other epidemiological models. Furthermore, people's beliefs about vaccination may affect their probability of getting infected by a disease, and in turn, getting infected may cause them to re-evaluate their beliefs.

Another example could involve an ecological network expressing predation and competition among species, and environmental factors affecting the natural resources in the system.

Interested: 
Sanja 
Fahad 
Brian 
Nhat (nhattdnguyen@gmail.com) 

== Consciousness as an emergent state of matter – what do you think?==

You’re conscious right now, reading this. How does subjective experience emerge out of the bundles of particles that we all are? 

Scholars of many fields have been deconstructing the mind/body dualism for a while, but consciousness remains a big, hard question. I’m no expert and by proposing this as a topic I’m not expecting that any of us will solve it, but I would be very interested in exchanging on the issue with the smart individuals that you are, grounded in so many backgrounds and unafraid of complex problems. 

So... physicians and physicists, social scientists, biologists, mathematicians, philosophers, computer scientists and others… what do you think? Don’t hold back – if beer is necessary for you to address this issue, it can be arranged. 

Contact Sarah L (laborde.7@osu.edu) 

Interested: 
Alireza (alireza.goudarzi at gmail.com)[totally agree with writing down something to figure out what are plausible ways to think about and study this] 
Fahad (fahad.khalid@hpi.uni-potsdam.de) [love the topic ... I'm glad someone brought it up ... I might have some ideas to contribute] 
Claire (lagesse.claire at gmail.com) [it sounds fascinating... :) ] 
Stefan (s.pfenninger12@imperial.ac.uk) 
Hiroshi (hashika1@jhmi.edu) [Happy to contribute from a medical and personal point of view] 
Sean Hayes(shaye004@ucr.edu) 
Cole Mathis (cole.mathis@asu.edu) [The origin and consciousness and the origin of life (my main research interest) have a lot in common, I'm always down to talk about consciousness with some beers, if something novel emerges that's great.] 
Emília [happy to contribute from various points of view, but I advance that, to me, it has a lot to do with memory] 
Ana María 
Brian (bthompso8784@gmail.com) 
Sean Gibbons (sgibbons at uchicago dot edu) [Definitely interested in joining the conversation]

Note: this doesn’t have to become a formal project, although it could. Let me know if you’re interested in a chat, writing an interdisciplinary dialogue piece, or anything related to this question. 

==Tradeoffs between division of labor and stability in networks==

The Black Queen Hypothesis [http://mbio.asm.org/content/3/2/e00036-12.abstract BQH] describes the evolution of functional dependencies in microbial ecosystems. This process results in a subset of a community providing necessary services for the rest of the community (see link). Organisms that can outsource essential functions escape the cost performing these functions and have more resources for growth and reproduction. However, this process makes the ecosystem more delicate, as the destruction of key species can eliminate their crucial service(s) and lead to system collapse. Thus, there is a tradeoff between the stability of a network (in the face of perturbations), and the degree of cooperation (how many tasks can be outsourced). As a result of this tradeoff, we could expect different community types to arise in stable vs. variable environments. There is likely some critical range between these two modes (high vs. low environmental variability), where some mixed strategy is optimal. 

This process may have an analogue in the development of multicellular life (vs. free-living single-celled organisms), where each cell type expresses a subset of the genome and provide a specific set of services to the whole (division of labor). This might also be reflected in social or economic networks (higher stability = more cooperative?). A connection could potentially be made to life-history tradeoffs for individual organisms (r vs. k selection - oligotrophs vs. copiotrophs), or in dissipative chemical systems (e.g. [http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.4818538 Stat-Mech of Self Replication]). 

Definitely a work in progress, please add your thoughts if you are interested!

Interested: 
Sean Gibbons (sgibbons at uchicago dot edu) 
Rohan Mehta 
Stojan 
Emília 

==How can evolutionary game theory be applied to electricity trading==

The interest of this project is the following: how can evolutionary game theory be used to find optimal strategies for consumers and/or producers that bid in the electricity market. Also some real data can be considered. 
Contact Blaz 

Interested: 
Degang Wu 

== Information Theory of the Heart ==

The heart is a complex system with simple rules of operation and minimal central control. Under normal conditions, it orchestrates a self-organized, emergent behavior of 2 to 3 billion heart cells to perform sophisticated, well-timed pumping of the blood. Under abnormal conditions, it can lead to sudden cardiac death due to cardiac arrhythmias, which are also emergent, collective behaviors of a large number of heart cells, where each heart cell doesn't necessarily need to be abnormal. 

Each heart cell is a dynamic information processing system, which transmits digital information (0 – resting, 1 – excited) in the form of electrical wave. We aim to establish a theoretical basis to quantify information transmission within the heart using information theory and network theory. Our hypothesis is that arrhythmias following heart attack result from an adaptive mechanism to optimize information transmission in abnormal hearts. 

If you want to discuss more please contact Hiroshi (hashika1@jhmi.edu). 

''Interested:'' 
Hiroshi 
Flavia 

== Cells and Software: Is Evolution a Software Engineer? ==

There appear to be striking similarities between how we design software, and how evolution designed cells. Some of the analogies are: 
- The concept of "Encapsulation". In object oriented programs, data inside an object is protected by an interface of functions. Similarly, processes within a cell (intra-cellular signaling cascades) are protected from the extra-cellular messaging activities through membrane-bound receptors acting as the interface. 
- Apoptosis (programmed cell death) is similar to proper memory deallocation in programs, while Necrosis is similar to dangling pointers and memory corruption. 
- Proteolysis (breaking down of proteins into constituent amino acids) is similar to automatic garbage collection. 

There are certain constraints (perhaps physical constraints) on the available solutions in biology. Solutions within this constrained solution space eventually result in the emergence of complex behavior. This emergent behavior has enabled humans to engineer solutions to everyday problems. These artificially engineered solutions are very similar in principal to the solutions that already exist in biological systems. 

Are our creative processes ultimately bound by the physical constraints that underlie molecular mechanisms? Or, do we just tend to interpret the phenomena at the molecular level according to our own understanding, which is limited by our senses and neurological processes? Is it all about optimization, and everything else is just a side effect?
Can/do “Patterns” transcend disciplines? 

Motifs (biological systems) – Patterns (software). Patterns/motifs transcending biological and software systems could perhaps, fill gaps in our knowledge of biological systems, and help us design better software systems. Deterministic patterns could perhaps indicate what is required for high level functions to emerge from molecular interactions. And perhaps these similarities occur at the interface between low level interaction and emergent phenomena.

So let's further explore biological and software systems, and try to find answers to these questions.

For more information, please contact Fahad (fahad.khalid@hpi.uni-potsdam.de). 

''Interested:'' 
Fahad 
Ernest 
Diana 
Degang 
Stojan 
Ana María 

==Susceptibility of Fields of Research to Interdisciplinary Influences (network perspective) ==

Fields of Research are more often than not isolated from one another in terms of their community, jargon, perspective, research programme (in the sense of Lakatos) and their journals and lots more.

This isolation stands in the way of a fruitful merging and interaction of fields. One needs to understand the obstructions. Hence an analysis of the determining factors for 'community inbreeding' is sought after. Eventually also a quantitative measure for the susceptibility of a research field could be formulated.

A clear-cut project could be based on data together with a network type analysis of a precise question around the determining factors.
We could look at citation data or journal based data or maybe there is a chance to get hold of data from Jessica's collegues, who works on the diffusion of knowledge.

It would be great also to discuss and gather our ideas and experiences.

