https://wiki.santafe.edu/api.php?action=feedcontributions&user=RobMills&feedformat=atomSanta Fe Institute Events Wiki - User contributions [en]2022-08-20T05:37:08ZUser contributionsMediaWiki 1.37.1https://wiki.santafe.edu/index.php?title=Rob_Mills&diff=18553Rob Mills2009-01-31T14:05:35Z<p>RobMills: </p>
<hr />
<div>[http://users.ecs.soton.ac.uk/rmm05r/ I'm] a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't repeat myself here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (hiking/running/skiing/biking..) and juggle too.<br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
My email address is: rob.mills@zepler.net<br />
My room extension is: 4160<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
My Project links<br />
*[[The_pollination_network_wiki_page| Pollination Model]]<br />
*[[HP_Modularity| Host-pathogen modularity]]<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=15859Rob Mills2008-08-04T21:20:41Z<p>RobMills: </p>
<hr />
<div>[http://www.ecs.soton.ac.uk/~rmm05r/ I'm] a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't repeat myself here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (hiking/running/skiing/biking..) and juggle too.<br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
My email address is: rob.mills@zepler.net<br />
My room extension is: 4160<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
My Project links<br />
*[[The_pollination_network_wiki_page| Pollination Model]]<br />
*[[HP_Modularity| Host-pathogen modularity]]<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Discovering_the_surroundings&diff=15208Discovering the surroundings2008-06-19T01:02:49Z<p>RobMills: </p>
<hr />
<div>{{CSSS 2008 Santa Fe}}<br />
<br />
<!-- put content below here --><br />
<br />
I'm especially interested in Nat. Parks and Nat. Monuments - they are just the best! I've an 'America the Beautiful' pass, which allows me (and the whole car I'm in) to visit each Park without fees. So if somebody is interested, just write it in here. I'd prefer White Sands, Petriefied Forest or Badlands. But I'm open for everything (how about Alaska? ;-)) - [[Ruben_Kubiak|Ruben]]<br />
<br />
Nish is planning on visiting White Sands, Carlsbad and perhaps the Grand Canyon (about 7 hours for the last one). I also could drive back up to Canyonlands if folks are interested. I'm told we have a full moon in two weeks, which is when I would like to visit White Sands. I'm guessing that makes the third weekend for the Grand Canyon... I have room for 4 more in my car, although it might be a little tight. Feel free to put your name here if you'd like to tag along.<br />
<br />
I'd like to come with you to White Sands. I've been to the Grand Canyon, and the Carlsbad Caverns are pretty far away, so this things maybe not. -[[Ruben_Kubiak|Ruben]]<br />
<br />
===White Sands===<br />
Drivers (3):<br />
<br />
Nish (+3), Justin (+3), Kolbjørn (+6)<br />
<br />
Passengers (16):<br />
<br />
Sonja, Giovanni, Dirk, Rob, Flávia, Antony, Jiang, Francois, Riley, Ana, Peter, Jean, Jeremie, Petr, Ruben, Paul<br />
<br />
Nish's car: Sonja, Petr, Ruben<br />
<br />
Justin's car: Jiang<br />
<br />
Kolbjørn's van: Ana, Jean, Peter, Rob<br />
<br />
Since the van Kolbjørn rented only seats an additional 6, we will need to rent one more car (or another van?).<br />
<br />
If you're interested in going, add yourself to the list above (updating the number appropriately) by Wednesday evening at the latest.<br />
<br />
==Plan==<br />
Leave Friday afternoon after Mitch Waldrop's lecture. It is a 4.5 hour drive from Santa Fe to White Sands, meaning we should be in the Las Cruces area for dinner.<br />
<br />
I have two cabins (all they have) reserved [http://www.roadrunnercampground.com/ here]. Each cabin sleeps 4 (however, some could presumably sleep on the floor). Regardless, we'll need at least one motel/hotel room in Alamogordo and I've booked two double rooms at the Motel 6. If someone has camping gear, I can also reserve a campsite (we'd obviously need to bring tents, etc) if folks want me to (and I can cancel one of the two hotel rooms (before Friday) if that is the case).<br />
<br />
Given that summer temperatures in White Sands approach 100 degrees Fahrenheit, I think we should be sensible about hiking and the like. Maybe do the White Sands drive (8 miles one way) in the morning and one or two of the short trails. Then hang out in town or somewhere local during mid-day and return to White Sands for a few more hikes in the late afternoon and for sunset/moonrise. For those that would like to stay in the park during the day, we can split up by car or something.<br />
<br />
Although I had mentioned going to Carlsbad Caverns, it's a 4 hour drive (through Texas! [TEXAS!!!! YEHAAAAAA!!!! :-) ([[Ruben_Kubiak|Ruben]])], so I'm unlikely to actually do it.</div>RobMillshttps://wiki.santafe.edu/index.php?title=HP_Modularity&diff=14879HP Modularity2008-06-12T21:48:35Z<p>RobMills: </p>
<hr />
<div>== Host-Pathogen Modularity ==<br />
<br />
This is the working space for our project. Everything written is a work in progress.<br />
<br />
=== Title Ideas ===<br />
*Evolution of modularity in a host-pathogen system<br />
*Modularity: a pathogen's answer to host interactions<br />
* Do host-pathogen interactions lead to the adaptive evolution for modularity?<br />
*more here<br />
<br />
=== ''Major'' Questions ===<br />
#Does modularity in pathogen ''genes'' responsible for an interaction with a host increase its ability to adapt to a host?<br />
#under what conditions does pathogen modularity arise? specifically,<br />
## Is modularity in the host required?<br />
## what configurations of the interaction matrix?<br />
## what influence does population structure have (in the hosts)?<br />
#additional ones here<br />
<br />
=== Questions to answer in proposal ===<br />
# why are we studying host-pathogen interactions?<br />
# what evidence suggests that modular allelic dependencies might be advantageous in such a host-pathogen system?<br />
# give a one-line description of this type of modularity<br />
# what conditions do we aim to test to show a benefit to modular dependencies/interaction structures?<br />
# what are our null models, i.e. why is (this) result a surprise?<br />
# what impact does this have for the understanding of host-pathogen interactions, and evolvability in general?<br />
<br />
<br />
=== Model Details ===<br />
<br />
==== Discrete or continuous? ====<br />
# Pros for discrete: easier to run iterated simulations; possible to run experiments on explicit graph structures<br />
# Pros for continuous: mathematical derivations cleaner<br />
<br />
== Glossary ==<br />
<br />
=== Modularity Concepts ===<br />
<br />
I'm quite sure that there is some overloading here; but these are the types of modularity that have come up in our discussions:<br />
# Modularity for reassortment (Molly)<br />
# Modularity for independence (Molly) (I call this 'functional decomposition' - Rob)<br />
# Repeated modularity: eg where a body segment occurs many times in an organism (Rob)<br />
# Modularity for robustness to antagonistic pleiotrophy (Molly)<br />
<br />
=== Pathogen-related terms ===<br />
<br />
# '''Epitope ''': the phenotype of a pathogen that interacts with a host<br />
## only need to consider a portion of the host's genome since the pathogen only targets a specialised portion of that genome.</div>RobMillshttps://wiki.santafe.edu/index.php?title=The_pollination_network_wiki_page&diff=14867The pollination network wiki page2008-06-12T21:16:59Z<p>RobMills: </p>
<hr />
<div>= An agent-based model for a pollination network. An evolutionary game theory approach =<br />
<br />
Members:<br />
<br />
* Ana Martín González<br />
* Carlos Yepez<br />
* Meritxell Vinyals<br />
* Petr Svarc<br />
* Michael Cox<br />
* [[Rob_Mills|Rob Mills]]<br />
<br />
=== Questions ===<br />
# is it possible to produce a model that generates qualitatively similar results to the data?<br />
# what type of model produces the best fit?<br />
# which parameters/variables are essential in explaining underlying patterns, and are any irrelevant?<br />
# please add more here!<br />
<br />
=== Data ===<br />
We have measured several attributes of both the flowers and the pollinators:<br />
<br />
{| class="wikitable" style="text-align:center" border="1"<br />
|'''Flowers''' || '''Pollinators'''<br />
|- <br />
| Floral display (size and color) || Size<br />
|- <br />
| Energy production || Energy demand/consumption <br />
|- <br />
| Tube restriction (length/width) || Foraging behavior<br />
|-<br />
| Floral density || Population abundance<br />
|-<br />
|}<br />
<br />
----<br />
<br />
=== Resources ===<br />
[[Image:Linkage Rules for Plant–Pollinator Networks.pdf|Paper with simple model]]<br />
<br />
[[Image:Game_Structures_in_Mutualistic_Interactions.pdf|Other interesting paper about modeling of those networks]]<br />
<br />
<br />
----</div>RobMillshttps://wiki.santafe.edu/index.php?title=HP_Modularity&diff=14863HP Modularity2008-06-12T21:10:41Z<p>RobMills: sketched an outline of what to touch on in the abstract/proposal</p>
<hr />
<div>== Host-Pathogen Modularity ==<br />
<br />
This is the working space for our project. Everything written is a work in progress.<br />
<br />
=== Title Ideas ===<br />
*Evolution of modularity in a host-pathogen system<br />
*Modularity: a pathogen's answer to host interactions<br />
*more here<br />
<br />
=== ''Major'' Questions ===<br />
#Does modularity in pathogen ''genes'' responsible for an interaction with a host increase its ability to adapt to a host?<br />
# Is modularity in the host required for pathogen modularity to arise/emerge?<br />
#additional ones here<br />
<br />
=== Questions to answer in proposal ===<br />
# why are we studying host-pathogen interactions?<br />
# what evidence suggests that modular allelic dependencies might be advantageous in such a host-pathogen system?<br />
# give a one-line description of this type of modularity<br />
# what conditions do we aim to test to show a benefit to modular dependencies/interaction structures?<br />
# what are our null models, i.e. why is (this) result a surprise?<br />
# what impact does this have for the understanding of host-pathogen interactions, and evolvability in general?<br />
<br />
<br />
=== Model Details ===<br />
<br />
==== Discrete or continuous? ====<br />
# Pros for discrete: easier to run iterated simulations; possible to run experiments on explicit graph structures<br />
# Pros for continuous: mathematical derivations cleaner<br />
<br />
== Glossary ==<br />
<br />
=== Modularity Concepts ===<br />
<br />
I'm quite sure that there is some overloading here; but these are the types of modularity that have come up in our discussions:<br />
# Modularity for reassortment (Molly)<br />
# Modularity for independence (Molly) (I call this 'functional decomposition' - Rob)<br />
# Repeated modularity: eg where a body segment occurs many times in an organism (Rob)<br />
# Modularity for robustness to antagonistic pleiotrophy (Molly)<br />
<br />
=== Pathogen-related terms ===<br />
<br />
# '''Epitope ''': the phenotype of a pathogen that interacts with a host<br />
## only need to consider a portion of the host's genome since the pathogen only targets a specialised portion of that genome.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=14786Rob Mills2008-06-12T05:02:36Z<p>RobMills: </p>
<hr />
<div>I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't repeat myself here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (eg hiking/running/skiing/biking) and juggle occasionally. <br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
My email address is: rob.mills@zepler.net<br />
My room extension is: 4160<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
My Project links<br />
*[[The_pollination_network_wiki_page| Pollination Model]]<br />
*[[HP_Modularity| Host-pathogen modularity]]<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=14785Rob Mills2008-06-12T05:01:43Z<p>RobMills: </p>
<hr />
<div>I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't repeat myself here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (eg hiking/running/skiing/biking) and juggle occasionally. <br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
My email address is: rob.mills@zepler.net<br />
My room extension is: 4160<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
My Project links<br />
*[[Pollination Model|The_pollination_network_wiki_page]]<br />
*[[Host-pathogen modularity|HP_Modularity]]<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=HP_Modularity&diff=14784HP Modularity2008-06-12T04:59:43Z<p>RobMills: </p>
<hr />
<div>== Host-Pathogen Modularity ==<br />
<br />
This is the working space for our project. Everything written is a work in progress.<br />
<br />
=== Title Ideas ===<br />
*Evolution of modularity in a host-pathogen system<br />
*Modularity: a pathogen's answer to host interactions<br />
*more here<br />
<br />
=== ''Major'' Questions ===<br />
#Does modularity in pathogen ''genes'' responsible for an interaction with a host increase its ability to adapt to a host?<br />
# Is modularity in the host required for pathogen modularity to arise/emerge?<br />
#additional ones here<br />
<br />
=== Model Details ===<br />
<br />
==== Discrete or continuous? ====<br />
# Pros for discrete: easier to run iterated simulations; possible to run experiments on explicit graph structures<br />
# Pros for continuous: mathematical derivations cleaner<br />
<br />
== Glossary ==<br />
<br />
=== Modularity Concepts ===<br />
<br />
I'm quite sure that there is some overloading here; but these are the types of modularity that have come up in our discussions:<br />
# Modularity for reassortment (Molly)<br />
# Modularity for independence (Molly) (I call this 'functional decomposition' - Rob)<br />
# Repeated modularity: eg where a body segment occurs many times in an organism (Rob)<br />
# Modularity for robustness to antagonistic pleiotrophy (Molly)<br />
<br />
=== Pathogen-related terms ===<br />
<br />
# '''Epitope ''': the phenotype of a pathogen that interacts with a host<br />
## only need to consider a portion of the host's genome since the pathogen only targets a specialised portion of that genome.</div>RobMillshttps://wiki.santafe.edu/index.php?title=The_pollination_network_wiki_page&diff=14782The pollination network wiki page2008-06-12T04:45:44Z<p>RobMills: /* An agent-based model for a pollination network. An evolutionary game theory approach */</p>
<hr />
<div>= An agent-based model for a pollination network. An evolutionary game theory approach =<br />
<br />
Members:<br />
<br />
* Ana Martín González<br />
* Carlos Yepez<br />
* Meritxell Vinyals<br />
* Petr Svarc<br />
* Michael Cox<br />
* [[Rob_Mills|Rob Mills]]<br />
<br />
<br />
We have measured several attributes of both the flowers and the pollinators:<br />
<br />
<br />
{| class="wikitable" style="text-align:center" border="1"<br />
|'''Flowers''' || '''Pollinators'''<br />
|- <br />
| Floral display (size and color) || Size<br />
|- <br />
| Energy production || Energy demand/consumption <br />
|- <br />
| Tube restriction (length/width) || Foraging behavior<br />
|-<br />
| Floral density || Population abundance<br />
|-<br />
|}</div>RobMillshttps://wiki.santafe.edu/index.php?title=Discovering_the_surroundings&diff=14781Discovering the surroundings2008-06-12T04:43:56Z<p>RobMills: </p>
<hr />
<div>{{CSSS 2008 Santa Fe}}<br />
<br />
<!-- put content below here --><br />
<br />
I'm especially interested in Nat. Parks and Nat. Monuments - they are just the best! I've an 'America the Beautiful' pass, which allows me (and the whole car I'm in) to visit each Park without fees. So if somebody is interested, just write it in here. I'd prefer White Sands, Petriefied Forest or Badlands. But I'm open for everything (how about Alaska? ;-)) - [[Ruben_Kubiak|Ruben]]<br />
