Santa Fe Institute Events Wiki - User contributions [en]

Complex Systems Summer School 2014-After Hours

2014-07-03T00:06:15Z

Corneliam: /* Friday July 4: Taxis to airports :-( */

{{Complex Systems Summer School 2014}}

==Friday July 4: Taxis to airports :-( ==

'''4.00AM to ABQ''' 
1. Fahad

'''8.15AM to Santa Fe Municipal''' 
1. Catherine 

'''4.15AM to Santa Fe Municipal - Roadrunner shuttle (already booked, feel free to contact the company to add your name - our reservation confirmation: #35822)''' 
1. Diego 
2. Alberto 
3. Brais 
4. Cornelia

==Dinner Off Campus==

[[JP]] hungers! Dinner off campus for those who would like a change of scene and palette. Let me know if you're interested here and we'll figure out how to get there. If anyone has any requests for a destination, please let me know. I think New Mexican tonight and then something a little more upscale on Wednesday might be appropriate, but I'm more than willing to accommodate desires.

Tuesday 7/1, 7:30pm, Maria's New Mexican

JP 
Anna 
Nix 
Sanja 
Catherine 
Heath 

Wednesday 7/2, 8:00, Pink Adobe 

JP 
Ana Maria 
Nix 
Fahad 
Renske 
Hiroshi 
Luis 
Alberto 
Massimo 
Sanja 
Flavia 
Francesca 
Leto 
Cole 
Emilia 
Sarah 
Claudius 
Brais 

==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. 
4. Morgan 
5. Renske 

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

==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!

'''Meet in the dorm circle at 4:30'''

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 
Jose 
Nicolas 
Brais 
Claire 
Luis 
Michael 
Morgan (could also leave around 6) 
George 
Nix 
Bernardo 
Vipin (I too would like to leave St. John's at around 6) 
Rohan 
Ernest 
Pooya (interested to leave St. John's at around 6) 
Massimo 
Leo (after 6) 
Brais, Also prefer to leave around 6 
Sanja 
Nhat (Also prefer leaving around 6) 
Leto 
Leta (after 6) 
Brian (leave SJC around 6) 
Renske 
Liz 

==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 
2. shai 

==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 
==July 2, 5:00am - Sunrise hike to Atalaya mountain==

Updated to an earlier time. I'm planning to to the Atalaya and Picacho Peaks. This is 9.1 miles and will give us 3 hours to do it. (maybe a little longer and be quick getting ready).

We'll meet at 5:00 am at the circle.

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

This is our last morning hike.

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-Projects & Working Groups

2014-06-19T20:48:23Z

Corneliam: /* Fractal-like structures in economic data */

{{Complex Systems Summer School 2014}}

==Dynamics of Norms Under Reinforcement Learning==

[[Dynamics of Reinforced Norms | Dynamics of Reinforced Norms]]

Summary: 
We investigate how societal/cultural norms are reinforced and how they affect decision making of an agent. Agent decision is conditioned by an identity saliency vector. Each identity of the agent connects it to a number of other agents that reinforce the choice of the agent. For instance, the role of agent as a daughter connects it to her family which may support decision to invest in education or not. We study how the the connection of agent with other agent may affect the saliency vector and cause the agent to change the decision rule.

Why do we study this? 
The application of this project is to inform policy making and designing the right intervention points (pressure points) that one can use to change norms in a society.

Interested: 
Francesca 
Alireza 
Brais 
Leo 

==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) 
George(qiaozhi827@gmail.com) 
Sean Hayes (shaye004@ucr.edu) 
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

==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 
Leo 
Cornelia (cornelia.metzig@hotmail.com) 

==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).

== The pollination problem from a game theory approach ==

The old title was: "Does Larger Memory Capacity Brings about Evolutionary Advantage?"