''Interested'' 
Leo (horstmey@mis.mpg.de ) 
Jennifer Hellmann 
Anna Olson 
Lin Li 
Stefan Pfenninger [other angles include: citation networks/academic generations and how they change through time (Diego's idea); citations between subfields to quantify interdisciplinarity and how it changes over time] 

==Simple case for studying about “from single-cell to multi-cell / species collaboration”==

QUESTION: how single-cell evolves to multi-cell, even they do not have so-called “intelligence”?

How to do:
Let’s imagine that there is a land where resources A, B, C are located, and a kind of creature which need all of these resources to survive (imagine many creatures live in this land). 
One surviving strategy is that every creature gathers A, B and C and eat them on its own. But maybe under some condition, specialization would automatically happen (e.g. one creature gather A and another gather B, and then they share). 
The goal is to find the necessary condition if possible (we could think out of many sufficient conditions, but finding necessary conditions seems not so easy).

Interested: 
Ernest Liu (yu.liu@math.uu.se) 

==An Analysis of the Hierarchies Present in Modern Economic Theory ==

The idea of this project is to provide a comprehensive survey of the hierarchical structure of economics (macro -> microeconomics) following the reductionist = constructionist + emergence framework of Anderson (N.B. This equation is my own interpretation of Anderson's paper and is open for discussion). Ideally, we would first investigate the microfoundations literature of macroeconomics and the possibility for ABM to rectify some of the redundancies therein after which we would reverse the direction and see how, given some 'fundamental' laws of economic behaviour, we could couple these with emergent phenomena (whatever they may be) to reconstruct the economy at the macro-level.

''Interested'' 
Nicolas ( nicolas dot scholtes at unamur dot be) 
Claudius

== The Topological Modeling of Infrastructure Networks ==

There is some disagreement on the topology of power networks in the literature. There are preferential attachment, small-world and random graph models proposed to explain the topology of power networks. There are caveats associated with each of these generative models. For instance, there is the cost of building new transmission lines that may question the validity of preferential models.

'''The broad question that we attempt to answer here is:''' 

-Can these previous network models create real-world power networks? 
-Can we come up with a better model that can replicate a power network or at least one with similar characteristics? 
-What about other infrastructure networks, e.g., natural gas network, water piping networks, etc? 

Interested:
Pooya Rezaei 
Tom McAndrew 

== Functional Networks and their evolution ==

We are interested in researching (possibly hierarchical) networks that have a function which can be quantified. We are interested in understanding how such networks evolve and may continue to deliver all or part of their function when they are damaged. As of now, we do not have a clear conceptualization of these ideas in formal network language, and our immediate task is to think of the formal network structure we wish to explore (e.g. b-partite, multileveled). Possible concrete cases to apply this formal characterization to are trees (i.e. plants), power grids, or financial networks.

Interested (please contact us to join the debate):

Alex Brummer (brummera@email.arizona.edu) 
Shai Gorsky (shai.gorsky@utah.edu) 
Beth Lusczek (lusc0006@umn.edu) 
Stefan Pfenninger (s.pfenninger12@imperial.ac.uk) 
Jessica Santana (jsant@stanford.edu)

Complex Systems Summer School 2014-Projects & Working Groups

2014-06-12T13:27:55Z

Pfenningers: /* Susceptibility of Fields of Research to Interdisciplinary Influences (network perspective) */

{{Complex Systems Summer School 2014}}

==Bitcoin==

Bitcoin is an online peer-to-peer currency which has gained popularity in recent years. With increased general interest and now more and more companies accepting transactions in Bitcoin, so to has its value and is currently priced at $633 for 1 Bitcoin!

'''So what is Bitcoin?'''

The idea behind Bitcoin was to remove the need for a centralised banking system. The way this works is to have all transactions made public and then have the Bitcoin community validate transactions by donating computational power (and rewarded in Bitcoins). For further details see this blog:

http://www.michaelnielsen.org/ddi/how-the-bitcoin-protocol-actually-works/

'''So why is it interesting?'''

Usually companies and individuals keep all of their financial records private, but ALL transaction in Bitcoin are publicly available, so this provides a unique opportunity to study financial transactions. While the transactions are public, the owners of Bitcoin remain (relatively) anonymous, and so this has led to associations with criminal activities (e.g. on the silk road) from illegal drugs to hired hit-men. In addition to illegal activities using the currency, there have also been a number of illegal activities against the currency, such as high valued heists of the order of $100 million.

''Oh, and of course its a big temporally evolving network.''

If you're interested in working on this then add your name below. If there is interest, then we can have a "Bitcoin, beers and blackboard" session to throw some ideas around.

Interested:

Leto 
Shai 
Flavia 
Jessica Santana jsant@stanford.edu 

==MITRE Data Sets==

To access the data please contact Juniper she has it on a hard drive. Here is a PDF that explains the datasets and gives some sample challenge questions.
[[Media:mitredata.pdf |MITRE DATA PDF]] If you have any specific questions about the data you can contact Matt Koehler at mkoehler@mitre.org

==Death in physical, biological and social systems==

Firms, nation states, human beings and stars all die. Do the causes of "death" in physical, biological and social systems have something in common? If yes, what is it?

''Interested''

Vipin 
Ana María (I really find this topic interesting) 

==Fractal-like structures in economic data==

In the 1960-70s Mandelbrot showed that some economic time series have fractal-like structures, i.e. they look the same at many time scales. The existence of these structures has been debated since. Do economic time series like S&P 500 index have fractal-like structures? If yes, how fractal-like are they?

''Interested'' 

Vipin 
Blaz 
Qiao Zhi 

==Microbial Community Data Sets==

The Earth Microbiome Project [http://www.earthmicrobiome.org/ EMP] is a massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. All data sets are processed in the same way (DNA extraction, PCR primers, sequencing, bioinformatics), making them inter-comparable. You can explore these data sets (including some time series, and a bunch of spatial samplings) at the following link [http://microbio.me/emp EMP Data] (no need to create a login ID, just scroll down to 'Download Public Data'). If you have questions, please contact Sean Gibbons (sgibbons at uchicago dot edu).

==Does Larger Memory Capacity Brings about Evolutionary Advantage?==

Evolutionary game theory modeling. Agents/players on lattice or networks. A player with n-step memory has responses to all 4^n past game outcomes. Intuitively, a player with longer memory can have more sophisticated strategy, which might be used to exploit player with smaller memory capacity. Yet according to the Prisoner's Dilemma tournament organized by Axelrod, Tit-for-Tat, which can be modeled using only one-step memory, fares better than a number of sophisticated strategies invented by experts in the field of game theory. From the game theory perspective, does smaller memory capacity actually have evolutionary benefits?
Please contact Degang Wu (dwuab@ust.hk).

''Interested:'' 
Blaz 
Brian 
Flavia 
Cole Mathis (cole.mathis@asu.edu) 
Claudius

==North American Breeding Birds Survey and tropical trees==

This dataset contains ~4500 sites where populations of birds (~600 species overall, ~60 species on average in every site) were sampled over the past 44 years. This gives numerous time series of both population sizes and the overall number of species. Some problems with this dataset include large observational errors. A dataset of tropical trees with the exact diameter, identity (from among 300 species) and location of ~250000 trees over 6 censuses is also available. Please contact Michael Kalyuzhny for these.

==Santa Fe tournament of time series analysis!==

Do fluctuations in timeseries arise from nonlinear dynamics or from stochasticity? Specifically, there are several examples of ecological time series where chaos/complex periodicity were found (and published in Science and other leading journals). But usually such analyses didn't examine alternative models of stochastic dynamics. I propose making some meta-analysis and trying to compare the predictive power of both kinds of models. This can also be done in other fields were such timeseries are available. If you want to talk about this - contact Michael Kalyuzhny

Interested:
Michael Kalyuzhny 
Degang Wu 

==The Multiplex Networks==

How does the structure of social networks affect the emergence and persistence of norms? Why are some norms (like fashion styles) less persistent than others (like religious beliefs)? Is this because different kinds of norms live on different social networks (with same individual participating in different networks)? If yes, how do these social networks interact?