<br />
Nish is planning on visiting White Sands, Carlsbad and perhaps the Grand Canyon (about 7 hours for the last one). I also could drive back up to Canyonlands if folks are interested. I'm told we have a full moon in two weeks, which is when I would like to visit White Sands. I'm guessing that makes the third weekend for the Grand Canyon... I have room for 4 more in my car, although it might be a little tight. Feel free to put your name here if you'd like to tag along.<br />
<br />
I'd like to come with you to White Sands. I've been to the Grand Canyon, and the Carlsbad Caverns are pretty far away, so this things maybe not. -[[Ruben_Kubiak|Ruben]]<br />
<br />
I'd be glad if I can go with you both to GC and WS. Thanks a lot, [[Petr Svarc|Petr]]<br />
I'm in; let me know ! [[Jeremie |Jeremie]]<br />
DEFINITELY DOWN W/ White Sands, Peter<br />
<br />
I'm interested - Paul.<br />
<br />
<br />
<br />
'''White Sands'''<br />
<br />
I'd love to come and keep the space in your car, Nish.. :) -- [[sonotto|Sonja*]]<br />
<br />
Interested in going there [[User:Giovanni|Giovanni]]<br />
<br />
I'd love to go -[[Molly_Rorick|Molly]]<br />
<br />
sounds good -[[User:Dirk|Dirk]]<br />
<br />
Count me in for full moon+sand dune experience! [[Rob_Mills|Rob]]</div>RobMillshttps://wiki.santafe.edu/index.php?title=CSSS_2008_Santa_Fe-After_Hours&diff=14776CSSS 2008 Santa Fe-After Hours2008-06-12T04:24:27Z<p>RobMills: /* Hiking Activities */</p>
<hr />
<div>{{CSSS 2008 Santa Fe}}<br />
<br />
<!-- put content below here --><br />
<br />
=Scheduled Fun=<br />
<br />
==Near Future==<br />
<br />
=== Ping-Pong tournament for the champion of the world ===<br />
<br />
----<br />
<br />
Playing Ping-Pong is fun...and so is setting up a needlessly complex, round robin style, double secret elimination tournament '''FOR THE CHAMPION OF THE WORLD'''. <br />
<br />
Anyone that likes ping-pong or setting things up should post and we can get the small plastic ball rolling.<br />
<br />
Player list:<br />
<br />
*Michael Cox<br />
*Walter Zesk<br />
*Mark Rivera<br />
*[[Jie_Ren | Jie Ren]]<br />
<br />
=== Singing ===<br />
<br />
This is the CSSS'08 Santa Fe officiel Anthem:<br />
http://youtube.com/watch?v=-klCBXcNNa4<br />
<br />
Learn it so we can all sing along!<br />
<br />
=== Case studies in complexity: The Wire ===<br />
'''Start time: 9pm, Monday, 6/9, lower dorms common area (upstairs or downstairs)'''<br />
<br />
I have obtained the DVD box set of Season 4 of [http://en.wikipedia.org/wiki/Wire%2C_The The Wire]. This show has already come up in several conversations I've had at this course, and pertains to such topics as: <br />
* How do you evolve an adaptive organization? (In Baltimore, you don't, apparently)<br />
* How does institutional dysfunction lead to complex functional systems?<br />
* What educational systems can have an impact on kids in low-income backgrounds ("corner kids"?)<br />
* How can informed, ethical people deal with the corrupt political process?<br />
* How do you combine http://en.wikipedia.org/wiki/Charles_Dickens Charles Dickens]-style extended novelistic narrative arcs with [http://en.wikipedia.org/wiki/Michael_Mann_(film_director) Michael Mann]-style asskicking?<br />
<br />
A couple of points. First, this show is immersive, and incredibly awesome. A nonlinear consequence of this is that people who haven't already become invested in the show may be hesitant to jump in with the fourth season. I'd like to encourage everyone to give it a shot who may be interested; it's far enough ahead that I think it actually won't spoil it for you if you later go back to the beginning. And this season is of particular interest for many of the issues I've discussed here, since it particularly focuses both on the educational system and electoral politics. The creators, David Simon and Ed Burns, both have had extensive real-life experience in the city of [http://en.wikipedia.org/wiki/Baltimore%2C_Maryland Baltimore]'s police system (Burns was a homicide detective for many years), political system (Simon was a political reporter) and educational systems. A lot of the plot points come from real life events, and the characterization is better than anything I've ever seen on TV. <br />
<br />
I'll start Monday 6/9 (punted from Sunday b/c of NBA Finals) and update this space to schedule continuations. There are 13 episodes this season, so it'll take 4 or 5 goes, at least, to get through it. <br />
<br />
Cheers, [[User:Sayres|Sayres]] 19:06, 8 June 2008 (MDT)<br />
<br />
==Wednesday June 11==<br />
=== Albuquerque Isotopes Baseball Game ===<br />
Any interest in going to see an Albuquerque Isotopes baseball game? Next Wednesday June 11 might be a good day since I don't think there are any after hours events scheduled. Game time is 7pm so we could leave after class and easily make it on time. Looks like tickets are $9 and $11 (plus $3 online fee).<br />
<br />
List your name if you want to attend. Let me know by Sunday and I'll buy the tickets.<br />
http://www.albuquerquebaseball.com/<br />
<br />
Justin Darkoch<br />
<br />
Please count me in - Mauricio<br />
<br />
I'll come, too. Also, I can drive as the minivan fits 6 people. - Cathy<br />
<br />
in for the isotopes [[walter_zesk|Walt]]<br />
<br />
Sounds like fun - Skyler<br />
<br />
=== Board Games ===<br />
'''Tired of learning about game theory? Let's play some games!'''<br />
<br />
Location: Lower Commons (upper floor)<br />
<br />
Time: 8pm (Wednesday June 11th)<br />
<br />
<br />
We haven't had a chance to play the classic ''Settlers of Catan'', so that's going to be the first order of business. After that, we've got lots of games to choose from. Let's get more people this time, so pass the word.<br />
<br />
==Post-CSSS==<br />
<br />
=Activities and Interests=<br />
<br />
== Euro championship 2008 ==<br />
The European championship just started yesterday (and the swiss just got defeated! LoL). What matches do we want to see? I guess there's an Italy - France we cannot avoid!<br />
<br />
Problem: matches are at 10am or 12:45am (local time). How to see them without interfering with the classes?<br />
<br />
Put matches you are interested in here:<br />
<br />
France vs Italy - 17/06 12:45am [[User:Giovanni|Giovanni]]<br />
<br />
More generally all the games of the group C [[User:Jeremie|Jeremie]] <br />
France vs Romania - 17/06 10:45am<br />
Italy vs Holland - 17/06 12:45am<br />
<br />
We can setup to see the replay of a particular game after classes provided we don't know the result already. Replay games are free and live games 3 euros in internet. For games on Saturday or Sunday we can go to a bar downtown. [[User:Mauricio|Mauricio]]<br />
<br />
== Discovering the surroundings ==<br />
Interested in discovering the surroundings? The meaning of "surrounding" is scale-free - this could be just Los Alamos but maybe also as far as the Grand Canyon. Are you interested? Got some ideas? Go [http://www.santafe.edu/events/workshops/index.php?title=Discovering_the_surroundings here] and write it down.<br />
<br />
==Hiking Activities==<br />
<br />
*<span style="color: red; font-weight: bold;">'''Hiking this Week end 6/14 and/or 6/15 - Wheelers Peak'''</span><br />
<br />
'''please edit or confirm until Thursday morning if possible !!!'''<br />
<br />
* '''over night trip, sleeping at lake:'''<br />
Richard <br><br />
Dirk <br><br />
Qiqi + friend <br><br />
Sonja <br><br />
Mark (?)(please let know early cuz of van-reservation) <br><br />
<br />
> i am trying to get sleeping bags, camping pads, tents for everybody <br><br />
> i have also a stove and mayba a water pump, I'll check <br><br />
> please lets meet to discuss details: start Saturday at 10am?, buy dinner/brekky/lunch stuff in Taos... etc.: <span style="color: red>Thursday morning at breakfirst at 8:30!?!?</span> <br><br />
> make sure you bring plenty of warm stuff, might get really cold at night! <br><br />
> who can drive? Sonja + _________ <br><br />
<br />
<br />
* ''' 1 big day on Sunday:'''<br />
Rob (I'll be in Taos for saturday night so don't need transport - will aim to coordinate meeting at the trail head on sunday, depending on timings) <br><br />
Cold-Björn <br><br />
Abby <br><br />
Francois <br><br />
Harald <br><br />
Carlos <br><br />
Juqui (?? sorry) <br><br />
<br />
> Kolbjörn: please lets organize the car thing together <br><br />
> you start at 6am <br><br />
> make sure to bring plenty of water and warm (!!) stuff for the high elevations <br><br />
> please make sure to get organized yourself <br><br />
<br />
<br />
* ''' either one big day or some small hike'''<br />
Molly <br><br />
Mery <br><br />
Lisa <br><br />
Shrideep <br><br />
Chris <br><br />
> please delete and subscripe above if you wish to do so, or get in touch and plan different<br />
(and have fun :) )<br />
<br />
<br />
<br />
<br />
<br />
<br />
* '''Hiking this Saturday 6/14'''<br />
<br />
So we are thinking about the next big hike. According to preferences we can have one big group like last time or divide in small groups to hike at different places.<br />
Here are a few options so far:<br />
<br />
'''1-Wheeler Peak.''' Altitute 13.000 ft. 15 miles overall. Near Taos, NM. (2hr drive)<br />
Need warm clothes for cold temp, especially at night: Some people are thinking on camping so equipment will be needed.<br />
<br />
*<span style="color: red; font-weight: bold;">'''Update'''</span> This could be done by overnight camping near a lake: Drive to Taos on Saturday, Hike in to lake (2 hours), stay overnight (or leave, if cars want to split), climb the steep peak on Sunday (4-5 hours), drive home.<br />
I am about to try to get gear from St Johns or the SANTA FE MOUNTAIN SPORTS<br><br />
'''please sign in if interested'''<br><br />
How many tents do we have / need<br><br />
How many large backpacks, sleeping packs, isomats...<br><br />
<br />
Sonja: 1 backback, tent, waterpump (i think), water-pills, mat<br><br />
Dirk: 2 backpacks, bivouac sack, mat <br><br />
<br />
<br />
<br />
'''2-Tent Rocks.''' 3 miles. Nice and easy day hike near Santa Fe.<br />
<br />
'''3-Nambe Lake.''' 11.000 ft. 6 miles.<br />
May be still covered with snow and cold. Location: Albuquerque area.<br />
This 6-mile out-and-back adventure serves up mountain forests, a peaceful creek, and an unbeatable lunch spot on the banks of a small alpine lake.<br />
<br />
<br />
Carlos<br />
<br />
<br />
'''4-Rio en Medio trail.''' a nice waterfall about 45 minutes from the trailhead, then <br />
continue up on the main trail for 4 miles out + 4 miles back (back at the junction with trail 150). So it's an 8-mile out and back, follows the Rio en Medio the whole way. <br />
There are nice small pools on the right as you go up (there's one in particular with a sandy bottom and a small waterfall), and a nice big meadow on the right. You can also do a<br />
longer hike by doing the whole "La Junta" circuit.<br />
<br />
<br />
Though the camping sounds great, realistically I'll probably only be up for a day hike. They all sound great. Maybe one that is not too far from here? (I want to hike more than drive) ~[[Molly_Rorick|Molly]]<br />
<br />
--------------<br />
<br />
Banderleros links:<br />
<br />
http://www.nps.gov/band/<br />
http://www.lanl.gov/museum/<br />
http://www.trails.com/tcatalog_trail.asp?trailid=XFA024-024<br />
<br />
Kolbjørn<br />
<br />
-----------<br />
<br />
Hola CSSS'ers,<br />
<br />
Let's get together and explore the beauty and wilderness of Santa Fe's mountains!<br />
<br />
Start by joining our Facebook group: <br />
<br />
CSSS'08 Hiking Group<br />
http://www.facebook.com/group.php?gid=17254991462<br />
<br />
Hasta la vista!<br />
Carlos<br />
<br />
<br />
<br />
I've always wanted to see the Native American cliff dwellings. There are ruins near Santa Fe! http://www.nmsu.edu/~redtt/Resources/html/Cliff%20Dwellings.html<br />
<br><br />
<br />
==Opera==<br />
Wayne continues his tireless effort to get a group in to a rehearsal; probably Tuesday, June 24. It would be late (9pm - midnight) and during "crunch time", but on the other hand definitely worth it, so we just need to plan ahead a bit. In the interim, [http://santafeopera.org/commprograms/onehouropera.php this] looks adorable, and might be an option for next weekend.<br />
<br />
== Santa Fe Complex (Downtown in the Railyard) ==<br />
When you are downtown, feel free to use the new Santa Fe Complex as a home away from St. John's. SFComplex is a non-profit dedicated to applied complexity, urban planning and computational art. We have a large 4000 square foot common space in the railyard where the train locomotives used to be repaired. In the space are projection screens and broadband access. Use the space for CSSS projects, film screenings, ad-hoc lectures or meeting others in Santa Fe in the Applied Complexity space. Or, just play some music and hang out into the wee hours. The address is 632 Agua Fria. More info at http://www.sfcomplex.org. Want to know more, contact Stephen Guerin at (505)577-5828 or Owen Densmore (505)570-0168.<br />
<br />
==Get A Bike (for the month)==<br />
Get a bicycle to ride around while in Santa Fe from a bike collective place called [http://chainbreakercollective.org/ Chain Breaker]. Their website is under maintenance right now, but [http://profile.myspace.com/index.cfm?fuseaction=user.viewprofile&friendID=92732509 here's] some info on them. <br />
<br />
==Board Games==<br />
I’ve seen a couple of other folks have interests in playing board games. It would be fun to get folks together to play some evenings. I’m always up for learning a new game and meeting other players. I’m going to bring a few that are small and compact enough to travel. Maybe others can bring some too? Cheers, Devin<br />
<br />
I started a list so we know what will be in Santa Fe. Add to the list if you'll bring it with you. [[Board Game List]]<br />
<br />
==Ultimate Frisbee==<br />
I (Nish) brought a disc and cones to play some Ultimate on the weekends (or after class). I'm happy to just throw around as well. Ultimate is, or can be, super casual and a lot of fun. Grab me some time if you want to throw (I always have a disc nearby) or if you're interested in playing a game (no prior experience necessary).<br />
<br />
Hi Nish! I just checked this ultimate frisbee on youtube. Kinda cool game!!! I think it should be played here in the morning--it will be too windy after the class.... Rio<br />
<br />
==Local Music==<br />
I love live music, especially folk/bluegrass. I did some quick searching and there are a few shows I think I will go to this month in Santa Fe:<br />
<br />
June 7, 1PM: [http://profile.myspace.com/index.cfm?fuseaction=user.viewprofile&friendID=20756842 Sharon Gilchrist] at Cowgirl<br />
<br />
June 20, evening: [http://www.caneraising.com/index.html Raising Cane]<br />
<br />
Those are just the two I've found, I'm up for whatever<br />
<br />
==Spa/Resort==<br />
[http://www.tenthousandwaves.com/ Ten Thousand Waves] is very close to St. John's. Any interest?<br />
<br />
Definitely. [[Kathleen_Sprouffske|Kathleen]]<br />
<br />
Me too! Peter<br />
<br />
==*Cough* *Cough* Drinking==<br />
Well, let's be honest, we all drink :) To facilitate the great discussions that occur with the act of imbibing, I'm volunteering to be our "Beer Baron". I will drive to Albertson's every day or two and pick up beer and any booze folks want me to. Please indicate your preferences. Every night, starting around 9pm, you will find folks in the Lower Commons (near the muse dorms) hanging out, drinking, playing (Swiffer) pool and Foos(pool)ball. I'm told the Upper Commons have pool cues and foosballs we may want to "steal" at night. Stop by whenever you would like and chip in a few bucks to help keep my costs down :)<br />
<br />
Update: Unfortunately, I was warned Wednesday evening by a St. John's student that keeping beer in the fridge in<br />