Pollination systems are amazing. The expected from a flower visitor , like a bee, is that it enters the flower looking for its resource (nectar) and when gets out, it is carrying many pollen grains in its body. Then, in the next visiting flower looking for more resource, it eventually pollinates this second flower with pollen bind on the body. But what happens is that this system can face up some free-riders, interested in getting their nectar quickly and easily. Yes, they exist! The nectar robbers (or cheaters) can rob nectar in different ways. One of the most amazing techniques is making a hole in the basal part of the flower and getting the nectar without touching the reproductive parts of the flower.

However, if you think that plants always evolve to avoid this cheaters, maybe you are very mistaken. The presence of the cheaters reduces the amount of nectar inside the flower, and when a pollinator visits this flower after the cheater, it must look for more flowers to get the necessary amount of nectar. It potentially increases the outcrossing reproduction, very necessary for some plant species (and it can also produce a higher fitness than the autopollination system in many other plants which can reproduce via both systems)

We plan to model this unexpected history using a game theory approach, with some flavor of Public Goods game, incorporating memory in the path made by the plant visitors.

We also still consider our initial idea of studying the influence of more/less memory on the qualitiy of evolved strategies in an evolutionary game theoretic context. The focus would be, however, on the fact that in nature more memory comes with a higher cost.

''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) 
Alberto (alberto.antonioni@unil.ch) 
Francesca 
Nhat (nhattdnguyen@gmail.com) 
Sanja (sanjakojasanja@gmail.com) 
Massimo 
Alireza (alireza.goudarzi at gmail.com) 
Claire (lagesse.claire at gmail.com) 
Cecilia (ci.andreazzi@gmail.com) 
Sean Hayes (shaye004@ucr.edu) 
Brais (brais.alvarez@eui.eu) 
Matthew Ayres (matthew.ayres@growthandinnovation.com.au) 

==Network Tolerance of Failure==
[[ Network Tolerance Page | Network Tolerance Page]]

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:

Junjian Qi (junjian.qi.2012@ieee.org) 
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) 
Lin Li (linnlii2495 at gmail dot 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* 

==Growth of Cities==

[[Cities Growth Page | Cities Growth Page]]

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 (morgane@mit.edu) 
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 
Alex Brummer brummera@email.arizoa.edu 
James Holdener (jholdener@mitre.org) 

==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 Gómez López (anamaria.gomezlopez@yale.edu) 
Sean Gibbons (sgibbons at uchicago dot edu) 

==Coupling of different types of networks==

[[Coupling of different types of networks | 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 (gotero@linuxprophet.com) 
Hiroshi (hashika1@jhmi.edu) 

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 
Cecilia (ci.andreazzi@gmail.com) 

== Consciousness as an emergent state of matter – what do you think?==
[[ Emergence of Consciousness Page | Emergence of consciousness ]] 
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) 
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!]
Tom McAndrew [Thomas.McAndrew@uvm.edu] 
Diego Barneche (digo.barneche@mq.edu.au)[glad to join the conversation over beers and maybe formalizing a project] 

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 

*Thanks Ernest! I have a copy of this paper and I added a link on the webpage: http://tuvalu.santafe.edu/events/workshops/index.php/Emergence_of_Consciousness_Page 
*As far as meeting, most people can meet tonight except Ana-Maria and myself (going to the opening of this arts festival: http://currentsnewmedia.org ).. otherwise it looks like sunday over lunch (in the cafeteria) is the go. It's so many of us, there will no doubt be many partial meetings, so let's keep updating Alireza's page! Yesterday Emilia and I had a chat about this with Alfred Hubler about this, we will add ideas to the page later today. Cheers! Sarah

*I'd like to toss this in here, in case I don't make it to the discussions. It's one of my favorite perspectives regarding consciousness and qualia and whatnot: http://en.wikipedia.org/wiki/Eliminative_materialism -Nix

==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: Data Analysis Group - Friday at lunch''' 

*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.

Rohan: Potential evolutionary network model: N different kinds of edges for N resources (so N separate networks). Directed graph, with self-loop signifying self-sufficiency for a particular resource, and a directed edge from A to B indicates that A relies on B for a particular resource. The weight of an edge corresponds to the proportion the population of node A relying on node B for that resource. Evolution: at each time step, random mutations change the weights of the edges, and fitness calculations based on the number of self-produced resources change the composition of each node over time. A perturbation would involve randomly converting all the edges of a particular node to self-loops (or possibly just deleting the node).