And finally, what do the answers to the above questions tell us about policy interventions? Can certain critical properties of network structures be exploited to change norms, like going to the moon without much fuel? If two networks interact, say religious belief and fashion styles, can interventions in one be used to bring about changes in another?

''Interested''

Vipin 
Sarah L 
Alberto 
Francesca 
Nhat (nhattdnguyen@gmail.com) 
Sanja 
Massimo 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Cecilia 
Sean Hayes (shaye004@ucr.edu) 
Claudius

==Network Tolerance of Failure==

How might a network endure non-catastrophic failure without isolating the failing components? Most network failure models consider resilience against failure as a result of isolating failing components. In contrast, is it possible for the network to be robust through "tolerance" of failure? Perhaps, for example, a symbiotic relationship sustains a weakened node until it has recovered its prior performance. Or perhaps a transmitting network retains a connection to an offline node to reduce an anticipated memory load of re-establishing the connection when it comes back online. What are some of the ways in which networks are able to maintain connection to a failing node without failing themselves in the process - how is the cascade halted without isolation? This is meant to be a broad question to generate more specific ideas. Importantly, this question refers to "tolerance of" failure in contrast to "resilience against" failure.
 Contact: Jessica Santana jsant@stanford.edu

Interested:

James Holdener 
Junjian Qi 
Ells Campbell 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Sean Hayes(shaye004@ucr.edu)

==Influence of different types of parasites and pathogens in networks on dynamics and stability of food webs==

In nature there is a number of infectious agents which have different evolutionary approaches in way how they influence their hosts. We want to built artificial ecological network and to compare how these evolutionary solutions affect stability of food webs.
 Contact: sanjakojasanja@gmail.com

Interested:

Stojan 
Nhat (nhattdnguyen@gmail.com) 
Sanja 
Cecilia: Are we going to discuss today at 9? No probably, but tomorrow, today is a free day! Relax!:D

==Growth of Cities==

Do foraging animals and growing cities utilize resources in the same way? We're interested in building an agent-based model which generates a road network on a map of varying resources by following a set of simple, probabilistic rules. How do the properties of this network evolve through time? How much of city growth can be explained by resource constraints? Do simple rules of growth parallel simple rules of animal foraging behavior? This project will explore agent-based modeling, but will also present opportunities to examine the limits of modeling. Contacts: Diana LaScala-Gruenewald (dianalg11 at gmail.com) and Claire Lagesse (lagesse.claire at gmail.com).

Interested: 
Morgan Edwards 
Rohan Mehta 
Alberto Antonioni 
Ernest Liu 
Michael Kalyuzhny 
Hiroshi Ashikaga (hashika1@jhmi.edu) 

==Towards a Unified Theory of Biodiversity==

The idea is to build on the Unified Neutral Theory of Biodiversity and create a realistic unified theory that incorporates important scaling phenomena following power laws, energetic constraints, and stochasticity that have been previously neglected. Basically, we want to modify the unrealistic assumptions that birth, death, speciation rates are stochastic uniform functions across all species within a given meta-community. In fact, these processes have recently been shown to scale with body size following power laws of the form Y= C * M^alpha, where C is a constant independent of body mass, M, and alpha is the scaling exponent. These constraints will also dictate how much energy is required at different trophic levels and body sizes, ultimately constraining abundance of organisms in natural systems. Stochasticity will still play a role, but it should be first bounded by energetic constraints. We also plan to incorporate environmental noise, that is to say, incorporate in the model the realistic assumption that the environment changes through time and therefore so will the fitness of different species in the meta-community.
The ultimate goal is to provide a Unified Theory that can make clear predictions about size-abundance-distributions in natural systems, and, perhaps, also make predictions about speciation-extinction dynamics. We currently hold data to test predictions on an 'ecological' time scale. At this point we are uncertain on whether we could obtain good fossil/contemporary data to calibrate/test models.

Interested: 
Diego Barneche Rosado 
Cornelia Metzig 
Michael Kalyuzhny 

==Coupling of different types of networks==

We want to develop a concept of how to work with networks of qualitatively different types of relationships or interactions that can influence each other (eg. natural and social). Sign up and come to brainstorm with us :) Contact: sanjakojasanja@gmail.com

For example, people's beliefs about the health benefits/risks of vaccination can be influenced by their social network, and may be studied using belief propagation models. Simultaneously, diseases may spread through a population, which can be studied using diffusion or other epidemiological models. Furthermore, people's beliefs about vaccination may affect their probability of getting infected by a disease, and in turn, getting infected may cause them to re-evaluate their beliefs.

Another example could involve an ecological network expressing predation and competition among species, and environmental factors affecting the natural resources in the system.

Interested: 
Sanja 
Fahad 
Brian 
Nhat (nhattdnguyen@gmail.com) 

== Consciousness as an emergent state of matter – what do you think?==

You’re conscious right now, reading this. How does subjective experience emerge out of the bundles of particles that we all are? 

Scholars of many fields have been deconstructing the mind/body dualism for a while, but consciousness remains a big, hard question. I’m no expert and by proposing this as a topic I’m not expecting that any of us will solve it, but I would be very interested in exchanging on the issue with the smart individuals that you are, grounded in so many backgrounds and unafraid of complex problems. 

So... physicians and physicists, social scientists, biologists, mathematicians, philosophers, computer scientists and others… what do you think? Don’t hold back – if beer is necessary for you to address this issue, it can be arranged. 

Contact Sarah L (laborde.7@osu.edu) 

Interested: 
Alireza (alireza.goudarzi at gmail.com)[totally agree with writing down something to figure out what are plausible ways to think about and study this] 
Fahad (fahad.khalid@hpi.uni-potsdam.de) [love the topic ... I'm glad someone brought it up ... I might have some ideas to contribute] 
Claire (lagesse.claire at gmail.com) [it sounds fascinating... :) ] 
Stefan (s.pfenninger12@imperial.ac.uk) 
Hiroshi (hashika1@jhmi.edu) [Happy to contribute from a medical and personal point of view] 
Sean Hayes(shaye004@ucr.edu) 
Cole Mathis (cole.mathis@asu.edu) [The origin and consciousness and the origin of life (my main research interest) have a lot in common, I'm always down to talk about consciousness with some beers, if something novel emerges that's great.] 
Emília [happy to contribute from various points of view, but I advance that, to me, it has a lot to do with memory] 
Ana María 
Brian (bthompso8784@gmail.com) 
Sean Gibbons (sgibbons at uchicago dot edu) [Definitely interested in joining the conversation]

Note: this doesn’t have to become a formal project, although it could. Let me know if you’re interested in a chat, writing an interdisciplinary dialogue piece, or anything related to this question. 

==Tradeoffs between division of labor and stability in networks==

The Black Queen Hypothesis [http://mbio.asm.org/content/3/2/e00036-12.abstract BQH] describes the evolution of functional dependencies in microbial ecosystems. This process results in a subset of a community providing necessary services for the rest of the community (see link). Organisms that can outsource essential functions escape the cost performing these functions and have more resources for growth and reproduction. However, this process makes the ecosystem more delicate, as the destruction of key species can eliminate their crucial service(s) and lead to system collapse. Thus, there is a tradeoff between the stability of a network (in the face of perturbations), and the degree of cooperation (how many tasks can be outsourced). As a result of this tradeoff, we could expect different community types to arise in stable vs. variable environments. There is likely some critical range between these two modes (high vs. low environmental variability), where some mixed strategy is optimal. 