the Lower Commons may result in said beer being stolen. So most of the beer is being stored in my room (Polyhymnia<br />
15). I will try and move it to the fridge each evening between 8 and 9PM, if I'm on campus. Sorry for the<br />
inconvenience.<br />
<br />
Further update: For St. John's sake and our own, let's also not be striving for crazy parties or anything. Just<br />
social activities with reasonable social drinking :) Thanks for your cooperation.<br />
<br />
[[Nish_Aravamudan|Nish]]<br />
<br />
==Basketball==<br />
<br />
A few of us have started what we hope is a bi-weekly (or more!) game of basketball. So far we've been playing between the end of classes and dinner (4:45 to 5:30ish), but this is mutable. I will update this page as soon as we have specific plans to play again. Email me ([[David Foster]]) if you have any questions. My email address is on my page. If your question is "I am not very good", the answer is: "Neither are we."<br />
<br />
I'm down for some hoops action (that time at Duke has to be good for something), let me know when you guys are playing - Justin<br />
<br />
=Old/Completed fun=<br />
<br />
==Early Arrivals==<br />
==Wednesday June 4==<br />
=== Board Game evening (around 8pm) ===<br />
Location: [http://www.santafe.edu/events/workshops/index.php/Image:Cr_map.JPG Common Room] (ground floor) #37 on the [http://conferenceservices.sjcsf.edu/map.htm map]<br />
<br />
Organizer: [[Devin_Drown|Devin]]<br />
<br />
Looks like Wednesday might be the first unscheduled evening, so let’s meet up! Interested folks should bring any games they have or just show up ready to play. Let's see if we can take over the Common Room (lower floor) in the lower dorm area. I really enjoy teaching new players and I’ve brought along several that take only minutes to learn, so come join even if you’re just looking for a way to pass some time. Also, I brought several games that can accommodate a large number of people (up to 8 people).</div>RobMillshttps://wiki.santafe.edu/index.php?title=CSSS_2008_Santa_Fe-Tutorials&diff=14664CSSS 2008 Santa Fe-Tutorials2008-06-11T02:15:17Z<p>RobMills: /* A Crash Course to Classical and Evolutionary Game Theory */</p>
<hr />
<div>{{CSSS 2008 Santa Fe}}<br />
<br />
<!-- put content below here --><br />
<br />
== The big opensource tutorial ==<br />
<br />
=== Open Source research software ===<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> [[Opensource software tutorial|Tutorial]] scheduled on Monday 9 from 7:00p<br />
<br />
Open (no pun intended...) your eyes to the wonderful world of FOSS -- Free and Open Source Software. While the distinction between Free and Open Source is a very interesting one (and highly contentious in the right crowds), for research purposes, we want to use the best tools for the job but some of us suffer from limited income, so I would like to talk about both. At the same time, FOSS is great to use for a non-economic reason: if you find bugs, or design extensions, you can fix them yourself (in OSS, at least) or at least report the problem back to a typically active community. Some potential tools to discuss/explore: R, Octave, Scilab, Gnuplot, perhaps some of the more useful languages in the field like Python and perhaps others I don't know as much about (a quick `apt-cache` on my Ubuntu Hardy install shows RasMol, ClustalW, SeaView, Achilles, complearn, EMBOSS, GENESIS, etc...)<br />
<br />
- I would like to give a "Brazilian" contribution. Those who are interested in GIS&Cia could have a look at [http://www.dpi.inpe.br/gilberto/software.html Free and Open Source GIS Source]. <br />
[[Flavia_Feitosa|Flavia]]<br />
<br />
I would be happy to contribute a little bit about freely available simulation environments like ns-2 (computer networks) and omnet++ (a generic DES) -- Laura<br />
<br />
- For Python I can offer a tutorial (see below). Nish, do you have any experience with [http://www.sagemath.org/ Sage]? [[User:Giovanni|Giovanni]]<br />
<br />
All great ideas and I would love to have more of a "You know how to use this tool or you know of this tool, you talk about it" style of tutorial :)<br />
Maybe we can do a general OSS tutorial/discussion and then transition to specific sub-topics in separate tutorials (Python, GIS, networks, etc)?<br />
I've not used Sage, before, but I'm happy to take a look before the tutorial. Thanks for the info, Giovanni!<br />
<br />
<br><br />
I'd like to learn more about open software. [[Holger_Keeler| Paul]]<br />
<br />
Some subtopics that we'll cover:<br />
<br />
==== R tutorial ====<br />
<br />
I (''[[Ruben_Kubiak|Ruben]]'') know a little bit about R (basic stuff such as common plots and regression analysis) but would like to enhance my R skills. Does anybody have an interest in a R tutorial, too? Please edit this if there is more interest.<br />
<br />
I am fairly familiar with R and could probably run a tutorial... what are you all interested in <br />
learning? - Skyler<br />
*I'd just like to get an understanding of some of it's practical uses. -Devin<br />
*Do you familiar with running social network analysis package in R? I want to learn more about it. [[Jiang_Wu| Jiang]]<br />
<br />
Interested folks<br />
#[[Devin_Drown|Devin]]<br />
#[[Mark_Rivera | Mark]]<br />
#[[Jiang_Wu| Jiang]]<br />
#[[Molly_Rorick|Molly]]<br />
#(Soumya)<br />
#[[Riley_Crane]]<br />
#[[Jeremie]]<br />
#[[Tanja_Gesell|Tanja]]<br />
<br />
==== Python tutorial ====<br />
<br />
I've (''also [[Ruben_Kubiak|Ruben]]'') interest in a Python tutorial. Please edit this if there is more interest.<br />
<br />
I can give a tutorial on python and on scipy/numpy. I can also talk about coding in general, as python is both a languange which is object oriented, imperative and functional (somehow). We can use the [http://docs.python.org/tut/tut.html python tutorial] itself as a reference for the part about the language, and then move to the basic concepts of the duo [http://numpy.org numpy] / [http://scipy.org scipy], which form a powerful tool to manipulate n-dimensional arrays of numbers and also talk about [http://ipython.scipy.org/moin/ ipython] (the enhanced interactive shell) and the [http://matplotlib.sourceforge.net/ pylab] interface, which gives a very nice environment for interactive programming and data analysis. Since pylab has been designed to mimic MATLAB's interface (the major plotting/statistical functions work as expected in both enviroments, which saves you a lot of time if you're used to MATLAB), I can also talk a bit about MATLAB, but being not a big fan of it, it would be better if somebody else stepped in to another tutorial on that. <br />
<br />
Leave a mark if interested! [[User:Giovanni|Giovanni]]<br />
<br />
I'd be interested in this as well [[User: Mark | Mark]]<br/><br />
<br />
I'm in. &mdash;[[User:Jreyes|Josh]]<br />
<br />
I'm in. [[Nish_Aravamudan|Nish]]<br />
<br />
Yes please. [[Molly_Rorick|Molly]]<br />
<br />
Me too. [[Rory_Sayres]] [[User:Sayres|Sayres]] 23:55, 4 June 2008 (MDT)<br />
<br />
I'd be interested in this as well [[Tanja_Gesell|Tanja]]<br />
<br />
I'm in [[Riley_Crane]]<br />
<br />
Another one. [[Petr Svarc|Petr]]<br />
<br />
== Neutral models in biology ==<br />
<br />
Already met. Big thanks to Molly! <br />
<br />
There is an interesting [http://arxiv.org/abs/0710.4911 paper] by Cosma Shalizi of SFI about methodological problems in social sciences research in which he talks about the concept of neutral models in evolution models. I was wondering if any of the bio-people can give a tutorial on this topic as I am pretty interested in understanding the concept. [[User:Giovanni|Giovanni]]<br />
<br />
I would be very interested in learning about neutral networks too! - Skyler<br />
<br />
== GIS / Spatial Analysis ==<br />
<br />
Space Matters!! Geographical information system (GIS) is a computational system (hardware + database engine) that is designed to assemble, store, update, analyze, manipulate, and display geographically referenced information (data identified by their locations).<br />
<br />
I'm thinking about introducing some basic GIS concepts and a free GIS software known as [http://www.dpi.inpe.br/~flavia/GIS/ Terraview]. We could also explore some spatial analysis techniques (this is the best part!) using Terraview and [http://www.geoda.uiuc.edu/downloadin.php GeoDa] (also free!). <br />
<br />
<br />
Please edit here if you are interested or send me an email. [mailto:flafeitosa@gmail.com Flávia]<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> It has been scheduled on Friday, June 13 from 1:30 p.m. - 2:45 p.m.<br />
<br />
<br />
I'm in [[Walter_Zesk|Walt]]<br/><br />
I'd do this. &mdash;[[User:Jreyes|Josh]]<br/><br />
let me know, I'm in, Sonja<br/><br />
Me too. &mdash;[[User:Lfriedl|Lisa]]<br/><br />
Can not wait for this! Rio<br><br />
Me too. [[Kathleen_Sprouffske|Kathleen]]<br><br />
Sounds like fun. If people are interested, I can bring some data sets to play around with. Alex<br />
<br />
== Statistical Physics for Non-Physicists == <br />
Problem: Textbooks about this are written for physicists. <br />
Solution: A Physicist (or mathematician) that would be so kind and spend few minutes (or maybe hours) to explain all that stuff to people like me(Petr):-)<br />
<br />
[[Ruben_Kubiak|Ruben]]: Do you seek for a general introduction or something specific?<br />
<br />
A crash course in Statistical Physics would be awesome. Let us know. &mdash; [[User:cyepez|Carlos]]<br />
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I am interested too. (Soumya)<br />
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Me too. (Jean)<br />
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Interested! [[User:Meritxell|Meritxell]]<br />
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Interested! [[User:Giovanni|Giovanni]]<br />
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Ditto - Skyler<br />
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Me too. &mdash;[[User:Lfriedl|Lisa]]<br/><br />
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Me three. [[User:RobMills|RobMills]]<br />
<br />
I'd be willing to run such a tutorial. However, I would have to consult with some/all of the interested parties to find out what kind of statphys you want to learn about. There are a huge number of possible topics, one could start with basics like ensembles, or perhaps people are interested in master equation and other non-equilibrium techniques, or maybe critical phenomena is what people are interested in. I really do not know. (Orion)<br />
<br />
Can you give us who are not physicists an introduction about a kind of special questions that you will think it from the viewpoint of physicists? Like complex network, dynamic, also something else, what is the most important measurement and dynamic process you want to observe? -[[Jiang_Wu|Jiang]]<br />
<br />
== Modern Logic and Reasoning ==<br />
Like I mentioned in the 'ice-breaking', I could tell something about application of modern logic into human reasoning. It's a very board topic, and very new. Criticisms are welcome and needed. I would give some basic examples. On top of that, I would also say some development of logic, and how I found it useful in research, which might seem un-related to logic, esp. in social science. I am planning to give a 15 to 20 minutes presentation, UNLESS people want to hear more, in that case, please let me know.<br />
QiQi<br />
<br />
<br />
<br />
I'm interested! [[Kathleen_Sprouffske|Kathleen]]<br/><br />
Me too! [[kolbjorn|Kolbjørn]]<br/><br />
Sign me up. &mdash; [[User:Jreyes|Josh]]<br/><br />
I'm interested too! (Flavia)<br/><br />
I'm in! [[Srideep_Musuvathy|srideep]]<br/><br />
I'm in too [[User:Giovanni|Giovanni]] <br/><br />
Count me in - Skyler<br/><br />
I'd be interested in this as well. [[Tanja_Gesell|Tanja]]<br />
<br/>Sounds great - i'll be there. [[User:RobMills|RobMills]]<br />
<br />
Please remind by email or somhow.. and sign me up! [[User:sonotto|Sonja]]<br />
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I am in Qi, But where? Rio<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Time at June 10th, 03.15 p.m. - 03.35 p.m.<br />
[[CSSS 2008 Santa Fe-Schedule]]<br />
<br />
== Introduction to the Design and Analysis of Computer Experiments ==<br />
How do you find "interesting" behavior when your computer model is too slow or the inputs are too many to try every possible combination? Using an Arctic sea ice simulator example, I will show you how modern statistical methods can help you explore your virtual world more efficiently. Check out this brief<br />
[http://www.stat.sfu.ca/~dbingham/NICDS_CompExpt/research.html overview] or a more technical paper about<br />
[http://www.schonlau.net/publication/jogo98.pdf global optimization]. Also see [http://www.gaussianprocess.org/ Gaussian Processes for Machine Learning] for a list of available resources. [[B%C3%A9la_Nagy|Béla]]<br />
<br />
<br />
== Genomics / Central dogma overview ==<br />
It seems like some of you might be interested in an overview of the central dogma of molecular biology to non-biologists. This could be an 1h tutorial on the major actors of gene expression: nucleus, chromosomes, chromatine, DNA, RNA (tRNA, mRNA), proteins, polymerases, ribosomes, transcription factors, and eventually a quick intro to small, non-coding RNAs as a bonus. Although being a bioinformatician by training, I'm happy to leave the way if a "hard core" biologist wants to do this tutorial (Molly ?). Edit if interested! Jean<br />
<br />
I'd be happy to attend a tutorial in 'genomics for idiots' -- Laura<br />
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Me too. I am also interested in metagenomics if this is not too much of course. -- Francois<br />
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I'd like to go to a 'genomics for idiots' tutorial as well. -- [[Srideep_Musuavthy|srideep]]<br />
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Ok, so I'll prepare some slides. How about Monday 9th, 5p - 6p (location TBA) ? -- Jean<br />
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== Artificial Intelligence/Machine Learning ==<br />
I (Nish) could introduce some of the basic methods in AI/ML. If there is significant interest in the two fields separately, I could do two tutorials. Would probably focus on the higher level, rather than the nitty-gritty details, as well as applications of the methods to real problems. I'm not necessarily an expert, although have a fair amount of experience in the area, so I would prefer a more interactive session, where questions can be answered by everyone.<br />
<br />
Sign me up. &mdash; [[User:cyepez|Carlos]]<br><br />
I'm also interested. -[[Sarah_Cobey|Sarah]] <br><br />
Me too! [[Flavia_Feitosa|Flávia]]<br />
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How about "AI/MI for dummies", Nish? I've been wondering about it.... Rio<br />
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sounds good [[Riley_Crane]]<br />
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== A Crash Course to Classical and Evolutionary Game Theory ==<br />
Game theory is the study of interactive decision making. Classical game theory aims to develop a general theory to describe how rational agents interact strategically. In many cases humans lack the kind of infinite computational power and time assumed by classical game theory. In the early 1970s the biologist John Maynard Smith introduced evolutionary methods to the field, dispensing with the assumption of hyper-rationality while changing many of the concepts central to the field along the way. The result was evolutionary game theory. This new framework has been used to model the behavior of fundamentally non-rational players (such as viruses) as well as humans. <br />
<br />