Ernest: a agent-based model: 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 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 (we could think out of many sufficient conditions, but finding necessary conditions seems not so easy). PS: My original plan is to investigate the process before labor-division, that is, define some creatures' behavior rules which would not directly tell them to collaborate, to see whether they would figure out some way to collaborate automatically. Of course, this kind of rules should satisfy some conditions, otherwise labor-division would not happen definitely. So these conditions matter, and it's what I want to investigate. Anyway, my future plan is flexible.

George: I am thinking of the dependency within the financial networks which you can see cascading failures in a lot of past crisis. i am interested in using the model Rohan mentioned above by adding some some mechanism like internal effect.

Sean: Here are some resources for modeling dynamical networks in python [http://pycx.sourceforge.net/ pycx]

*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) 
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) 
George (qiaozhi827@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: 
Alberto 
Leo 
Ali ali [at] pp.u-tokyo.ac.jp 

The project is currently not active. Due to the fact that I am just starting this research, I still don't have a project-appropriate well-defined idea on which we could work on. Still, it might happen that we can start the project towards the end of the school and then continue to work on it after the school is ended. Thank you all so much for your interest in the project. I wish you best luck with your other projects.

== Information Theory of the Heart ==
'''[[Information Theory of the Heart Page]]''' 
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 (hashika1@jhmi.edu) 
Flavia (flamarquitti@gmail.com) 
Brian (bthompso8784@gmail.com) 
Bernardo Furtado (furtadobb@gmail.com) 
José Aguilar-Rodríguez (jose.aguilar@ieu.uzh.ch) 
Nix (nix@math.ucdavis.edu) 
Degang (samuelandjw@gmail.com) 
Josh (garland.joshua@gmail.com>) 

== 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 (dianalg11@gmail.com) 
Degang (dwuab@ust.hk) 
Stojan 
Ana María (anamaria.gomezlopez@yale.edu) 
Brian (bthompso8784@gmail.com) 
George (qiaozhi827@gmail.com) 
Glen (gotero@linuxprophet.com) 
Renske 

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

[[Interdisciplinary research networks | Interdisciplinary research networks]]

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 
Sarah Laborde [laborde.7@osu.edu - sorry I probably missed a lot of the initial discussion.. but I would love to listen to/participate in the next meeting]

@ Diego's idea, I remembered this quote by Max Planck:
“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

==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 
stojan (stojand at mpib dash berlin dot mpg dot de) i'm happy to discuss this with you guys..and hear your opinion 

== 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) 
Nicolas K. Scholtes (nicolas dot scholtes at unamur dot be 
Ali Kharrazi 
Renske Vroomans (R.M.A.Vroomans@uu.nl) 

== Exploring regime shifts in the Logone Floodplain of Cameroon: complex systems approaches applied to data scarce environments ==

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. We want to experiment with the benefits and limits of complex systems approaches and tools (starting with a common pool resources model) when applied to a complex case study. 
 
Next meeting '''2:45 Tuesday in lecture room (to start with)'''. 
 

Sarah L 
Ana María 
Claudius 
Luis Martínez (fnxabraxas@gmail.com) 
Ali Kharrazi 
Francesca Lipari 
Brian (bthompso8784@gmail.com) 

== 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 far away 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 Aguilar-Rodríguez (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: 
José Aguilar-Rodríguez 
Cole Mathis 
Renske Vroomans 
Leto Peel 
Massimo Stella 
 Glen Otero (gotero@linuxprophet.com) 
 Leo Horstmeyer (horstmey@mis.mpg.de) 
 Brian Thompson (bthompso8784@gmail.com) 
 Sean G. (sgibbons@uchicago.edu) 
stojan (stojand@mpib-berlin.mpg.de) 

==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 
Alireza Goudarzi (alireza.goudarzi at gmail dot com) 
Tom McAndrew 

==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.