This process may have an analogue in the development of multicellular life (vs. free-living single-celled organisms), where each cell type expresses a subset of the genome and provide a specific set of services to the whole (division of labor). This might also be reflected in social or economic networks (higher stability = more cooperative?). A connection could potentially be made to life-history tradeoffs for individual organisms (r vs. k selection - oligotrophs vs. copiotrophs), or in dissipative chemical systems (e.g. [http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.4818538 Stat-Mech of Self Replication]). 

Definitely a work in progress, please add your thoughts if you are interested!

Interested: 
Sean Gibbons (sgibbons at uchicago dot edu) 
Rohan Mehta 
Stojan 
Emília 

==How can evolutionary game theory be applied to electricity trading==

The interest of this project is the following: how can evolutionary game theory be used to find optimal strategies for consumers and/or producers that bid in the electricity market. Also some real data can be considered. 
Contact Blaz 

Interested: 
Degang Wu 

== Information Theory of the Heart ==

The heart is a complex system with simple rules of operation and minimal central control. Under normal conditions, it orchestrates a self-organized, emergent behavior of 2 to 3 billion heart cells to perform sophisticated, well-timed pumping of the blood. Under abnormal conditions, it can lead to sudden cardiac death due to cardiac arrhythmias, which are also emergent, collective behaviors of a large number of heart cells, where each heart cell doesn't necessarily need to be abnormal. 

Each heart cell is a dynamic information processing system, which transmits digital information (0 – resting, 1 – excited) in the form of electrical wave. We aim to establish a theoretical basis to quantify information transmission within the heart using information theory and network theory. Our hypothesis is that arrhythmias following heart attack result from an adaptive mechanism to optimize information transmission in abnormal hearts. 

If you want to discuss more please contact Hiroshi (hashika1@jhmi.edu). 

''Interested:'' 
Hiroshi 
Flavia 

== Cells and Software: Is Evolution a Software Engineer? ==

There appear to be striking similarities between how we design software, and how evolution designed cells. Some of the analogies are: 
- The concept of "Encapsulation". In object oriented programs, data inside an object is protected by an interface of functions. Similarly, processes within a cell (intra-cellular signaling cascades) are protected from the extra-cellular messaging activities through membrane-bound receptors acting as the interface. 
- Apoptosis (programmed cell death) is similar to proper memory deallocation in programs, while Necrosis is similar to dangling pointers and memory corruption. 
- Proteolysis (breaking down of proteins into constituent amino acids) is similar to automatic garbage collection. 

There are certain constraints (perhaps physical constraints) on the available solutions in biology. Solutions within this constrained solution space eventually result in the emergence of complex behavior. This emergent behavior has enabled humans to engineer solutions to everyday problems. These artificially engineered solutions are very similar in principal to the solutions that already exist in biological systems. 

Are our creative processes ultimately bound by the physical constraints that underlie molecular mechanisms? Or, do we just tend to interpret the phenomena at the molecular level according to our own understanding, which is limited by our senses and neurological processes? Is it all about optimization, and everything else is just a side effect?
Can/do “Patterns” transcend disciplines? 

Motifs (biological systems) – Patterns (software). Patterns/motifs transcending biological and software systems could perhaps, fill gaps in our knowledge of biological systems, and help us design better software systems. Deterministic patterns could perhaps indicate what is required for high level functions to emerge from molecular interactions. And perhaps these similarities occur at the interface between low level interaction and emergent phenomena.

So let's further explore biological and software systems, and try to find answers to these questions.

For more information, please contact Fahad (fahad.khalid@hpi.uni-potsdam.de). 

''Interested:'' 
Fahad 
Ernest 
Diana 
Degang 
Stojan 
Ana María 

==Susceptibility of Fields of Research to Interdisciplinary Influences (network perspective) ==

Fields of Research are more often than not isolated from one another in terms of their community, jargon, perspective, research programme (in the sense of Lakatos) and their journals and lots more.

This isolation stands in the way of a fruitful merging and interaction of fields. One needs to understand the obstructions. Hence an analysis of the determining factors for 'community inbreeding' is sought after. Eventually also a quantitative measure for the susceptibility of a research field could be formulated.

A clear-cut project could be based on data together with a network type analysis of a precise question around the determining factors.
We could look at citation data or journal based data or maybe there is a chance to get hold of data from Jessica's collegues, who works on the diffusion of knowledge.

It would be great also to discuss and gather our ideas and experiences.

''Interested'' 
Leo (horstmey@mis.mpg.de ) 
Jennifer Hellmann 
Anna Olson 
Lin Li 
Stefan Pfenninger [other angles include: citation networks/academic generations and how they change through time (Diego's idea); citations between subfields to quantify interdisciplinarity and how it changes over time] 

==Simple case for studying about “from single-cell to multi-cell / species collaboration”==

QUESTION: how single-cell evolves to multi-cell, even they do not have so-called “intelligence”?

How to do:
Let’s imagine that there is a land where resources A, B, C are located, and a kind of creature which need all of these resources to survive (imagine many creatures live in this land). 
One surviving strategy is that every creature gathers A, B and C and eat them on its own. But maybe under some condition, specialization would automatically happen (e.g. one creature gather A and another gather B, and then they share). 
The goal is to find the necessary condition if possible (we could think out of many sufficient conditions, but finding necessary conditions seems not so easy).

Interested: 
Ernest Liu (yu.liu@math.uu.se) 

==An Analysis of the Hierarchies Present in Modern Economic Theory ==

The idea of this project is to provide a comprehensive survey of the hierarchical structure of economics (macro -> microeconomics) following the reductionist = constructionist + emergence framework of Anderson (N.B. This equation is my own interpretation of Anderson's paper and is open for discussion). Ideally, we would first investigate the microfoundations literature of macroeconomics and the possibility for ABM to rectify some of the redundancies therein after which we would reverse the direction and see how, given some 'fundamental' laws of economic behaviour, we could couple these with emergent phenomena (whatever they may be) to reconstruct the economy at the macro-level.

''Interested'' 
Nicolas ( nicolas dot scholtes at unamur dot be) 
Claudius

== The Topological Modeling of Infrastructure Networks ==

There is some disagreement on the topology of power networks in the literature. There are preferential attachment, small-world and random graph models proposed to explain the topology of power networks. There are caveats associated with each of these generative models. For instance, there is the cost of building new transmission lines that may question the validity of preferential models.

'''The broad question that we attempt to answer here is:''' 

-Can these previous network models create real-world power networks? 
-Can we come up with a better model that can replicate a power network or at least one with similar characteristics? 
-What about other infrastructure networks, e.g., natural gas network, water piping networks, etc? 

Interested:
Pooya Rezaei 
Tom McAndrew 

== Functional Networks and their evolution ==

We are interested in researching (possibly hierarchical) networks that have a function which can be quantified. We are interested in understanding how such networks evolve and may continue to deliver all or part of their function when they are damaged. As of now, we do not have a clear conceptualization of these ideas in formal network language, and our immediate task is to think of the formal network structure we wish to explore (e.g. b-partite, multileveled). Possible concrete cases to apply this formal characterization to are trees (i.e. plants), power grids, or financial networks.

Interested (please contact us to join the debate):

Alex Brummer (brummera@email.arizona.edu) 
Shai Gorsky (shai.gorsky@utah.edu) 
Beth Lusczek (lusc0006@umn.edu) 
Stefan Pfenninger (s.pfenninger12@imperial.ac.uk) 
Jessica Santana (jsant@stanford.edu)

Complex Systems Summer School 2014-Projects & Working Groups

2014-06-12T02:32:50Z

Pfenningers: /* Consciousness as an emergent state of matter – what do you think? */

{{Complex Systems Summer School 2014}}

==Bitcoin==

Bitcoin is an online peer-to-peer currency which has gained popularity in recent years. With increased general interest and now more and more companies accepting transactions in Bitcoin, so to has its value and is currently priced at $633 for 1 Bitcoin!