In this tutorial, I'd try to introduce the basic concepts in both of these fields, namely, the definition of a game, payoffs, the Nash equilibirum and evolutionarily stable strategies, the replicator dynamics. I'll briefly mention the three basic classes of two-strategy games represented by the Prisoner's Dilemma, the Snowdrift Game (sometimes called the Hawk-Dove game or Chicken), and the Stag Hunt Game. Depending on particular interests of the group, we could prove the Bishop-Cannings theorem and give a classification of all symmetric two-strategy games; or look at updating methods and spatial chaos; reputation and image scoring; rock-paper-scissors in biological systems; or evolutionary branching and specialization.<br />
<br />
If there's something else you'd like to know about EGT, shoot me ([mailto:joshua.reyes@removeme.gmail.com Josh]) an email, and I'll see if I can dig up something I know on your topic. I'm not going to require any fancy mathematical background. If you've seen a 2&times;2 matrix before, great. Otherwise, it's not a big deal. We won't multiply them or calculate their eigenvalues. They'll just serve as a means for bookkeeping.<br />
<br />
<span style="color: red; font-weight: bold;">Note:</span> Some of us are also thinking about setting up a [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Evolutionary_Game_Theory|working group]] as well.<br/><br />
<span style="color: red; font-weight: bold;">Update:</span> The next meeting has been scheduled for Tuesday, June 10 from 7&ndash;8pm in a location TBD.<br />
<br />
=== Lecture Notes ===<br />
Lecture 1. [[Media:EGT-01.pdf|Classical Game Theory]]<br />
<br />
Please let me know about any typos, errors, or flat-out lies. Suggestions are good, too. Thanks.<br />
<br />
=== Resources ===<br />
# Hofbauer & Sigmund '''Evolutionary Games and Population Dynamics''' [http://www.amazon.com/Evolutionary-Games-Population-Dynamics-Hofbauer/dp/052162570X]<br />
# Cressman R '''Evolutionary Dynamics and Extensive Form Games''' [http://www.amazon.com/Evolutionary-Dynamics-Extensive-Economic-Evolution/dp/0262033054/ref=sr_1_2?ie=UTF8&s=books&qid=1213149279&sr=1-2]<br />
# Nowak, Martin (to be found)<br />
# Sandholm, Bill (to be found -- is it this: '''Evolution in games with randomly disturbed payoffs''', J. Economic Theory?)<br />
<br />
<br />
*I'll sign up for this. Kolbjørn<br />
*I'm interested too! (Flavia) <br />
*I'll be there too. Kathleen<br />
*I'm in. Jean<br />
*I'm interested as well. Steve<br />
*will be there at 3 [[Walter_Zesk|Walt]]<br />
*I'll be there, Petr<br />
*Good stuff. I could also say a few things about [http://www.iiasa.ac.at/Research/EEP/AdaptiveDynamics.html adaptive dynamics], if there's interest. [[Sarah_Cobey|Sarah]]<br />
*I'll be there. [[Jiang_Wu|Jiang]]<br />
*Count me in (Chris)<br />
*I'm in. Tanja<br />
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== Resilience of social-ecological systems ==<br />
The resilience perspective is increasingly used as an approach for understanding the dynamics of social–ecological systems. Essential for the resilience perspective is the recognition that living systems are not in equilibrium but rather in a domain of attraction. <br />
Many dynamic systems, however, have multiple domains of attraction. Moreover, self-organizing processes can create or change the shape and depth of this domain of attraction. Within the resilience perspective, new pathways of sustainable development can be represented by crossing a threshold from a domain of attraction and/or by creating new domains. Resilience is a measure of how much change or disruption is required to transform a system from being maintained by one set of mutually reinforcing processes and structures to a different set of processes and structures.<br />
If you are interested we (Mike and Dirk) can introduce you to some of the insights developed by the [http://www.resalliance.org/1.php resiliance alliance] and the challenges we face in understanding these kind of systems.<br />
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I am interested in this too. Richard<br />
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Very interested, any idea of when you will do it? [[Walter_Zesk|Walt]]<br />
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I'm interested as well. Steve<br />
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I'm interested too. - Skyler<br />
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I think to contribute from my previous work on SES. Rio<br />
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== Introduction to classical control theory ==<br />
I (Srideep) can offer a 'quick' tutorial on control theory/control systems. This is will be a simple introduction to the motivation, basic ideas, issues and jargon in the field. If you are interested, please let me know about your background in linear algebra, complex analysis and calculus. Depending on the background, I might spend more or less time introducing the field. <br />
<br />
Ideally, if you know what eigenvalues and eigenvectors of a matrix are, what a pole of a complex function is and how the solution of a linear differential equation looks like, you are ready to jump right into controls. If the words above don't mean much at all, then we can run a quick 'review' of what they mean intuitively. <br />
you can sign up here or send me an email [mailto:srideep.musuvathy@gmail.com srideep]<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Lets plan on discussing this early next week. Will fix up a time by the end of this week. Liz bradley will be done with her introduction to dynamics and the eigenvalue, eigenvector tutorial will be done this friday. This will make my life easier! :-)<br />
<br />
I'd be very interested in this tutorial. I think I'm basically OK on the prerequisites, <br />
but I wouldn't be annoyed by a review. Perhaps Monday? -- Laura<br />
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I'm in too. I guess I should be ok on linear algebra, calculus and linear ODEs, but I don't know what the pole of a complex function is. Jean<br />
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I'm in. If we can start with 'pole' thing, that would be wonderful. - Masayoshi<br />
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Hi Srideep, please put me in this group. About my background on the subjects you asked; zero!!! Sorry. Rio<br />
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Definitely interested in this. - Jacob<br />
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I'm in. Paul<br />
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Looks cool. -[[Sarah_Cobey|Sarah]]<br />
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Me too! [[Rory_Sayres|Rory]]<br />
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I'm interested. Don't have any complex analysis background though. [[User:Lfriedl|Lisa]]<br />
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== Topology/algebra ==<br />
I (Srideep) will also be happy to talk about topology, introducing the concepts of point-set topology. The language of modern mathematics is enshrined in the concepts of point-set topology. I can also talk about group theory and introduce abstract algebra to those interested. In my opinion, it is the most powerful gateway into abstract thinking. sign here or email me [mailto:srideep.musuvathy@gmail.com srideep]<br />
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I'd be very interested in that. Jean<br />
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I'd be interested to see what you cover in the topology section. Algebra, however, is for the birds :) Paul<br />
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Srideep, can you do an introduction to category theory? Or would you be interested in co-organizing a tutorial with me? - Jacob<br />
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I'm very interested. Abby<br />
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Sounds like fun (Chris)<br />
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Interested. Category theory also would be fun [[User:Giovanni|Giovanni]]<br />
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== Eigenvalues - what are they and how to find them? ==<br />
I (Kolbjørn) can put together a brief and elementary introduction to eigenvalues and eigenvectors if anyone have an urge for this. Sign up or e-mail and we'll schedule something. [mailto:kolbjorn@chalmers.se Kolbjørn]<br />
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<span style="color: red; font-weight: bold;">UPDATE 06062008: SLIDES</span><br />
<br />
[http://www.santafe.edu/events/workshops/images/e/e7/Linear_algebra_tutorial.pdf Tutorial slides]<br />
<br />
<span style="color: red; font-weight: bold;">UPDATE!</span> Time: Friday June 6th, 01.00 p.m. - 03.00 p.m. If this collides with other stuff, please yell out! [[CSSS 2008 Santa Fe-Schedule]]<br />
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Yes please. [[Kathleen_Sprouffske|Kathleen]]<br />
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I am also very interested [[Walter_Zesk|Walt]]<br />
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I'm in as well [[ Mark_Rivera|Mark]]<br />
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Please - have always been kind of confusing to me. [[Jonathan_Zelner|Jon]]<br />
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Let me in - Masayoshi<br />
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I'm also interested! [[ Flavia_Feitosa|Flavia]]<br />
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I'll be there. -[[Molly_Rorick|Molly]]<br />
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I'm in as well. -[[Tanja_Gesell|Tanja]]<br />
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Me too! '''Just to remind'''; I think Classical and Evolutionary Game Theory (Josh)will be started at 3 PM. Rio<br />
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== How your computer works ==<br />
<br />
Nish and Laura can give a joint tutorial on 'how your computer works'. What happens when I type 'www.santafe.edu' in my browser? How does a web server at santafe.edu handle all those incoming requests? What happens when I use a WiFi access point? Basically, we'd be happy to take your questions about how your computer works and do our best to answer them - we're also happy to have other co-tutors. <br />
<br />
Let us know if there's interest [mailto:lmfeeney@sics.se Laura], we'd probably schedule later next week, to not conflict with tutorials that focus on maths and other project prerequisites.<br />
<br />
I would love this. -[[Sarah_Cobey|Sarah]]<br />
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== How your hardware works ==<br />
Along the same lines as the computer tutorial, I've found myself discussing hardware with a number of folks. And why hardware matters from a massive parallelism perspective (which is quite common in the complex research areas I've encountered). If folks are interested, I can give a rough overview of the way hardware works in different types of computers and supercomputers (as much as I understand of it) as well as how to best leverage that knowledge.<br />
<br />
Not sure how this differs from the the one above it, but def. interested (Chris)<br />
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== Computational Physics for Non-physicists or A small introduction into Applied Physics ==<br />
<br />
I've seen that many people are interested in physics. I could give an introduction to "computational" physics - this means physics with a PC. Actually, it is very broad and gives some basics for simulations (interesting for all simulation-folks):<br />
<br />
- What is a 'random number generator' and why should I know something about it?<br />
<br />
- What are Master-equations?<br />
<br />
- The Ising-model / Voter-model<br />
<br />
- The Central Limit Theorem or why does it make sense to average over multiple runs of a simulation?<br />
<br />
- ...<br />
<br />
[[Ruben Kubiak|Ruben]]<br />
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I'm very interested [[Nish_Aravamudan|Nish]]<br />
<br />
I'm in too. [[Jiang_Wu|Jiang]]<br />
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[[Srideep_Musuvathy|srideep]] is in.<br />
Sounds great. [[Molly_Rorick|Molly]]<br />
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Looking forward to it. [[Petr Svarc|Petr]]<br />
<br />
Interested [[User:Giovanni|Giovanni]]<br />
<br />
==Information Theory==<br />
An open discussion of Shannon information theory (would like some help in presenting this part clearly) and then some newer results from its application to cellular automata (and potentially other complex systems).<br />
<br />
Interesting. I remember something from the master course I took. [[User:Giovanni|Giovanni]]<br><br />
I'd love to participate. -[[Sarah_Cobey|Sarah]]<br><br />
I'm interested.[[Holger_Keeler|Paul]]<br><br />
I'm in. --[[User:Lfriedl|Lisa]]<br />
<br />
I'm in. --[[User:meritxell|Meritxell]]<br />
<br />
FYI: Tom Carter is going to be talking about Information Theory a bit tomorrow from 2-3pm, not sure of a location yet, but its on the schedule.<br />
<br />
==Cellular Automata==<br />
CAs (particularly ECAs) are a very interested model of computation. How do 8 rules (ECA 110, e.g.) emulate a Turing Machine? Why is that interesting? What can we learn about what defines computation given CAs? Maybe we can also discuss some simple computational (Turing) theory.<br />
<br />
I'd go to that twice. &mdash;[[User:Jreyes|Josh]]<br />
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Sounds like fun. [[Christopher Vitale|Chris]]<br />
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==A little analytical tool-box: Non-linear dynamics, ODEs, PDEs...==<br />
The [[David_Foster|Brothers]] [[Jacob_Foster|Foster]] would be happy to offer some tutorials on analytical methods. Depending on what Alfred Hubler covers, we can do some fraction of Strogatz (flows on the line & circle, bifurcations, maybe linear systems, index theorem, etc.), as well as offering a basic introduction to solving linear ODEs (no theorems, just techniques) and simple PDEs like the heat equation, with boundary conditions. Ideally this would come after Kolbjørn's eigen-stuff course, so we can just assume familiarity with that.<br />
<br />
We've put a tentative time for our tutorial on the schedule: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 3:15pm]]. Let us know if this doesn't work out for some reason and we can try to change it.<br />
<br />
These are fun topics! I never get enough of them! -- [[Srideep_Musuvathy|srideep]]<br><br />
Sounds great. [[Molly_Rorick|Molly]]<br><br />
Interesting -- sure. [[User:Lfriedl|Lisa]]<br><br />
Very useful! [[Kathleen_Sprouffske|Kathleen]]<br><br />
Need this.... Rio <br><br />
I'm in! [[Flavia_Feitosa|Flávia]]<br />
great! [[Riley_Crane]]<br />
<br />
Brothers Foster rulez! I'll be there. [[Petr Svarc|Petr]]<br />
Count me in! [[User:Giovanni|Giovanni]]<br />
<br />
==Linguistics==<br />
Can someone (I don't know [[Peter_Graff|who]]) perhaps offer a tutorial on basic linguistics stuff? I am particularly interested in generative grammar and coverage of the Chomsky "Three Models" paper, but maybe there are more interesting topics to be discussed these days... -Jacob<br />
<br />
I could easily do a Saussure/Pierce tutorial, along with how this has been applied from everything to kinship structure to film theory to table manners, but this is continental structural linguistics, very diff from the chomsky stuff. I think Peter Graff can do the chomsky stuff, though, perhaps we could work on this together (Chris)<br />
<br />
Would love both tutorials. Esp. the kinship structure stuff (is this Andre Weil's algebra chapter on kinship, from Levi-Strauss I think?) -Jacob<br />
<br />
I'd love to participate. -Tanja<br />
<br />
==Fitting models to data==<br />