Interested: 

== [[Cough analysis]] ==
This project will investigate if signal analysis of a person's cough coupled with collection of other data (such as: age, height, weight, ''etc.'') can be used to distinguish between a healthy and an unhealthy lung. Our idea is that humans have evolved a specific sound/frequency of coughing so as to break up mucus in the lungs and that diseased lungs will have different sounds/frequencies than a healthy lung. Using the collected data, we will be able to determine if coughs are specific to individuals or if there are qualities about them that span a population. If there are qualities that span a population, then the data can lead to answering deeper questions about how to care for individuals with cystic fibrosis. For instance, treatment of this disease state could lead to adjusting their cough—through external means—to help move stagnant mucus in their lungs.

=== Project goals ===
* Create a website that allows users to submit cough sound files and enter appropriate metadata to.
* Determine relevant signal analysis techniques that can be used to analyze coughs.
* Create a classifier that can separate coughs into different categories.
* Display any analysis on the website.

We will be using standard techniques to create the website (Ruby on Rails), host the data (Postgres and Amazon S3), generate a classifier (Mahout), and display the data (D3). If you are interested in learning some of the standard technologies that companies use, you are welcome to join the group. The project is engineering heavy, however, the scientific goal is to determine if a cough is either specific to a person or if there are principles about it that are similar within a population. If there are similarities, then this can lead to interesting biological questions such as how did the cough evolve.

=== Interested ===
* [http://tuvalu.santafe.edu/events/workshops/index.php/Andy_Maloney Andy] [[Special:Emailuser/Maloneya|Email Andy using the wiki if you are interested.]] amaloney theatthingy austin.utexas.edu
* [http://tuvalu.santafe.edu/events/workshops/index.php/Ellsworth_Campbell Ells]
* Nix has a nasty chest cold and would be interested in learning about some of the software used here.
* Glen
* Pooya (pooya.rezaei@uvm.edu)
* Renske -would be interested in learning the techniques, probably can't contribute much else

== Using Natural Network Lessons in Modern Network Environments ==

There is a significant set of natural and biological network data that has been investigated. How can insights, lessons and parallels be applied to modern organisations, modern networks and modern contexts? Can innovation, idea diffusion and increased resilience be informed by key insights?

This group has met twice to form initial views and if there is enough interest (>3-4 people) will continue or if not may merge with other innovation and network related areas.

Group Members 

Matthew Ayres (matthew.ayres@growthandinnnovtion.com.au) 
{members please add names!}

Interested 

Diego Barneche (diego.barneche@mq.edu.au)[glad to provide some insights in terms of ecological resilience and learn of possible parallels in modern organisations]

As the original 5 members have joined similar groups in Ecology, Innovation and Resilience - this group will not be further pursued.

==Economic inequality, kinship networks, and political transitions==

[[Economic inequality, kinship networks, and political transitions project page | Economic inequality, kinship networks, and political transitions project page]] 

Summary: 
It has been argued that political institutions are central to long-term economic development. Acemoglu and Robinson (2006) suggested that economic factors, namely the distribution of wealth, play a central role in political transitions (e.g. transition from non-democratic to democratic regimes). Building on Demetrius and Manke (2004), we would like to additionally consider the role of kinship networks in political transitions. That is, for a given state of the economy and distribution of wealth, what role do kinship networks play in facilitating or precluding institutional change? How might the outcome change with an altered distribution of wealth? As such, we implement a simple agent-based model to gain insight into the institutional outcomes of select historic events and, if possible, inform policy-making.

Group members: 
Bernardo 
Catherine 
James G. 
Heath (hendersonhl@gmail.com) 
Leo 
Brais 

== Chocolate and Coffee Trade as a Power Grid ==

Motivation: 
Previous research on global resource trade networks has mostly viewed trade flows as a static state. Global resource trade networks however are dynamic and are responsive to fluctuations and perturbations. As a new research approach this group intends to explore common properties between global resource trade networks as an electric power grid. We will strike analogies between the trade flows of chocolate and coffee and power grid dynamic measures. Specifically, we intend to describe an chocolate and coffee trade systems in terms of voltage, current, capacitor, resistance, and inductance.