'''So what is Bitcoin?'''

The idea behind Bitcoin was to remove the need for a centralised banking system. The way this works is to have all transactions made public and then have the Bitcoin community validate transactions by donating computational power (and rewarded in Bitcoins). For further details see this blog:

http://www.michaelnielsen.org/ddi/how-the-bitcoin-protocol-actually-works/

'''So why is it interesting?'''

Usually companies and individuals keep all of their financial records private, but ALL transaction in Bitcoin are publicly available, so this provides a unique opportunity to study financial transactions. While the transactions are public, the owners of Bitcoin remain (relatively) anonymous, and so this has led to associations with criminal activities (e.g. on the silk road) from illegal drugs to hired hit-men. In addition to illegal activities using the currency, there have also been a number of illegal activities against the currency, such as high valued heists of the order of $100 million.

''Oh, and of course its a big temporally evolving network.''

If you're interested in working on this then add your name below. If there is interest, then we can have a "Bitcoin, beers and blackboard" session to throw some ideas around.

Interested:

Leto

==MITRE Data Sets==

To access the data please contact Juniper she has it on a hard drive. Here is a PDF that explains the datasets and gives some sample challenge questions.
[[Media:mitredata.pdf |MITRE DATA PDF]] If you have any specific questions about the data you can contact Matt Koehler at mkoehler@mitre.org

==Death in physical, biological and social systems==

Firms, nation states, human beings and stars all die. Do the causes of "death" in physical, biological and social systems have something in common? If yes, what is it?

''Interested''

Vipin

==Fractal-like structures in economic data==

In the 1960-70s Mandelbrot showed that some economic time series have fractal-like structures, i.e. they look the same at many time scales. The existence of these structures has been debated since. Do economic time series like S&P 500 index have fractal-like structures? If yes, how fractal-like are they?

''Interested'' 

Vipin 
Blaz 

==Microbial Community Data Sets==

The Earth Microbiome Project [http://www.earthmicrobiome.org/ EMP] is a massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. All data sets are processed in the same way (DNA extraction, PCR primers, sequencing, bioinformatics), making them inter-comparable. You can explore these data sets (including some time series, and a bunch of spatial samplings) at the following link [http://microbio.me/emp EMP Data] (no need to create a login ID, just scroll down to 'Download Public Data'). If you have questions, please contact Sean Gibbons (sgibbons at uchicago dot edu).

==Does Larger Memory Capacity Brings about Evolutionary Advantage?==

Evolutionary game theory modeling. Agents/players on lattice or networks. A player with n-step memory has responses to all 4^n past game outcomes. Intuitively, a player with longer memory can have more sophisticated strategy, which might be used to exploit player with smaller memory capacity. Yet according to the Prisoner's Dilemma tournament organized by Axelrod, Tit-for-Tat, which can be modeled using only one-step memory, fares better than a number of sophisticated strategies invented by experts in the field of game theory. From the game theory perspective, does smaller memory capacity actually have evolutionary benefits?
Please contact Degang Wu (dwuab@ust.hk).

''Interested:'' 
Blaz 
Brian 

==North American Breeding Birds Survey and tropical trees==

This dataset contains ~4500 sites where populations of birds (~600 species overall, ~60 species on average in every site) were sampled over the past 44 years. This gives numerous time series of both population sizes and the overall number of species. Some problems with this dataset include large observational errors. A dataset of tropical trees with the exact diameter, identity (from among 300 species) and location of ~250000 trees over 6 censuses is also available. Please contact Michael Kalyuzhny for these.

==Santa Fe tournament of time series analysis!==

Do fluctuations in timeseries arise from nonlinear dynamics or from stochasticity? Specifically, there are several examples of ecological time series where chaos/complex periodicity were found (and published in Science and other leading journals). But usually such analyses didn't examine alternative models of stochastic dynamics. I propose making some meta-analysis and trying to compare the predictive power of both kinds of models. This can also be done in other fields were such timeseries are available. If you want to talk about this - contact Michael Kalyuzhny

Interested:
Michael Kalyuzhny

==The Multiplex Networks==

How does the structure of social networks affect the emergence and persistence of norms? Why are some norms (like fashion styles) less persistent than others (like religious beliefs)? Is this because different kinds of norms live on different social networks (with same individual participating in different networks)? If yes, how do these social networks interact?

And finally, what do the answers to the above questions tell us about policy interventions? Can certain critical properties of network structures be exploited to change norms, like going to the moon without much fuel? If two networks interact, say religious belief and fashion styles, can interventions in one be used to bring about changes in another?

''Interested''

Vipin 
Sarah L 
Alberto 
Francesca 
Nhat 
Sanja 
Massimo 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com)

==Network Tolerance of Failure==

How might a network endure non-catastrophic failure without isolating the failing components? Most network failure models consider resilience against failure as a result of isolating failing components. In contrast, is it possible for the network to be robust through "tolerance" of failure? Perhaps, for example, a symbiotic relationship sustains a weakened node until it has recovered its prior performance. Or perhaps a transmitting network retains a connection to an offline node to reduce an anticipated memory load of re-establishing the connection when it comes back online. What are some of the ways in which networks are able to maintain connection to a failing node without failing themselves in the process - how is the cascade halted without isolation? This is meant to be a broad question to generate more specific ideas. Importantly, this question refers to "tolerance of" failure in contrast to "resilience against" failure.
 Contact: Jessica Santana jsant@stanford.edu

Interested:

James Holdener 
Junjian Qi 
Ells Campbell 
Leto 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com)

==Influence of different types of parasites and pathogens in networks on dynamics and stability of food webs==

In nature there is a number of infectious agents which have different evolutionary approaches in way how they influence their hosts. We want to built artificial ecological network and to compare how these evolutionary solutions affect stability of food webs.
 Contact: sanjakojasanja@gmail.com

Interested:

Stojan 
Nhat 
Sanja 
Cecilia: Are we going to discuss today at 9? No probably, but tomorrow, today is a free day! Relax!:D

==Growth of Cities==

Do foraging animals and growing cities utilize resources in the same way? We're interested in building an agent-based model which generates a road network on a map of varying resources by following a set of simple, probabilistic rules. How do the properties of this network evolve through time? How much of city growth can be explained by resource constraints? Do simple rules of growth parallel simple rules of animal foraging behavior? This project will explore agent-based modeling, but will also present opportunities to examine the limits of modeling. Contacts: Diana LaScala-Gruenewald (dianalg11 at gmail.com) and Claire Lagesse (lagesse.claire at gmail.com).

Interested: 
Morgan Edwards 
Rohan Mehta 
Alberto Antonioni 
Ernest Liu 
Michael Kalyuzhny 

==Towards a Unified Theory of Biodiversity==

The idea is to build on the Unified Neutral Theory of Biodiversity and create a realistic unified theory that incorporates important power-scaling laws, energetic constraints, and stochasticity that have been previously neglected. Still checking with external collaborators if they are not working on the idea.
Interested: 
Diego Barneche Rosado 
Cornelia Metzig 
Michael Kalyuzhny 

==Coupling of different types of networks==

We want to develop a concept of how to work with networks of qualitatively different types of relationships or interactions that can influence each other (eg. natural and social). Sign up and come to brainstorm with us :) Contact: sanjakojasanja@gmail.com

For example, people's beliefs about the health benefits/risks of vaccination can be influenced by their social network, and may be studied using belief propagation models. Simultaneously, diseases may spread through a population, which can be studied using diffusion or other epidemiological models. Furthermore, people's beliefs about vaccination may affect their probability of getting infected by a disease, and in turn, getting infected may cause them to re-evaluate their beliefs.