A few people have asked me for a brief review of fitting models to data, but I'd like to know what methods interest you. I could start with least squares and progress to Bayesian approaches, maximum likelihood, and some more recent developments in methods for exploring space (GAs, particle filters, MCMC) with which I'm familiar. I'm by no means an expert in all these topics, so please add your name below if there's something you'd like to learn about (a particular method or method for a particular context) or teach. I feel like this tutorial would be most appropriate for the third or fourth week. -[[Sarah_Cobey|Sarah]]<br />
<br />
I am really interested in this. (Soumya)<br />
<br />
cool [[Riley_Crane]]<br />
<br />
<br />
==Semiotics, Sign Systems, and the Mind==<br />
<br />
UPDATE: TUTORIAL NOW SCHEDULED MONDAY NIGHT, 4:30-6 - bring dinner with you to coffee shop!<br />
<br />
This tutorial will be a general overview of theories of language (Saussure, Pierce, French Structuralism, Lacan) and how they impact philosophy of mind (Freud, Fodor, Minsky, Edelman, ANNs). <br />
<br />
Probably start off with the first real theory of language and the brain, Freud's topological theory, and then move to how this was absorbed into structuralist linguistics/semiotics in the 1950's (Saussure's theory of signifiers, Jakobsen on axes of discourse, paradigms/syntagms, metaphoric value transfer, and how this was applied to kinship structures, social institutions, etc.) From there we could look at how Jacques Lacan built upon this with his 'mathemic' algebraic notation for discourse analysis. We could then look at how networked theories of mind challenge both the Lacanian model and its American counterparts (Fodor's psychosemantics, for example), particularly in regard to connectionist architectures in artificial neural networks, and how this leads to more distributed notions of linguistic structure. These new paradigms can allow us to move beyond notions of discrete 'signs' existing somewhere in the brain to models based on research in microfeature maps, dynamic network synchronization, spreading activation, and feature vectores. When synthesized with Lacan's insights, and blended with some ideas from object-relations theory and by thinkers like Marvin Minsky and Gerald Edelman, its possible to come up with models that actually reflect the impact of complex systems theories. Likely wayy too much stuff to squeeze in, but certainly enough to get a conversation going, even if we don't get to half of it! <br />
<br />
(-Chris)<br />
<br />
== Questions at the Intersection of Neuroscience and Complexity ==<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> This tutorial is scheduled for 10:30 AM Wedenesday (June 11), in the <br> small library on the upper floor of Petersen student center, just behind the main conference room.<br />
<br />
Related to Chris' proposal above, but perhaps on the flip side, I'd be happy to give a tutorial / lead a discussion on issues where questions of complexity intersect with problems in neuroscience. I'll distinguish this topic from the idea above, in that I'll focus a bit more on bottom-up questions rather than purely theory-motivated questions. Neuroscience is a very large field, so I'll talk about some of the things I know, but encourage others to bring their own knowledge and curiosity. <br />
<br />
I'll start with a short background on neuroanatomy of humans and other species. Then I'll do a survey of what's sometimes termed "systems neuroscience". This is the branch of neuroscience that asks about behavior roughly on the level of neural circuits -- but which often jumps up and down scales, and overlaps pretty significantly with ideas in "cognitive neuroscience" where the focus is on a lot of the interesting, higher-order behaviors unique to relatively few species. Then I'll go over a couple of papers which I think start on a road to using complex systems. Examples of what I might talk about would be:<br />
<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/17428910?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Kiani et al J. Neurophys 2007] '''Does the visual system naturally group objects into heirarchical categories?''' These authors tried to apply some dimensionality reduction techniques to neural data from monkey inferotemporal cortex. The ideas from Dr. Newman's lectures may be very appropriate here.<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/17660812?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Assisi et al. Nature Neuroscience 2007] '''Sparseness in representation of odors'''. The Laurent lab has been combining high-quality experimental methods in the insect olfactory system with computational models (including network models) to look at how the insect system (and more recently the mammalian system) represent odors. The system presents a very interesting contrast to the visual system, in terms of the sparseness of representations at the early levels. There's some elegant circuitry mapped out here. '''BONUS QUESTION!''' I remember one of the questions they investigated earlier was how locusts transition from 'happy grasshopper' mode to 'Biblical swarm' mode. This has something to do with olfaction. This population behavior is probably a very intersting bifurcation; we can dig into what this reflects.<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/18047414?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Machens and Brody, Neural Computation 2008]. [[http://www.molbio.princeton.edu/index.php?option=content&task=view&id=335 Carlos Brody]] does a lot of work on how neural circuits dynamics can allow for short term memory behavior. This includes comparing a perceived sensation to something you experienced a few seconds or minutes ago, and constructing an internal sense of how time elapses. His group uses tools like attractor networks to model this behavior.<br />
* '''Walter Freeman's work'''. Freeman studies the mammalian visual system, but also has a background in talking about how neural circuits encode meaning. This will be an opportunity for me to go back and find some interesting results to discuss. We may also highlight the questions of information theory and oscillatory behavior in neural circuits, which covers researchers like Pascal Fries, John Huguenard, and David McCormick. I'll update this part with a more specific paper when I find a good one. <br />
<br />
'''Timing?''' Right now I'll focus on Wednesday morning, June 11. Please let me know below if you're interested. If it's a small group we can meet in the small library next to the main room; this might encourage discussion. And of course, let me know if there's something within this area in which you're more or less interested.<br />
<br />
Cheers, [[Rory_Sayres | Rory]]<br />
<br />
I'll be there Wednesday AM. Teach me, oh wise Neuroscientist! [[Nish_Aravamudan|Nish]]<br />
<br />
Hellsyeah. [[Christopher Vitale|Chris]]<br />
<br />
cool [[User:Giovanni|Giovanni]]<br />
<br />
==Network Economics and Value Theory==<br />
<br />
So, for the third week of CSSS, I'm thinking of maybe doing a session on 'Network Economics and Value Theory' for whoever's interested. Likely start off with Marx's three levels of value (use, exchange, surplus), move to his theories on production, formulas for capital, commodity fetishism, sticky points of his famous 'labor theory of value,' then on to his analysis of modes of production, and his thesis on the falling rate of profit that was supposed to bring down capitalism (but which obviously didn't). From there we could discuss critiques/updates of this theory via the growth of Keynesianism/Stalinism/Neoliberalism, in order to get to David Harvey's new work on how neoliberal economies largely avoid demand crises by engineering carefully managed accumulation crises whose effects can be easily passed off to poorer nations using multi-national postwar institutions like the IMF/WTO. This leads to examples of how networked models can help us understand today's economic crises (for example, how evolutionary search models can help us understand the ways in which 'overleveraging' economies via 'market derivatives' can help funnel capital to hedge funds in rich countries). From there we could look at critiques of economic theories of value, particularly Deleuze and Guattari's notion of 'desiring-production' as that which links production of commodities to the production of consumers by the social unit of production, namely, the family, and how even this model needs to be rethought in terms of shifts in mass media. Other topics could include theories of network political activism, namely those of Hardt and Negri (Empire/Multitude) and Ernesto Laclau on social dislocations and crisis management via counterhegemonic blocs. <br />
<br />
Anyone interested in any of this stuff, lemme know! (-Chris)<br />
<br />
== Topological and Symbolic Dynamical Systems ==<br />
<br />
I would like to address the perceived interest among [[Jacob_Foster|few]] of us here in topics relating to the topological dynamics and symbolic dynamics. I can talk a bit about ideas relating to the topological properties of dynamical systems and systems with very little structure to them (i.e., systems whose state spaces are merely a hausdorff space and a dynamic shift which is a continuous function). The symbolic dynamics part will deal with spaces of sequences of symbols and the dynamics being a shift map. I would like to wrap things up with a powerful tool - topological conjugacy - which allows us to define an 'equivalence' between two dynamical systems, one of which might be easier to understand and analyze. Ideally, this discussion will come after my topology tutorial, but I'll spend a few minutes describing formally and intuitively, the terms I use. Alternatively, we can form small discussion groups and chat about this over a cup of tea. [[Srideep_Musuvathy|srideep]]<br />
<br />
absolutely interested. [[Christopher Vitale|Chris]]<br />
<br />
Interested! [[User:Giovanni|Giovanni]]<br />
<br />
== Economics & Finance 101 ==<br />
A 1 hour mini crash-course on the basic principles of Economics and Finance. The aim of this tutorial is -hopefully- to give a heads up for the upcoming Economics/Finance week for people who do not have a background in Economics. <br />
I will introduce 3 simple models of microeconomics, macroeconomics and finance that can give an idea of what economists do. [[Carlos_Yepez|Carlos]]<br />
<br />
'''Date and time:''' Friday June 13, 3:00-4:00pm.<br />
<br />
'''Note:''' Reply to this page if you are interested in taking this tutorial.<br />
*[[Devin_Drown|Devin]]<br />
*[[Kolbjorn_Tunstrom|Kolbjørn]]<br />
*[[Jacob_Foster|Jacob]]<br />
*[[Flavia_Feitosa|Flávia]]<br />
*[[Holger_Keeler|Paul]]<br />
<br />
==Theory of computation==<br />
[[Adam_Campbell|Adam Campbell]] will be holding a tutorial on the theoretical side of Computer Science. This will be a high level overview of the mathematical foundation on which computability theory is based and won't be a discussion on practical algorithms or programming methods. I will discuss Turing Machines, the various classes of problems (P, NP, NP-Complete, etc.), decidability, computational complexity, etc. What does it mean when an algorithm is in O(n), O(n^2), etc.? What makes a problem in NP-Complete, and how can you take your problem and prove that it is in NP-Complete or in P? What is the P = NP question all about? These questions and more will be discussed.<br />
<br />
The tutorial is scheduled for: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 6:00pm]].</div>RobMillshttps://wiki.santafe.edu/index.php?title=Tuesday_4:30_Lab_Signup&diff=14236Tuesday 4:30 Lab Signup2008-06-06T14:03:39Z<p>RobMills: </p>
<hr />
<div># Flávia Feitosa<br />
# Kathleen Sprouffske<br />
# Kolbjørn Tunstrøm<br />
# Meritxell Vinyals<br />
# Tolaya<br />
# John Gonzales<br />
# Lisa Friedland<br />
# Tanja<br />
# Qi Qi<br />
# Harold<br />
# Maria<br />
# Jean<br />
# Peter G.<br />
# Francois<br />
# Mauricio<br />
# Jacob<br />
# Orion<br />
# Masayoshi Kubo<br />
# Abby<br />
# Rob</div>RobMillshttps://wiki.santafe.edu/index.php?title=CSSS_2008_Santa_Fe-Tutorials&diff=14137CSSS 2008 Santa Fe-Tutorials2008-06-05T19:24:33Z<p>RobMills: /* Modern Logic and Reasoning */</p>
<hr />
<div>{{CSSS 2008 Santa Fe}}<br />
<br />
<!-- put content below here --><br />
<br />
== Open Source research software ==<br />
<br />
Open (no pun intended...) your eyes to the wonderful world of FOSS -- Free and Open Source Software. While the distinction between Free and Open Source is a very interesting one (and highly contentious in the right crowds), for research purposes, we want to use the best tools for the job but some of us suffer from limited income, so I would like to talk about both. At the same time, FOSS is great to use for a non-economic reason: if you find bugs, or design extensions, you can fix them yourself (in OSS, at least) or at least report the problem back to a typically active community. Some potential tools to discuss/explore: R, Octave, Scilab, Gnuplot, perhaps some of the more useful languages in the field like Python and perhaps others I don't know as much about (a quick `apt-cache` on my Ubuntu Hardy install shows RasMol, ClustalW, SeaView, Achilles, complearn, EMBOSS, GENESIS, etc...)<br />
<br />
- I would like to give a "Brazilian" contribution. Those who are interested in GIS&Cia could have a look at [http://www.dpi.inpe.br/gilberto/software.html Free and Open Source GIS Source]. <br />
[[Flavia_Feitosa|Flavia]]<br />
<br />
I would be happy to contribute a little bit about freely available simulation environments like ns-2 (computer networks) and omnet++ (a generic DES) -- Laura<br />
<br />
- For Python I can offer a tutorial (see below). Nish, do you have any experience with [http://www.sagemath.org/ Sage]? [[User:Giovanni|Giovanni]]<br />
<br />
All great ideas and I would love to have more of a "You know how to use this tool or you know of this tool, you talk about it" style of tutorial :)<br />
Maybe we can do a general OSS tutorial/discussion and then transition to specific sub-topics in separate tutorials (Python, GIS, networks, etc)?<br />
I've not used Sage, before, but I'm happy to take a look before the tutorial. Thanks for the info, Giovanni!<br />
<br />
<br><br />
I'd like to learn more about open software. [[Holger_Keeler| Paul]]<br />
<br />
== R tutorial ==<br />
I (''[[Ruben_Kubiak|Ruben]]'') know a little bit about R (basic stuff such as common plots and regression analysis) but would like to enhance my R skills. Does anybody have an interest in a R tutorial, too? Please edit this if there is more interest.<br />
<br />
Would be interested in learning about this as well. -[[Devin_Drown|Devin]]<br />
<br />
I would be interested as well. [[Mark_Rivera | Mark]]<br />
<br />
I am fairly familiar with R and could probably run a tutorial... what are you all interested in learning? - Skyler<br />
<br />
I am interesed in it too. Do you familiar with running social network analysis package in R? I want to learn more about it. [[Jiang_Wu| Jiang]]<br />
<br />
== Python tutorial ==<br />
I've (''also [[Ruben_Kubiak|Ruben]]'') interest in a Python tutorial. Please edit this if there is more interest.<br />
<br />
I can give a tutorial on python and on scipy/numpy. I can also talk about coding in general, as python is both a languange which is object oriented, imperative and functional (somehow). We can use the [http://docs.python.org/tut/tut.html python tutorial] itself as a reference for the part about the language, and then move to the basic concepts of the duo [http://numpy.org numpy] / [http://scipy.org scipy], which form a powerful tool to manipulate n-dimensional arrays of numbers and also talk about [http://ipython.scipy.org/moin/ ipython] (the enhanced interactive shell) and the [http://matplotlib.sourceforge.net/ pylab] interface, which gives a very nice environment for interactive programming and data analysis. Since pylab has been designed to mimic MATLAB's interface (the major plotting/statistical functions work as expected in both enviroments, which saves you a lot of time if you're used to MATLAB), I can also talk a bit about MATLAB, but being not a big fan of it, it would be better if somebody else stepped in to another tutorial on that. <br />