The resulting dynamic matrix of chocolate and coffee trade will allow us to make delicious evaluations of the resiliency of these trade networks. Insightful questions can be approached, such as: how responsive are these networks to perturbations and disruptions - that is, are we in danger of chocolate/coffee blackouts ... !

Group members: 
Tom 
Pooya 
Junjian 
Ali 
Stefan 
Nicolas

Physics Lab 2014

2014-06-12T21:16:19Z

Corneliam: /* Saturday June 14, 7:00 - 9:00 */

{{Complex Systems Summer School 2014}}

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

1. Diana LaScala-Gruenewald 
2. Brian Thompson 
3. Flavia Marquitti 
4. Alireza Goudarzi 
5. Stefan Pfenninger 
6. Hiroshi Ashikaga 
7. Jennifer Hellmann 
8. Alex Brummer 
9. Andy Maloney 
10. Glen Otero 
11. Bernardo Furtado 
12. Sean Gibbons 
13. Fahad Khalid 
14. Diego Barneche 
15. Morgan Edwards 
16. Madeleine Fort 

==Saturday June 14, 7:00 - 9:00==

1. Sean Hayes 
2. Massimo Stella 
3. Francesca Lipari 
4. James Holdener 
5. Cole Mathis 
6. Tom McAndrew 
7. Ells Campbell 
8. Pooya Rezaei 
9. Qiao Zhi (George) 
10. Brais 
11. stojan 
12.Cornelia Metzig 
13. 
14. 
15. 

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

1. Jessica Santana 
2. Degang Wu 
3. James Gentile 
4. José Aguilar-Rodríguez 
5. Alberto Antonioni 
6. Claire Lagesse 
7. Junjian Qi 
8. Michael Kalyuzhny 
9. Blaz Krese 
10. Rohan Mehta 
11. Beth Lusczek 
12. Ernest Yu Liu 
13. Heath Henderson 
14. Nicolas K. Scholtes 
15. Vipin P. Veetil 

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

1. Catherine Bale 
2. Ana Maria Gomez Lopez 
3. Sarah Laborde 
4. Claudius Gräbner 
5. Lin Li 
6. Matthew Ayres 
7. Renske Vroomans 
8. Anna Olson 
9. Nhat Nguyen 
10. Cecilia Andreazzi 
11. Emília Garcia Casademont 
12. Luis Martínez Vaquero 
13. Leto Peel 
14. Sanja Selakovic 
15. Shai Gorsky

Complex Systems Summer School 2014-Projects & Working Groups

2014-06-12T18:55:54Z

Corneliam: /* Towards a Unified Theory of Biodiversity */

{{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 (flamarquitti@gmail.com) 
Jessica Santana jsant@stanford.edu 
Stefan 
Ana María 
Brais (brais.alvarez@eui.eu) 

Meeting today (Jun 12) indicate your availability here:http://doodle.com/w5bys3zfmpeamf32

==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 

==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==

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 
Luis Martínez (fnxabraxas@gmail.com) 
Brais (brais.alvarez@eui.eu) 

==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) 
Ali Kharrazi 

*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 
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 (yu.liu@math.uu.se) 
Michael Kalyuzhny 
Hiroshi Ashikaga (hashika1@jhmi.edu) 
Bernardo Furtado bernardo.furtado at ipea.gov.br 
Luis Martínez (fnxabraxas@gmail.com) 
Alex Brummer 

* >> For those interested in this project, we will be meeting at 6 pm in the cafeteria

==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 

==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 

== 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) 

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]). 

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

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

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

==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 

== 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 

==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] 
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) 

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 

== 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) 

== 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. 
 

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

== 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 the evolutionary exploration of genotype space? 
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 
Leto 
Massimo 
José 
Renske