Another example could involve an ecological network expressing predation and competition among species, and environmental factors affecting the natural resources in the system.

Interested: 
Sanja 
Fahad 
Brian 

== Consciousness as an emergent state of matter – what do you think?==

You’re conscious right now, reading this. There are many ways to define consciousness, I’m talking here about subjective experience – how does it emerge out of the bundles of particles that we all are? 

Scholars of all fields have been deconstructing the mind/body dualism for a while, but consciousness remains a big, hard question. I’m no expert and by proposing this as a topic I’m not expecting that any of us will solve it, but I would be very interested in exchanging on the issue with the smart individuals that you are, grounded in so many backgrounds and unafraid of complex problems. 

So... physicians and physicists, social scientists, biologists, mathematicians, philosophers, computer scientists and others… what do you think? Don’t hold back – if beer is necessary for you to address this issue, it can be arranged. 

Contact Sarah L (laborde.7@osu.edu) 

Interested: 
Alireza (alireza.goudarzi at gmail.com)[totally agree with writing down something to figure out what are plausible ways to think about and study this] 
Fahad (fahad.khalid@hpi.uni-potsdam.de) [love the topic ... I'm glad someone brought it up ... I might have some ideas to contribute] 
Claire (lagesse.claire at gmail.com) [it sounds fascinating... :) ] 
Stefan (s.pfenninger12@imperial.ac.uk) 

Note: this doesn’t have to become a formal project, although it could. Let me know if you’re interested in a chat, writing an interdisciplinary dialogue piece, or anything related to this question. 

==Tradeoffs between division of labor and stability in networks==

The Black Queen Hypothesis [http://mbio.asm.org/content/3/2/e00036-12.abstract BQH] describes the evolution of functional dependencies in microbial ecosystems. This process results in a subset of a community providing necessary services for the rest of the community (see link). Organisms that can outsource essential functions escape the cost performing these functions and have more resources for growth and reproduction. However, this process makes the ecosystem more delicate, as the destruction of key species can eliminate their crucial service(s) and collapse the system. Thus, division of labor, which can result in higher functional efficiency (needs to be defined), comes at a cost. There is a tradeoff between the stability of a network in the face of perturbations, and the number of tasks outsourced to a subset of the community. As a result of this tradeoff, we might expect different community types to arise in stable vs. variable environments. There is likely some critical range between these two modes (high vs. low environmental variability), where some mixed strategy is optimal. 

This process may have an analogue in the development of multicellular life (vs. free-living single-celled organisms), where each cell type expresses a subset of the genome and provide a specific set of services to the whole (division of labor). This might also be reflected in social or economic networks (higher stability = more cooperative?). A connection could potentially be made to life-history tradeoffs for individual organisms (r vs. k selection), or in dissipative chemical systems (e.g. [http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.4818538 Stat-Mech of Self Replication]). 

Definitely a work in progress, please add your thoughts if you are interested!

Interested: 
Sean Gibbons (sgibbons at uchicago dot edu) 
Rohan Mehta 

==How can evolutionary game theory be applied to electricity trading==

The interest of this project is the following: how can evolutionary game theory be used to find optimal strategies for consumers and/or producers that bid in the electricity market. Also some real data can be considered. 
Contact Blaz 

Interested: 
Degang Wu 

== Information Theory of the Heart ==

The heart is a complex system with simple rules of operation and minimal central control. Under normal conditions, it orchestrates a self-organized, emergent behavior of 2 to 3 billion heart cells to perform sophisticated, well-timed pumping of the blood. Under abnormal conditions, it can lead to sudden cardiac death due to cardiac arrhythmias, which are also emergent, collective behaviors of a large number of heart cells, where each heart cell doesn't necessarily need to be abnormal. 

Each heart cell is a dynamic information processing system, which transmits digital information (0 – resting, 1 – excited) in the form of electrical wave. We aim to establish a theoretical basis to quantify information transmission within the heart using information theory and network theory. Our hypothesis is that arrhythmias following heart attack result from an adaptive mechanism to optimize information transmission in abnormal hearts. 

If you want to discuss more please contact Hiroshi (hashika1@jhmi.edu). 

''Interested:'' 
Hiroshi Ashikaga 

== Cells and Software: Is Evolution a Software Engineer? ==

There appear to be striking similarities between how we design software, and how evolution designed cells. Some of the analogies are: 
- The concept of "Encapsulation". In object oriented programs, data inside an object is protected by an interface of functions. Similarly, processes within a cell (intra-cellular signaling cascades) are protected from the extra-cellular messaging activities through membrane-bound receptors acting as the interface. 
- Apoptosis (programmed cell death) is similar to proper memory deallocation in programs, while Necrosis is similar to dangling pointers and memory corruption. 
- Proteolysis (breaking down of proteins into constituent amino acids) is similar to automatic garbage collection. 

There are certain constraints (perhaps physical constraints) on the available solutions in biology. Solutions within this constrained solution space eventually result in the emergence of complex behavior. This emergent behavior has enabled humans to engineer solutions to everyday problems. These artificially engineered solutions are very similar in principal to the solutions that already exist in biological systems. 

Are our creative processes ultimately bound by the physical constraints that underlie molecular mechanisms? Or, do we just tend to interpret the phenomena at the molecular level according to our own understanding, which is limited by our senses and neurological processes? Is it all about optimization, and everything else is just a side effect?
Can/do “Patterns” transcend disciplines? 

Motifs (biological systems) – Patterns (software). Patterns/motifs transcending biological and software systems could perhaps, fill gaps in our knowledge of biological systems, and help us design better software systems. Deterministic patterns could perhaps indicate what is required for high level functions to emerge from molecular interactions. And perhaps these similarities occur at the interface between low level interaction and emergent phenomena.

So let's further explore biological and software systems, and try to find answers to these questions.

For more information, please contact Fahad (fahad.khalid@hpi.uni-potsdam.de). 

''Interested:'' 
Fahad

Complex Systems Summer School 2014-After Hours

2014-06-11T00:52:39Z

Pfenningers: /* Still Needs a Ride */

{{Complex Systems Summer School 2014}}

==June <strike> 10</strike>11, 5:00pm - Supplies Run==

JP is going down to buy the stuff everyone needs. He'll take you if you would like.

JP's GTI (5 seats)

1.JP 
2.Anna Olson 
3.Bernardo Furtado 
4.Ali Kharrazi 
5.Ana Maria Gomez Lopez 

Still needs a ride:

7. Leonhard Horstmeyer (converter for power plug, groceries, bike, stuff) 

Common Supplies:

What kinds of supplies can we all split? Make a list here and JP will buy a big box or two for everyone.

1). Laundry Soap 
2). Bottles of water (for the hikes) ? Otherwise, please buy a big one (or multiple small ones) for Renske :) 
3) 3 Flashlights and batteries for James 
4) Earplugs. If nobody needs them, please buy a pack for Pooya. Thanks!

Individual Supplies:

1) Olive oil-- 1 liter bottle---Vipin 
2) Downy Dryer Sheet -- a small box enough for ~6-8 loads--- Nhat Nguyen
3) Please buy converter for power plug (Europe- US) for Sanja

==June 11, 5:30am - Sunrise hike to Atalaya mountain==

The plan is to meet at 5:30 a.m. and hike up to the summit. From today's (6/10) trip 5:30 might be early enough to get there. Even if we miss the sunrise the sun sitting just over the mountains is a great site.