<br />
Leave a mark if interested! [[User:Giovanni|Giovanni]]<br />
<br />
I'd be interested in this as well [[User: Mark | Mark]]<br/><br />
<br />
I'm in. &mdash;[[User:Jreyes|Josh]]<br />
<br />
I'm in. [[Nish_Aravamudan|Nish]]<br />
<br />
Yes please. [[Molly_Rorick|Molly]]<br />
<br />
Me too. [[Rory_Sayres]] [[User:Sayres|Sayres]] 23:55, 4 June 2008 (MDT)<br />
<br />
I'd be interested in this as well [[Tanja_Gesell|Tanja]]<br />
<br />
== Neutral models in biology ==<br />
<br />
Already met. Big thanks to Molly! <br />
<br />
There is an interesting [http://arxiv.org/abs/0710.4911 paper] by Cosma Shalizi of SFI about methodological problems in social sciences research in which he talks about the concept of neutral models in evolution models. I was wondering if any of the bio-people can give a tutorial on this topic as I am pretty interested in understanding the concept. [[User:Giovanni|Giovanni]]<br />
<br />
I would be very interested in learning about neutral networks too! - Skyler<br />
<br />
== GIS / Spatial Analysis ==<br />
<br />
Space Matters!! Geographical information system (GIS) is a computational system (hardware + database engine) that is designed to assemble, store, update, analyze, manipulate, and display geographically referenced information (data identified by their locations).<br />
<br />
I'm thinking about introducing some basic GIS concepts and a free GIS software known as [http://www.dpi.inpe.br/~flavia/GIS/ Terraview]. We could also explore some spatial analysis techniques (this is the best part!) using Terraview and [http://www.geoda.uiuc.edu/downloadin.php GeoDa] (also free!). <br />
<br />
<br />
Please edit here if you are interested or send me an email. [mailto:flafeitosa@gmail.com Flávia]<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> It has been scheduled on Friday, June 13 from 1:30 p.m. - 2:45 p.m.<br />
<br />
<br />
I'm in [[Walter_Zesk|Walt]]<br/><br />
I'd do this. &mdash;[[User:Jreyes|Josh]]<br/><br />
let me know, I'm in, Sonja<br/><br />
Me too. &mdash;[[User:Lfriedl|Lisa]]<br/><br />
Can not wait for this! Rio<br><br />
Me too. [[Kathleen_Sprouffske|Kathleen]]<br />
<br />
== Statistical Physics for Non-Physicists == <br />
Problem: Textbooks about this are written for physicists. <br />
Solution: A Physicist (or mathematician) that would be so kind and spend few minutes (or maybe hours) to explain all that stuff to people like me(Petr):-)<br />
<br />
[[Ruben_Kubiak|Ruben]]: Do you seek for a general introduction or something specific?<br />
<br />
A crash course in Statistical Physics would be awesome. Let us know. &mdash; [[User:cyepez|Carlos]]<br />
<br />
I am interested too. (Soumya)<br />
<br />
Me too. (Jean)<br />
<br />
Interested! [[User:Meritxell|Meritxell]]<br />
<br />
Interested! [[User:Giovanni|Giovanni]]<br />
<br />
Ditto - Skyler<br />
<br />
Me too. &mdash;[[User:Lfriedl|Lisa]]<br/><br />
<br />
Me three. [[User:RobMills|RobMills]]<br />
<br />
I'd be willing to run such a tutorial. However, I would have to consult with some/all of the interested parties to find out what kind of statphys you want to learn about. There are a huge number of possible topics, one could start with basics like ensembles, or perhaps people are interested in master equation and other non-equilibrium techniques, or maybe critical phenomena is what people are interested in. I really do not know. (Orion)<br />
<br />
Can you give us who are not physicists an introduction about a kind of special questions that you will think it from the viewpoint of physicists? Like complex network, dynamic, also something else, what is the most important measurement and dynamic process you want to observe? -[[Jiang_Wu|Jiang]]<br />
<br />
== Modern Logic and Reasoning ==<br />
Like I mentioned in the 'ice-breaking', I could tell something about application of modern logic into human reasoning. It's a very board topic, and very new. Criticisms are welcome and needed. I would give some basic examples. On top of that, I would also say some development of logic, and how I found it useful in research, which might seem un-related to logic, esp. in social science. I am planning to give a 15 to 20 minutes presentation, UNLESS people want to hear more, in that case, please let me know.<br />
QiQi<br />
<br />
<br />
<br />
I'm interested! [[Kathleen_Sprouffske|Kathleen]]<br/><br />
Me too! [[kolbjorn|Kolbjørn]]<br/><br />
Sign me up. &mdash; [[User:Jreyes|Josh]]<br/><br />
I'm interested too! (Flavia)<br/><br />
I'm in! [[Srideep_Musuvathy|srideep]]<br/><br />
I'm in too [[User:Giovanni|Giovanni]] <br/><br />
Count me in - Skyler<br/><br />
I'd be interested in this as well. [[Tanja_Gesell|Tanja]]<br />
<br/>Sounds great - i'll be there. [[User:RobMills|RobMills]]<br />
<br />
Please remind by email or somhow.. and sign me up! [[User:sonotto|Sonja]]<br />
<br />
I am in Qi, But where? Rio<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Time at June 10th, 03.15 p.m. - 03.35 p.m.<br />
[[CSSS 2008 Santa Fe-Schedule]]<br />
<br />
== Introduction to the Design and Analysis of Computer Experiments ==<br />
How do you find "interesting" behavior when your computer model is too slow or the inputs are too many to try every possible combination? Using an Arctic sea ice simulator example, I will show you how modern statistical methods can help you explore your virtual world more efficiently. Check out this brief<br />
[http://www.stat.sfu.ca/~dbingham/NICDS_CompExpt/research.html overview] or a more technical paper about<br />
[http://www.schonlau.net/publication/jogo98.pdf global optimization].<br />
Time permitting we could also touch on some of the statistical concepts involved, e.g. cross-validation, maximum likelihood estimation, or Bayesian statistics.<br />
[[B%C3%A9la_Nagy|Béla]]<br />
<br />
== Genomics / Central dogma overview ==<br />
It seems like some of you might be interested in an overview of the central dogma of molecular biology to non-biologists. This could be an 1h tutorial on the major actors of gene expression: nucleus, chromosomes, chromatine, DNA, RNA (tRNA, mRNA), proteins, polymerases, ribosomes, transcription factors, and eventually a quick intro to small, non-coding RNAs as a bonus. Although being a bioinformatician by training, I'm happy to leave the way if a "hard core" biologist wants to do this tutorial (Molly ?). Edit if interested! Jean<br />
<br />
I'd be happy to attend a tutorial in 'genomics for idiots' -- Laura<br />
<br />
Me too. I am also interested in metagenomics if this is not too much of course. -- Francois<br />
<br />
I'd like to go to a 'genomics for idiots' tutorial as well. -- [[Srideep_Musuavthy|srideep]]<br />
<br />
Ok, so I'll prepare some slides. How about Monday 9th, 5p - 6p (location TBA) ? -- Jean<br />
<br />
== Artificial Intelligence/Machine Learning ==<br />
I (Nish) could introduce some of the basic methods in AI/ML. If there is significant interest in the two fields separately, I could do two tutorials. Would probably focus on the higher level, rather than the nitty-gritty details, as well as applications of the methods to real problems. I'm not necessarily an expert, although have a fair amount of experience in the area, so I would prefer a more interactive session, where questions can be answered by everyone.<br />
<br />
Sign me up. &mdash; [[User:cyepez|Carlos]]<br><br />
I'm also interested. -[[Sarah_Cobey|Sarah]] <br><br />
Me too! [[Flavia_Feitosa|Flávia]]<br />
<br />
How about "AI/MI for dummies", Nish? I've been wondering about it.... Rio<br />
<br />
== A Crash Course to Classical and Evolutionary Game Theory ==<br />
Game theory is the study of interactive decision making. Classical game theory aims to develop a general theory to describe how rational agents interact strategically. In many cases humans lack the kind of infinite computational power and time assumed by classical game theory. In the early 1970s the biologist John Maynard Smith introduced evolutionary methods to the field, dispensing with the assumption of hyper-rationality while changing many of the concepts central to the field along the way. The result was evolutionary game theory. This new framework has been used to model the behavior of fundamentally non-rational players (such as viruses) as well as humans. <br />
<br />
In this tutorial, I'd try to introduce the basic concepts in both of these fields, namely, the definition of a game, payoffs, the Nash equilibirum and evolutionarily stable strategies, the replicator dynamics. I'll briefly mention the three basic classes of two-strategy games represented by the Prisoner's Dilemma, the Snowdrift Game (sometimes called the Hawk-Dove game or Chicken), and the Stag Hunt Game. Depending on particular interests of the group, we could prove the Bishop-Cannings theorem and give a classification of all symmetric two-strategy games; or look at updating methods and spatial chaos; reputation and image scoring; rock-paper-scissors in biological systems; or evolutionary branching and specialization.<br />
<br />
If there's something else you'd like to know about EGT, shoot me ([mailto:joshua.reyes@removeme.gmail.com Josh]) an email, and I'll see if I can dig up something I know on your topic. I'm not going to require any fancy mathematical background. If you've seen a 2&times;2 matrix before, great. Otherwise, it's not a big deal. We won't multiply them or calculate their eigenvalues. They'll just serve as a means for bookkeeping.<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Some of us are also thinking about setting up a [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Evolutionary_Game_Theory|working group]] as well.<br />
<span style="color: red; font-weight: bold;"><br />
<br/>Update 2!</span> This has been scheduled on Friday from 3 - 5, location TBD. <br />
<br />
*I'll sign up for this. Kolbjørn<br />
*I'm interested too! (Flavia) <br />
*I'll be there too. Kathleen<br />
*I'm in. Jean<br />
*I'm interested as well. Steve<br />
*will be there at 3 [[Walter_Zesk|Walt]]<br />
*I'll be there, Petr<br />
*Good stuff. I could also say a few things about [http://www.iiasa.ac.at/Research/EEP/AdaptiveDynamics.html adaptive dynamics], if there's interest. [[Sarah_Cobey|Sarah]]<br />
*I'll be there. [[Jiang_Wu|Jiang]]<br />
<br />
== Resilience of social-ecological systems ==<br />
The resilience perspective is increasingly used as an approach for understanding the dynamics of social–ecological systems. Essential for the resilience perspective is the recognition that living systems are not in equilibrium but rather in a domain of attraction. <br />
Many dynamic systems, however, have multiple domains of attraction. Moreover, self-organizing processes can create or change the shape and depth of this domain of attraction. Within the resilience perspective, new pathways of sustainable development can be represented by crossing a threshold from a domain of attraction and/or by creating new domains. Resilience is a measure of how much change or disruption is required to transform a system from being maintained by one set of mutually reinforcing processes and structures to a different set of processes and structures.<br />
If you are interested we (Mike and Dirk) can introduce you to some of the insights developed by the [http://www.resalliance.org/1.php resiliance alliance] and the challenges we face in understanding these kind of systems.<br />
<br />
I am interested in this too. Richard<br />
<br />
Very interested, any idea of when you will do it? [[Walter_Zesk|Walt]]<br />
<br />
I'm interested as well. Steve<br />
<br />
I'm interested too. - Skyler<br />
<br />
I think to contribute from my previous work on SES. Rio<br />
<br />
== Introduction to classical control theory ==<br />
I (Srideep) can offer a 'quick' tutorial on control theory/control systems. This is will be a simple introduction to the motivation, basic ideas, issues and jargon in the field. If you are interested, please let me know about your background in linear algebra, complex analysis and calculus. Depending on the background, I might spend more or less time introducing the field. <br />
<br />
Ideally, if you know what eigenvalues and eigenvectors of a matrix are, what a pole of a complex function is and how the solution of a linear differential equation looks like, you are ready to jump right into controls. If the words above don't mean much at all, then we can run a quick 'review' of what they mean intuitively. <br />
you can sign up here or send me an email [mailto:srideep.musuvathy@gmail.com srideep]<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Lets plan on discussing this early next week. Will fix up a time by the end of this week. Liz bradley will be done with her introduction to dynamics and the eigenvalue, eigenvector tutorial will be done this friday. This will make my life easier! :-)<br />
<br />
I'd be very interested in this tutorial. I think I'm basically OK on the prerequisites, <br />
but I wouldn't be annoyed by a review. Perhaps Monday? -- Laura<br />
<br />
I'm in too. I guess I should be ok on linear algebra, calculus and linear ODEs, but I don't know what the pole of a complex function is. Jean<br />
<br />
I'm in. If we can start with 'pole' thing, that would be wonderful. - Masayoshi<br />
<br />
Hi Srideep, please put me in this group. About my background on the subjects you asked; zero!!! Sorry. Rio<br />
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Definitely interested in this. - Jacob<br />
<br />
I'm in. Paul<br />
<br />
Looks cool. -[[Sarah_Cobey|Sarah]]<br />
<br />
== Topology/algebra ==<br />
I (Srideep) will also be happy to talk about topology, introducing the concepts of point-set topology. The language of modern mathematics is enshrined in the concepts of point-set topology. I can also talk about group theory and introduce abstract algebra to those interested. In my opinion, it is the most powerful gateway into abstract thinking. sign here or email me [mailto:srideep.musuvathy@gmail.com srideep]<br />
<br />
I'd be very interested in that. Jean<br />
<br />
I'd be interested to see what you cover in the topology section. Algebra, however, is for the birds :) Paul<br />
<br />
Srideep, can you do an introduction to category theory? Or would you be interested in co-organizing a tutorial with me? - Jacob<br />
<br />
I'm very interested. Abby<br />
<br />
== Eigenvalues - what are they and how to find them? ==<br />
I (Kolbjørn) can put together a brief and elementary introduction to eigenvalues and eigenvectors if anyone have an urge for this. Sign up or e-mail and we'll schedule something. [mailto:kolbjorn@chalmers.se Kolbjørn]<br />
<br />
<span style="color: red; font-weight: bold;">UPDATE!</span> Time: Friday June 6th, 01.00 p.m. - 03.00 p.m. If this collides with other stuff, please yell out! [[CSSS 2008 Santa Fe-Schedule]]<br />
<br />
Yes please. [[Kathleen_Sprouffske|Kathleen]]<br />
<br />
I am also very interested [[Walter_Zesk|Walt]]<br />
<br />
I'm in as well [[ Mark_Rivera|Mark]]<br />
<br />
Please - have always been kind of confusing to me. [[Jonathan_Zelner|Jon]]<br />
<br />
Let me in - Masayoshi<br />
<br />
I'm also interested! [[ Flavia_Feitosa|Flavia]]<br />
<br />
I'll be there. -[[Molly_Rorick|Molly]]<br />
<br />
I'm in as well. -[[Tanja_Gesell|Tanja]]<br />
<br />
Me too! '''Just to remind'''; I think Classical and Evolutionary Game Theory (Josh)will be started at 3 PM. Rio<br />
<br />
== How your computer works ==<br />
<br />
Nish and Laura can give a joint tutorial on 'how your computer works'. What happens when I type 'www.santafe.edu' in my browser? How does a web server at santafe.edu handle all those incoming requests? What happens when I use a WiFi access point? Basically, we'd be happy to take your questions about how your computer works and do our best to answer them - we're also happy to have other co-tutors. <br />
<br />
Let us know if there's interest [mailto:lmfeeney@sics.se Laura], we'd probably schedule later next week, to not conflict with tutorials that focus on maths and other project prerequisites.<br />
<br />
I would love this. -[[Sarah_Cobey|Sarah]]<br />
<br />
== How your hardware works ==<br />
Along the same lines as the computer tutorial, I've found myself discussing hardware with a number of folks. And why hardware matters from a massive parallelism perspective (which is quite common in the complex research areas I've encountered). If folks are interested, I can give a rough overview of the way hardware works in different types of computers and supercomputers (as much as I understand of it) as well as how to best leverage that knowledge.<br />
<br />
== Computational Physics for Non-physicists or A small introduction into Applied Physics ==<br />
<br />
I've seen that many people are interested in physics. I could give an introduction to "computational" physics - this means physics with a PC. Actually, it is very broad and gives some basics for simulations (interesting for all simulation-folks):<br />
<br />
- What is a 'random number generator' and why should I know something about it?<br />
<br />
- What are Master-equations?<br />
<br />
- The Ising-model / Voter-model<br />
<br />
- The Central Limit Theorem or why does it make sense to average over multiple runs of a simulation?<br />
<br />
- ...<br />
<br />
[[Ruben Kubiak|Ruben]]<br />
<br />
I'm very interested [[Nish_Aravamudan|Nish]]<br />
<br />
I'm in too. [[Jiang_Wu|Jiang]]<br />
<br />
[[Srideep_Musuvathy|srideep]] is in.<br />
Sounds great. [[Molly_Rorick|Molly]]<br />
<br />
==Information Theory==<br />
An open discussion of Shannon information theory (would like some help in presenting this part clearly) and then some newer results from its application to cellular automata (and potentially other complex systems).<br />
<br />
Interesting. I remember something from the master course I took. [[User:Giovanni|Giovanni]]<br><br />
I'd love to participate. -[[Sarah_Cobey|Sarah]]<br><br />
I'm interested.[[Holger_Keeler|Paul]]<br><br />
I'm in. --[[User:Lfriedl|Lisa]]<br />
<br />
I'm in. --[[User:meritxell|Meritxell]]<br />
<br />
==Cellular Automata==<br />
CAs (particularly ECAs) are a very interested model of computation. How do 8 rules (ECA 110, e.g.) emulate a Turing Machine? Why is that interesting? What can we learn about what defines computation given CAs? Maybe we can also discuss some simple computational (Turing) theory.<br />
<br />
==A little analytical tool-box: Non-linear dynamics, ODEs, PDEs...==<br />
The [[David_Foster|Brothers]] [[Jacob_Foster|Foster]] would be happy to offer some tutorials on analytical methods. Depending on what Alfred Hubler covers, we can do some fraction of Strogatz (flows on the line & circle, bifurcations, maybe linear systems, index theorem, etc.), as well as offering a basic introduction to solving linear ODEs (no theorems, just techniques) and simple PDEs like the heat equation, with boundary conditions. Ideally this would come after Kolbjørn's eigen-stuff course, so we can just assume familiarity with that.<br />
<br />
We've put a tentative time for our tutorial on the schedule: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 3:15pm]]. Let us know if this doesn't work out for some reason and we can try to change it.<br />
<br />
These are fun topics! I never get enough of them! -- [[Srideep_Musuvathy|srideep]]<br><br />
Sounds great. [[Molly_Rorick|Molly]]<br><br />
Interesting -- sure. [[User:Lfriedl|Lisa]]<br><br />
Very useful! [[Kathleen_Sprouffske|Kathleen]]<br><br />
Need this.... Rio <br><br />
I'm in! [[Flavia_Feitosa|Flávia]]<br />
<br />
==Linguistics==<br />
Can someone (I don't know [[Peter_Graff|who]]) perhaps offer a tutorial on basic linguistics stuff? I am particularly interested in generative grammar and coverage of the Chomsky "Three Models" paper, but maybe there are more interesting topics to be discussed these days... -Jacob<br />
<br />
==Fitting models to data==<br />
A few people have asked me for a brief review of fitting models to data, but I'd like to know what methods interest you. I could start with least squares and progress to Bayesian approaches, maximum likelihood, and some more recent developments in methods for exploring space (GAs, particle filters, MCMC) with which I'm familiar. I'm by no means an expert in all these topics, so please add your name below if there's something you'd like to learn about (a particular method or method for a particular context) or teach. I feel like this tutorial would be most appropriate for the third or fourth week. -[[Sarah_Cobey|Sarah]]</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=14136Rob Mills2008-06-05T19:20:47Z<p>RobMills: added contact details</p>
<hr />
<div>I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't repeat myself here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (eg hiking/running/skiing/biking) and juggle occasionally. <br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
My email address is: rob.mills@zepler.net<br />
My room extension is: 4160<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=CSSS_2008_Santa_Fe-Tutorials&diff=14135CSSS 2008 Santa Fe-Tutorials2008-06-05T19:18:27Z<p>RobMills: /* Statistical Physics for Non-Physicists */</p>
<hr />
<div>{{CSSS 2008 Santa Fe}}<br />
<br />
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<br />
== Open Source research software ==<br />
<br />
Open (no pun intended...) your eyes to the wonderful world of FOSS -- Free and Open Source Software. While the distinction between Free and Open Source is a very interesting one (and highly contentious in the right crowds), for research purposes, we want to use the best tools for the job but some of us suffer from limited income, so I would like to talk about both. At the same time, FOSS is great to use for a non-economic reason: if you find bugs, or design extensions, you can fix them yourself (in OSS, at least) or at least report the problem back to a typically active community. Some potential tools to discuss/explore: R, Octave, Scilab, Gnuplot, perhaps some of the more useful languages in the field like Python and perhaps others I don't know as much about (a quick `apt-cache` on my Ubuntu Hardy install shows RasMol, ClustalW, SeaView, Achilles, complearn, EMBOSS, GENESIS, etc...)<br />
<br />
- I would like to give a "Brazilian" contribution. Those who are interested in GIS&Cia could have a look at [http://www.dpi.inpe.br/gilberto/software.html Free and Open Source GIS Source]. <br />
[[Flavia_Feitosa|Flavia]]<br />
<br />
I would be happy to contribute a little bit about freely available simulation environments like ns-2 (computer networks) and omnet++ (a generic DES) -- Laura<br />
<br />
- For Python I can offer a tutorial (see below). Nish, do you have any experience with [http://www.sagemath.org/ Sage]? [[User:Giovanni|Giovanni]]<br />
<br />
All great ideas and I would love to have more of a "You know how to use this tool or you know of this tool, you talk about it" style of tutorial :)<br />
Maybe we can do a general OSS tutorial/discussion and then transition to specific sub-topics in separate tutorials (Python, GIS, networks, etc)?<br />
I've not used Sage, before, but I'm happy to take a look before the tutorial. Thanks for the info, Giovanni!<br />
<br />
<br><br />
I'd like to learn more about open software. [[Holger_Keeler| Paul]]<br />
<br />
== R tutorial ==<br />
I (''[[Ruben_Kubiak|Ruben]]'') know a little bit about R (basic stuff such as common plots and regression analysis) but would like to enhance my R skills. Does anybody have an interest in a R tutorial, too? Please edit this if there is more interest.<br />
<br />
Would be interested in learning about this as well. -[[Devin_Drown|Devin]]<br />
<br />
I would be interested as well. [[Mark_Rivera | Mark]]<br />
<br />
I am fairly familiar with R and could probably run a tutorial... what are you all interested in learning? - Skyler<br />
<br />
I am interesed in it too. Do you familiar with running social network analysis package in R? I want to learn more about it. [[Jiang_Wu| Jiang]]<br />
<br />
== Python tutorial ==<br />
I've (''also [[Ruben_Kubiak|Ruben]]'') interest in a Python tutorial. Please edit this if there is more interest.<br />
<br />
I can give a tutorial on python and on scipy/numpy. I can also talk about coding in general, as python is both a languange which is object oriented, imperative and functional (somehow). We can use the [http://docs.python.org/tut/tut.html python tutorial] itself as a reference for the part about the language, and then move to the basic concepts of the duo [http://numpy.org numpy] / [http://scipy.org scipy], which form a powerful tool to manipulate n-dimensional arrays of numbers and also talk about [http://ipython.scipy.org/moin/ ipython] (the enhanced interactive shell) and the [http://matplotlib.sourceforge.net/ pylab] interface, which gives a very nice environment for interactive programming and data analysis. Since pylab has been designed to mimic MATLAB's interface (the major plotting/statistical functions work as expected in both enviroments, which saves you a lot of time if you're used to MATLAB), I can also talk a bit about MATLAB, but being not a big fan of it, it would be better if somebody else stepped in to another tutorial on that. <br />
<br />
Leave a mark if interested! [[User:Giovanni|Giovanni]]<br />
<br />
I'd be interested in this as well [[User: Mark | Mark]]<br/><br />
<br />
I'm in. &mdash;[[User:Jreyes|Josh]]<br />
<br />
I'm in. [[Nish_Aravamudan|Nish]]<br />
<br />
Yes please. [[Molly_Rorick|Molly]]<br />
<br />
Me too. [[Rory_Sayres]] [[User:Sayres|Sayres]] 23:55, 4 June 2008 (MDT)<br />
<br />
I'd be interested in this as well [[Tanja_Gesell|Tanja]]<br />
<br />
== Neutral models in biology ==<br />
<br />
Already met. Big thanks to Molly! <br />
<br />
There is an interesting [http://arxiv.org/abs/0710.4911 paper] by Cosma Shalizi of SFI about methodological problems in social sciences research in which he talks about the concept of neutral models in evolution models. I was wondering if any of the bio-people can give a tutorial on this topic as I am pretty interested in understanding the concept. [[User:Giovanni|Giovanni]]<br />
<br />
I would be very interested in learning about neutral networks too! - Skyler<br />
<br />
== GIS / Spatial Analysis ==<br />
<br />
Space Matters!! Geographical information system (GIS) is a computational system (hardware + database engine) that is designed to assemble, store, update, analyze, manipulate, and display geographically referenced information (data identified by their locations).<br />
<br />
I'm thinking about introducing some basic GIS concepts and a free GIS software known as [http://www.dpi.inpe.br/~flavia/GIS/ Terraview]. We could also explore some spatial analysis techniques (this is the best part!) using Terraview and [http://www.geoda.uiuc.edu/downloadin.php GeoDa] (also free!). <br />
<br />
<br />
Please edit here if you are interested or send me an email. [mailto:flafeitosa@gmail.com Flávia]<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> It has been scheduled on Friday, June 13 from 1:30 p.m. - 2:45 p.m.<br />
<br />
<br />
I'm in [[Walter_Zesk|Walt]]<br/><br />
I'd do this. &mdash;[[User:Jreyes|Josh]]<br/><br />
let me know, I'm in, Sonja<br/><br />
Me too. &mdash;[[User:Lfriedl|Lisa]]<br/><br />
Can not wait for this! Rio<br><br />
Me too. [[Kathleen_Sprouffske|Kathleen]]<br />
<br />
== Statistical Physics for Non-Physicists == <br />
Problem: Textbooks about this are written for physicists. <br />
Solution: A Physicist (or mathematician) that would be so kind and spend few minutes (or maybe hours) to explain all that stuff to people like me(Petr):-)<br />
<br />
[[Ruben_Kubiak|Ruben]]: Do you seek for a general introduction or something specific?<br />
<br />
A crash course in Statistical Physics would be awesome. Let us know. &mdash; [[User:cyepez|Carlos]]<br />
<br />
I am interested too. (Soumya)<br />
<br />
Me too. (Jean)<br />
<br />
Interested! [[User:Meritxell|Meritxell]]<br />
<br />
Interested! [[User:Giovanni|Giovanni]]<br />
<br />
Ditto - Skyler<br />
<br />
Me too. &mdash;[[User:Lfriedl|Lisa]]<br/><br />
<br />
Me three. [[User:RobMills|RobMills]]<br />
<br />
I'd be willing to run such a tutorial. However, I would have to consult with some/all of the interested parties to find out what kind of statphys you want to learn about. There are a huge number of possible topics, one could start with basics like ensembles, or perhaps people are interested in master equation and other non-equilibrium techniques, or maybe critical phenomena is what people are interested in. I really do not know. (Orion)<br />
<br />
Can you give us who are not physicists an introduction about a kind of special questions that you will think it from the viewpoint of physicists? Like complex network, dynamic, also something else, what is the most important measurement and dynamic process you want to observe? -[[Jiang_Wu|Jiang]]<br />
<br />
== Modern Logic and Reasoning ==<br />
Like I mentioned in the 'ice-breaking', I could tell something about application of modern logic into human reasoning. It's a very board topic, and very new. Criticisms are welcome and needed. I would give some basic examples. On top of that, I would also say some development of logic, and how I found it useful in research, which might seem un-related to logic, esp. in social science. I am planning to give a 15 to 20 minutes presentation, UNLESS people want to hear more, in that case, please let me know.<br />
QiQi<br />
<br />
<br />
<br />
I'm interested! [[Kathleen_Sprouffske|Kathleen]]<br/><br />
Me too! [[kolbjorn|Kolbjørn]]<br/><br />
Sign me up. &mdash; [[User:Jreyes|Josh]]<br/><br />
I'm interested too! (Flavia)<br/><br />
I'm in! [[Srideep_Musuvathy|srideep]]<br/><br />
I'm in too [[User:Giovanni|Giovanni]] <br/><br />
Count me in - Skyler<br/><br />
I'd be interested in this as well. [[Tanja_Gesell|Tanja]]<br />
<br />
Please remind by email or somhow.. and sign me up! [[User:sonotto|Sonja]]<br />
<br />
I am in Qi, But where? Rio<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Time at June 10th, 03.15 p.m. - 03.35 p.m.<br />
[[CSSS 2008 Santa Fe-Schedule]]<br />
<br />
== Introduction to the Design and Analysis of Computer Experiments ==<br />
How do you find "interesting" behavior when your computer model is too slow or the inputs are too many to try every possible combination? Using an Arctic sea ice simulator example, I will show you how modern statistical methods can help you explore your virtual world more efficiently. Check out this brief<br />
[http://www.stat.sfu.ca/~dbingham/NICDS_CompExpt/research.html overview] or a more technical paper about<br />
[http://www.schonlau.net/publication/jogo98.pdf global optimization].<br />
Time permitting we could also touch on some of the statistical concepts involved, e.g. cross-validation, maximum likelihood estimation, or Bayesian statistics.<br />
[[B%C3%A9la_Nagy|Béla]]<br />
<br />
== Genomics / Central dogma overview ==<br />
It seems like some of you might be interested in an overview of the central dogma of molecular biology to non-biologists. This could be an 1h tutorial on the major actors of gene expression: nucleus, chromosomes, chromatine, DNA, RNA (tRNA, mRNA), proteins, polymerases, ribosomes, transcription factors, and eventually a quick intro to small, non-coding RNAs as a bonus. Although being a bioinformatician by training, I'm happy to leave the way if a "hard core" biologist wants to do this tutorial (Molly ?). Edit if interested! Jean<br />