Route data:
http://www.summitpost.org/atalaya-mountain/625480 
- Distance: 8 miles (14km) 
- Elevation Gain: 1,800 feet (600m) 
- Type of route: circular 

Equipment: 
- Walking sneakers or mountain boots 
- Backpack 
- Liquids: at least 1.5 litres 
- Different warm layers (it could be windy and chilly) 
- A flashlight might be useful at the start 

For more information, contact James HOldener
 
 
Participants: 
 
1. James Holdener 
2. Anna Olson (maybe) 
3. Ali Kharazi 
4. Nicolas K. Scholtes 
5. Claudius Gräbner 
6. Blaz Krese 
7. Stefan Pfenninger 
 

 

==June 11, 6:00pm - Sunset hike to Atalaya mountain==

The plan is to meet at 6:00 pm and hike up to the summit. Then we decide if we wait for the sunset there and go back with last lights or just do it faster.

Route data:
http://www.summitpost.org/atalaya-mountain/625480 
- Distance: 8 miles (14km) 
- Elevation Gain: 1,800 feet (600m) 
- Type of route: circular 

Forecast:
http://www.meteoblue.com/en/united-states/weather-atalaya-mountain?day=2

Equipment: 
- Walking sneakers or mountain boots 
- Backpack 
- Liquids: at least 1.5 litres 
- Different warm layers (it could be windy and chilly) 

If you have a torch, please bring it. It would not be necessary, but just in case... ;)

For more information, just contact with Luis Martínez
 
 
Participants: 
 
1. Luis Martinez 
2. Ernest Yu Liu 
3. Qiao Zhi 
4. 
5. 
6. 
... 
 
 

 

==June 14, 10:00am - Bandelier Field Trip==

We're taking a trip to [http://www.nps.gov/band/index.htm Bandelier National Monument] on Saturday June 14th. Please visit the [[Bandelier 2014 | Bandelier Field Trip]] Page to sign up!

==June 21, 6:00-9:00pm Santa Fe Fuego Baseball Game==

Come heckle and drink beer while watching some minor league baseball - [http://www.santafe.com/calendar/event/santa-fe-fuego-vs.-trinidad-triggers1 Fuego v. Trinidad Triggers]

1. Juniper

2. Mathew Ayres

3. Lin Li

4. Flavia Marquitti

5. Leto Peel

6. Claire Lagesse

7. Ernest Yu Liu

==June 27, 6:00-9:00pm Todd and the Fox==

See Juniper's brother's band [https://www.facebook.com/events/306176446198443/ Todd and the Fox] play on the Plaza at the Santa Fe Band Stand. For full line up of the Santa Fe Bandstand (June 23-August 28) visit [http://santafebandstand.org/ here]

1. Juniper

2. Matthew Ayres

3. Flavia Marquitti

4. Leto Peel

5. Morgan Edwards

6. Claire Lagesse

7. Leo

8. Ernest Yu Liu

==Rodeo de Santa Fe==

Wednesday, June 18!

Come on down for the 65th annual Rodeo de Santa Fe! Watch real-life cowboys get thrown off of various species of raging livestock for their competition and your entertainment. Starts at 7:00pm, we should leave SJC about 6:00.

===JP's GTI===
1. JP 
2. Alireza Goudarzi 
3.Matthew Ayres

4.Nhat Nguyen 
5.Lin Li 

===Juniper's Car===
1. Juni 
2. Catherine Bale 
3. Leto Peel 
4. Morgan Edwards 
5. Claire Lagesse 

===Still Needs a Ride===

1. Alberto Antonioni 
2. Luis Martinez Vaquero 
3. Jennifer Hellmann 
4. José Aguilar-Rodríguez 
5. Ernest Yu Liu 
6. Pooya Rezaei 
7. Stefan Pfenninger 

==World Cup==
 
*All times are Santa Fe (MST)
 
Thursday, June 12 
1) Brazil vs. Croatia - 1400 (MST) 
 
Friday, June 13 
1) Mexico vs. Cameroon - 1000 (MST) 
2) Spain vs. Netherlands - 1300 (MST) 
3) Chile vs. Australia - 1600 (MST) 
 
Saturday, June 14 
1) Columbia vs. Greece - 1000 (MST) 
2) Uruguay vs. Costa Rica - 1300 (MST) 
3) England vs. Italy - 1600 (MST) 
4) Côte d'Ivoire vs. Japan - 1900 (MST) 
 
Sunday, June 15 
1) Switzerland vs. Ecuador - 1000 (MST) 
2) France vs. Honduras - 1300 (MST) 
3) Argentina vs. Bosnia and Herzegovina - 1900 (MST) 

'''Sports Bars in Santa Fe: ''' 
[http://junctionsantafe.com/ Junction] 
[http://www.yelp.com/biz/el-paseo-bar-and-grill-santa-fe El Paseo Bar] 
[http://www.santafenewmexican.com/news/business/on-tap-craft-beers-from-around-state-at-downtown-s/article_de6b6182-fdcd-58ef-9f2e-6e9cc5bf5a85.html Santa Fe Tap Room] 
[http://www.cowgirlsantafe.com/ Cowgirl Cafe] 
[http://www.riochamasteakhouse.com/ Rio Chama Steak House] 

'''On campus viewing opportunities:''' Lower Campus Common's Room has a TV that can air the games, and on some occasions we can project the games after-hours in the Great Hall

==Santa Fe Railyard Events==

There are a ton of really fun and cool events happening all summer at the Santa Fe Railyard, check the calendar out [http://www.railyardsantafe.com/ here]

Complex Systems Summer School 2014-After Hours

2014-06-11T00:52:15Z

Pfenningers: /* June 11, 5:30am - Sunrise hike to Atalaya mountain */

{{Complex Systems Summer School 2014}}

==June <strike> 10</strike>11, 5:00pm - Supplies Run==

JP is going down to buy the stuff everyone needs. He'll take you if you would like.

JP's GTI (5 seats)

1.JP 
2.Anna Olson 
3.Bernardo Furtado 
4.Ali Kharrazi 
5.Ana Maria Gomez Lopez 

Still needs a ride:

7. Leonhard Horstmeyer (converter for power plug, groceries, bike, stuff) 

Common Supplies:

What kinds of supplies can we all split? Make a list here and JP will buy a big box or two for everyone.

1). Laundry Soap 
2). Bottles of water (for the hikes) ? Otherwise, please buy a big one (or multiple small ones) for Renske :) 
3) 3 Flashlights and batteries for James 
4) Earplugs. If nobody needs them, please buy a pack for Pooya. Thanks!

Individual Supplies:

1) Olive oil-- 1 liter bottle---Vipin 
2) Downy Dryer Sheet -- a small box enough for ~6-8 loads--- Nhat Nguyen
3) Please buy converter for power plug (Europe- US) for Sanja

==June 11, 5:30am - Sunrise hike to Atalaya mountain==

The plan is to meet at 5:30 a.m. and hike up to the summit. From today's (6/10) trip 5:30 might be early enough to get there. Even if we miss the sunrise the sun sitting just over the mountains is a great site.

Route data:
http://www.summitpost.org/atalaya-mountain/625480 
- Distance: 8 miles (14km) 
- Elevation Gain: 1,800 feet (600m) 
- Type of route: circular 

Equipment: 
- Walking sneakers or mountain boots 
- Backpack 
- Liquids: at least 1.5 litres 
- Different warm layers (it could be windy and chilly) 
- A flashlight might be useful at the start 

For more information, contact James HOldener
 
 
Participants: 
 
1. James Holdener 
2. Anna Olson (maybe) 
3. Ali Kharazi 
4. Nicolas K. Scholtes 
5. Claudius Gräbner 
6. Blaz Krese 
7. Stefan Pfenninger 
 

 

==June 11, 6:00pm - Sunset hike to Atalaya mountain==

The plan is to meet at 6:00 pm and hike up to the summit. Then we decide if we wait for the sunset there and go back with last lights or just do it faster.

Route data:
http://www.summitpost.org/atalaya-mountain/625480 
- Distance: 8 miles (14km) 
- Elevation Gain: 1,800 feet (600m) 
- Type of route: circular 

Forecast:
http://www.meteoblue.com/en/united-states/weather-atalaya-mountain?day=2

Equipment: 
- Walking sneakers or mountain boots 
- Backpack 
- Liquids: at least 1.5 litres 
- Different warm layers (it could be windy and chilly) 

If you have a torch, please bring it. It would not be necessary, but just in case... ;)

For more information, just contact with Luis Martínez
 
 
Participants: 
 
1. Luis Martinez 
2. Ernest Yu Liu 
3. Qiao Zhi 
4. 
5. 
6. 
... 
 
 

 

==June 14, 10:00am - Bandelier Field Trip==

We're taking a trip to [http://www.nps.gov/band/index.htm Bandelier National Monument] on Saturday June 14th. Please visit the [[Bandelier 2014 | Bandelier Field Trip]] Page to sign up!

==June 21, 6:00-9:00pm Santa Fe Fuego Baseball Game==

Come heckle and drink beer while watching some minor league baseball - [http://www.santafe.com/calendar/event/santa-fe-fuego-vs.-trinidad-triggers1 Fuego v. Trinidad Triggers]

1. Juniper

2. Mathew Ayres

3. Lin Li

4. Flavia Marquitti

5. Leto Peel

6. Claire Lagesse

7. Ernest Yu Liu

==June 27, 6:00-9:00pm Todd and the Fox==

See Juniper's brother's band [https://www.facebook.com/events/306176446198443/ Todd and the Fox] play on the Plaza at the Santa Fe Band Stand. For full line up of the Santa Fe Bandstand (June 23-August 28) visit [http://santafebandstand.org/ here]

1. Juniper

2. Matthew Ayres

3. Flavia Marquitti

4. Leto Peel

5. Morgan Edwards

6. Claire Lagesse

7. Leo

8. Ernest Yu Liu

==Rodeo de Santa Fe==

Wednesday, June 18!

Come on down for the 65th annual Rodeo de Santa Fe! Watch real-life cowboys get thrown off of various species of raging livestock for their competition and your entertainment. Starts at 7:00pm, we should leave SJC about 6:00.

===JP's GTI===
1. JP 
2. Alireza Goudarzi 
3.Matthew Ayres

4.Nhat Nguyen 
5.Lin Li 

===Juniper's Car===
1. Juni 
2. Catherine Bale 
3. Leto Peel 
4. Morgan Edwards 
5. Claire Lagesse 

===Still Needs a Ride===

1. Alberto Antonioni 
2. Luis Martinez Vaquero 
3. Jennifer Hellmann 
4. José Aguilar-Rodríguez 
5. Ernest Yu Liu 
6. Pooya Rezaei 

==World Cup==
 
*All times are Santa Fe (MST)
 
Thursday, June 12 
1) Brazil vs. Croatia - 1400 (MST) 
 
Friday, June 13 
1) Mexico vs. Cameroon - 1000 (MST) 
2) Spain vs. Netherlands - 1300 (MST) 
3) Chile vs. Australia - 1600 (MST) 
 
Saturday, June 14 
1) Columbia vs. Greece - 1000 (MST) 
2) Uruguay vs. Costa Rica - 1300 (MST) 
3) England vs. Italy - 1600 (MST) 
4) Côte d'Ivoire vs. Japan - 1900 (MST) 
 
Sunday, June 15 
1) Switzerland vs. Ecuador - 1000 (MST) 
2) France vs. Honduras - 1300 (MST) 
3) Argentina vs. Bosnia and Herzegovina - 1900 (MST) 

'''Sports Bars in Santa Fe: ''' 
[http://junctionsantafe.com/ Junction] 
[http://www.yelp.com/biz/el-paseo-bar-and-grill-santa-fe El Paseo Bar] 
[http://www.santafenewmexican.com/news/business/on-tap-craft-beers-from-around-state-at-downtown-s/article_de6b6182-fdcd-58ef-9f2e-6e9cc5bf5a85.html Santa Fe Tap Room] 
[http://www.cowgirlsantafe.com/ Cowgirl Cafe] 
[http://www.riochamasteakhouse.com/ Rio Chama Steak House] 

'''On campus viewing opportunities:''' Lower Campus Common's Room has a TV that can air the games, and on some occasions we can project the games after-hours in the Great Hall

==Santa Fe Railyard Events==

There are a ton of really fun and cool events happening all summer at the Santa Fe Railyard, check the calendar out [http://www.railyardsantafe.com/ here]

Stefan Pfenninger

2014-06-10T13:33:40Z

Pfenningers:

{{Complex Systems Summer School 2014}}

[[File:Stefan.jpg]]

I am doing a PhD in energy systems modeling at Imperial College London, and am particularly interested in understanding the opportunities and threats presented by the transition to clean and renewable energy technologies at a national and continental scale.

My general research interests are focused on energy policy and energy systems modeling. I am also interested in climate policy more generally, including resilience and strategies for adapting society and infrastructure to a changing climate. My background is in environmental science and policy.

For projects, I'm interested in the topics above but also in many other areas such as sustainable economic systems, ecology, or agriculture, amongst others.

I am an experienced Python programmer, and also know Javascript and some C and R.

[http://pfenninger.org website]

File:Stefan.jpg

2014-06-10T13:33:18Z

Pfenningers:

Stefan Pfenninger

2014-06-10T13:32:17Z

Pfenningers:

{{Complex Systems Summer School 2014}}

I am doing a PhD in energy systems modeling at Imperial College London, and am particularly interested in understanding the opportunities and threats presented by the transition to clean and renewable energy technologies at a national and continental scale.

My general research interests are focused on energy policy and energy systems modeling. I am also interested in climate policy more generally, including resilience and strategies for adapting society and infrastructure to a changing climate. My background is in environmental science and policy.

For projects, I'm interested in the topics above but also in many other areas such as sustainable economic systems, ecology, or agriculture, amongst others.

I am an experienced Python programmer, and also know Javascript and some C and R.

[http://pfenninger.org website]

Bandelier 2014

2014-06-08T21:15:06Z

Pfenningers:

{{Complex Systems Summer School 2014}}

Please sign up here so we know who's going. 
Also: If you have a car, please put it down. The more cars we have, the more people we can take. 

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

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

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

==Cars:==

===[[JP]]'s GTI (5 seats)===
1. JP 
2. Blaz Krese 
3. Nicolas Scholtes 
4. Claudius Graebner 
5. Riley Burkart 

===JP's 4Runner (5 seats)===
1. Alireza Goudarzi (I do have a NM driver's license and can follow directions or other two vehicles) 
2. Michael Kalyuzhny 
3. Stefan Pfenninger 
4. anybody else? 
5. 

===Juniper's Car (3 seats)===
1. Juni 
2. Bernardo Furtado 
3. Anna Olson 
4. Jennifer Hellmann

Physics Lab 2014

2014-06-08T14:38:49Z

Pfenningers: /* Thursday June 12, 7:00 - 9:00 PM */

{{Complex Systems Summer School 2014}}

==Thursday June 12, 7:00 - 9:00 PM==

1. Diana LaScala-Gruenewald 
2. Brian Thompson 
3. Claudius Gräbner 
4. Alireza Goudarzi 
5. Stefan Pfenninger 
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==Saturday June 14, 7:00 - 9:00==

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==Sunday June 15, 7:00 - 9:00==

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==Monday June 16, 7:00 - 9:00==

1. Catherine Bale 
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