<br />
I'd be happy to attend a tutorial in 'genomics for idiots' -- Laura<br />
<br />
Me too. I am also interested in metagenomics if this is not too much of course. -- Francois<br />
<br />
I'd like to go to a 'genomics for idiots' tutorial as well. -- [[Srideep_Musuavthy|srideep]]<br />
<br />
Ok, so I'll prepare some slides. How about Monday 9th, 5p - 6p (location TBA) ? -- Jean<br />
<br />
== Artificial Intelligence/Machine Learning ==<br />
I (Nish) could introduce some of the basic methods in AI/ML. If there is significant interest in the two fields separately, I could do two tutorials. Would probably focus on the higher level, rather than the nitty-gritty details, as well as applications of the methods to real problems. I'm not necessarily an expert, although have a fair amount of experience in the area, so I would prefer a more interactive session, where questions can be answered by everyone.<br />
<br />
Sign me up. &mdash; [[User:cyepez|Carlos]]<br><br />
I'm also interested. -[[Sarah_Cobey|Sarah]] <br><br />
Me too! [[Flavia_Feitosa|Flávia]]<br />
<br />
How about "AI/MI for dummies", Nish? I've been wondering about it.... Rio<br />
<br />
== A Crash Course to Classical and Evolutionary Game Theory ==<br />
Game theory is the study of interactive decision making. Classical game theory aims to develop a general theory to describe how rational agents interact strategically. In many cases humans lack the kind of infinite computational power and time assumed by classical game theory. In the early 1970s the biologist John Maynard Smith introduced evolutionary methods to the field, dispensing with the assumption of hyper-rationality while changing many of the concepts central to the field along the way. The result was evolutionary game theory. This new framework has been used to model the behavior of fundamentally non-rational players (such as viruses) as well as humans. <br />
<br />
In this tutorial, I'd try to introduce the basic concepts in both of these fields, namely, the definition of a game, payoffs, the Nash equilibirum and evolutionarily stable strategies, the replicator dynamics. I'll briefly mention the three basic classes of two-strategy games represented by the Prisoner's Dilemma, the Snowdrift Game (sometimes called the Hawk-Dove game or Chicken), and the Stag Hunt Game. Depending on particular interests of the group, we could prove the Bishop-Cannings theorem and give a classification of all symmetric two-strategy games; or look at updating methods and spatial chaos; reputation and image scoring; rock-paper-scissors in biological systems; or evolutionary branching and specialization.<br />
<br />
If there's something else you'd like to know about EGT, shoot me ([mailto:joshua.reyes@removeme.gmail.com Josh]) an email, and I'll see if I can dig up something I know on your topic. I'm not going to require any fancy mathematical background. If you've seen a 2&times;2 matrix before, great. Otherwise, it's not a big deal. We won't multiply them or calculate their eigenvalues. They'll just serve as a means for bookkeeping.<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Some of us are also thinking about setting up a [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Evolutionary_Game_Theory|working group]] as well.<br />
<span style="color: red; font-weight: bold;"><br />
<br/>Update 2!</span> This has been scheduled on Friday from 3 - 5, location TBD. <br />
<br />
*I'll sign up for this. Kolbjørn<br />
*I'm interested too! (Flavia) <br />
*I'll be there too. Kathleen<br />
*I'm in. Jean<br />
*I'm interested as well. Steve<br />
*will be there at 3 [[Walter_Zesk|Walt]]<br />
*I'll be there, Petr<br />
*Good stuff. I could also say a few things about [http://www.iiasa.ac.at/Research/EEP/AdaptiveDynamics.html adaptive dynamics], if there's interest. [[Sarah_Cobey|Sarah]]<br />
*I'll be there. [[Jiang_Wu|Jiang]]<br />
<br />
== Resilience of social-ecological systems ==<br />
The resilience perspective is increasingly used as an approach for understanding the dynamics of social–ecological systems. Essential for the resilience perspective is the recognition that living systems are not in equilibrium but rather in a domain of attraction. <br />
Many dynamic systems, however, have multiple domains of attraction. Moreover, self-organizing processes can create or change the shape and depth of this domain of attraction. Within the resilience perspective, new pathways of sustainable development can be represented by crossing a threshold from a domain of attraction and/or by creating new domains. Resilience is a measure of how much change or disruption is required to transform a system from being maintained by one set of mutually reinforcing processes and structures to a different set of processes and structures.<br />
If you are interested we (Mike and Dirk) can introduce you to some of the insights developed by the [http://www.resalliance.org/1.php resiliance alliance] and the challenges we face in understanding these kind of systems.<br />
<br />
I am interested in this too. Richard<br />
<br />
Very interested, any idea of when you will do it? [[Walter_Zesk|Walt]]<br />
<br />
I'm interested as well. Steve<br />
<br />
I'm interested too. - Skyler<br />
<br />
I think to contribute from my previous work on SES. Rio<br />
<br />
== Introduction to classical control theory ==<br />
I (Srideep) can offer a 'quick' tutorial on control theory/control systems. This is will be a simple introduction to the motivation, basic ideas, issues and jargon in the field. If you are interested, please let me know about your background in linear algebra, complex analysis and calculus. Depending on the background, I might spend more or less time introducing the field. <br />
<br />
Ideally, if you know what eigenvalues and eigenvectors of a matrix are, what a pole of a complex function is and how the solution of a linear differential equation looks like, you are ready to jump right into controls. If the words above don't mean much at all, then we can run a quick 'review' of what they mean intuitively. <br />
you can sign up here or send me an email [mailto:srideep.musuvathy@gmail.com srideep]<br />
<br />
<span style="color: red; font-weight: bold;">Update!</span> Lets plan on discussing this early next week. Will fix up a time by the end of this week. Liz bradley will be done with her introduction to dynamics and the eigenvalue, eigenvector tutorial will be done this friday. This will make my life easier! :-)<br />
<br />
I'd be very interested in this tutorial. I think I'm basically OK on the prerequisites, <br />
but I wouldn't be annoyed by a review. Perhaps Monday? -- Laura<br />
<br />
I'm in too. I guess I should be ok on linear algebra, calculus and linear ODEs, but I don't know what the pole of a complex function is. Jean<br />
<br />
I'm in. If we can start with 'pole' thing, that would be wonderful. - Masayoshi<br />
<br />
Hi Srideep, please put me in this group. About my background on the subjects you asked; zero!!! Sorry. Rio<br />
<br />
Definitely interested in this. - Jacob<br />
<br />
I'm in. Paul<br />
<br />
Looks cool. -[[Sarah_Cobey|Sarah]]<br />
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== Topology/algebra ==<br />
I (Srideep) will also be happy to talk about topology, introducing the concepts of point-set topology. The language of modern mathematics is enshrined in the concepts of point-set topology. I can also talk about group theory and introduce abstract algebra to those interested. In my opinion, it is the most powerful gateway into abstract thinking. sign here or email me [mailto:srideep.musuvathy@gmail.com srideep]<br />
<br />
I'd be very interested in that. Jean<br />
<br />
I'd be interested to see what you cover in the topology section. Algebra, however, is for the birds :) Paul<br />
<br />
Srideep, can you do an introduction to category theory? Or would you be interested in co-organizing a tutorial with me? - Jacob<br />
<br />
I'm very interested. Abby<br />
<br />
== Eigenvalues - what are they and how to find them? ==<br />
I (Kolbjørn) can put together a brief and elementary introduction to eigenvalues and eigenvectors if anyone have an urge for this. Sign up or e-mail and we'll schedule something. [mailto:kolbjorn@chalmers.se Kolbjørn]<br />
<br />
<span style="color: red; font-weight: bold;">UPDATE!</span> Time: Friday June 6th, 01.00 p.m. - 03.00 p.m. If this collides with other stuff, please yell out! [[CSSS 2008 Santa Fe-Schedule]]<br />
<br />
Yes please. [[Kathleen_Sprouffske|Kathleen]]<br />
<br />
I am also very interested [[Walter_Zesk|Walt]]<br />
<br />
I'm in as well [[ Mark_Rivera|Mark]]<br />
<br />
Please - have always been kind of confusing to me. [[Jonathan_Zelner|Jon]]<br />
<br />
Let me in - Masayoshi<br />
<br />
I'm also interested! [[ Flavia_Feitosa|Flavia]]<br />
<br />
I'll be there. -[[Molly_Rorick|Molly]]<br />
<br />
I'm in as well. -[[Tanja_Gesell|Tanja]]<br />
<br />
Me too! '''Just to remind'''; I think Classical and Evolutionary Game Theory (Josh)will be started at 3 PM. Rio<br />
<br />
== How your computer works ==<br />
<br />
Nish and Laura can give a joint tutorial on 'how your computer works'. What happens when I type 'www.santafe.edu' in my browser? How does a web server at santafe.edu handle all those incoming requests? What happens when I use a WiFi access point? Basically, we'd be happy to take your questions about how your computer works and do our best to answer them - we're also happy to have other co-tutors. <br />
<br />
Let us know if there's interest [mailto:lmfeeney@sics.se Laura], we'd probably schedule later next week, to not conflict with tutorials that focus on maths and other project prerequisites.<br />
<br />
I would love this. -[[Sarah_Cobey|Sarah]]<br />
<br />
== How your hardware works ==<br />
Along the same lines as the computer tutorial, I've found myself discussing hardware with a number of folks. And why hardware matters from a massive parallelism perspective (which is quite common in the complex research areas I've encountered). If folks are interested, I can give a rough overview of the way hardware works in different types of computers and supercomputers (as much as I understand of it) as well as how to best leverage that knowledge.<br />
<br />
== Computational Physics for Non-physicists or A small introduction into Applied Physics ==<br />
<br />
I've seen that many people are interested in physics. I could give an introduction to "computational" physics - this means physics with a PC. Actually, it is very broad and gives some basics for simulations (interesting for all simulation-folks):<br />
<br />
- What is a 'random number generator' and why should I know something about it?<br />
<br />
- What are Master-equations?<br />
<br />
- The Ising-model / Voter-model<br />
<br />
- The Central Limit Theorem or why does it make sense to average over multiple runs of a simulation?<br />
<br />
- ...<br />
<br />
[[Ruben Kubiak|Ruben]]<br />
<br />
I'm very interested [[Nish_Aravamudan|Nish]]<br />
<br />
I'm in too. [[Jiang_Wu|Jiang]]<br />
<br />
[[Srideep_Musuvathy|srideep]] is in.<br />
Sounds great. [[Molly_Rorick|Molly]]<br />
<br />
==Information Theory==<br />
An open discussion of Shannon information theory (would like some help in presenting this part clearly) and then some newer results from its application to cellular automata (and potentially other complex systems).<br />
<br />
Interesting. I remember something from the master course I took. [[User:Giovanni|Giovanni]]<br><br />
I'd love to participate. -[[Sarah_Cobey|Sarah]]<br><br />
I'm interested.[[Holger_Keeler|Paul]]<br><br />
I'm in. --[[User:Lfriedl|Lisa]]<br />
<br />
I'm in. --[[User:meritxell|Meritxell]]<br />
<br />
==Cellular Automata==<br />
CAs (particularly ECAs) are a very interested model of computation. How do 8 rules (ECA 110, e.g.) emulate a Turing Machine? Why is that interesting? What can we learn about what defines computation given CAs? Maybe we can also discuss some simple computational (Turing) theory.<br />
<br />
==A little analytical tool-box: Non-linear dynamics, ODEs, PDEs...==<br />
The [[David_Foster|Brothers]] [[Jacob_Foster|Foster]] would be happy to offer some tutorials on analytical methods. Depending on what Alfred Hubler covers, we can do some fraction of Strogatz (flows on the line & circle, bifurcations, maybe linear systems, index theorem, etc.), as well as offering a basic introduction to solving linear ODEs (no theorems, just techniques) and simple PDEs like the heat equation, with boundary conditions. Ideally this would come after Kolbjørn's eigen-stuff course, so we can just assume familiarity with that.<br />
<br />
We've put a tentative time for our tutorial on the schedule: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 3:15pm]]. Let us know if this doesn't work out for some reason and we can try to change it.<br />
<br />
These are fun topics! I never get enough of them! -- [[Srideep_Musuvathy|srideep]]<br><br />
Sounds great. [[Molly_Rorick|Molly]]<br><br />
Interesting -- sure. [[User:Lfriedl|Lisa]]<br><br />
Very useful! [[Kathleen_Sprouffske|Kathleen]]<br><br />
Need this.... Rio <br><br />
I'm in! [[Flavia_Feitosa|Flávia]]<br />
<br />
==Linguistics==<br />
Can someone (I don't know [[Peter_Graff|who]]) perhaps offer a tutorial on basic linguistics stuff? I am particularly interested in generative grammar and coverage of the Chomsky "Three Models" paper, but maybe there are more interesting topics to be discussed these days... -Jacob<br />
<br />
==Fitting models to data==<br />
A few people have asked me for a brief review of fitting models to data, but I'd like to know what methods interest you. I could start with least squares and progress to Bayesian approaches, maximum likelihood, and some more recent developments in methods for exploring space (GAs, particle filters, MCMC) with which I'm familiar. I'm by no means an expert in all these topics, so please add your name below if there's something you'd like to learn about (a particular method or method for a particular context) or teach. I feel like this tutorial would be most appropriate for the third or fourth week. -[[Sarah_Cobey|Sarah]]</div>RobMillshttps://wiki.santafe.edu/index.php?title=User:RobMills&diff=14134User:RobMills2008-06-05T19:18:17Z<p>RobMills: </p>
<hr />
<div>Please see my [[Rob_Mills|profile]]</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=13259Rob Mills2008-05-15T09:55:55Z<p>RobMills: </p>
<hr />
<div>I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't repeat myself here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (eg hiking/running/skiing/biking) and juggle occasionally. <br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=13258Rob Mills2008-05-15T09:55:30Z<p>RobMills: </p>
<hr />
<div>I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. My answers to Dan Rockmore's questions below are a good introduction to my research, so I shan't say any more here. I have a general love for the outdoors, and in my free time I enjoy travelling and many sports (eg hiking/running/skiing/biking) and juggle occasionally. <br />
<br />
I am very much looking forwards to meeting all of you out in Santa Fe!<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=13090Rob Mills2008-05-07T22:03:42Z<p>RobMills: </p>
<hr />
<div>I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. I'll say some more about myself very soon, but for now I'll just post my answers to Dan Rockmore's questions.<br />
<br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
----<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=13089Rob Mills2008-05-07T22:02:19Z<p>RobMills: </p>
<hr />
<div>=== Rob Mills === <br />
[[Image:Rmm-kai-iwi.JPG | right]]<br />
<br />
<br />
I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. I'll say some more about myself very soon, but for now I'll just post my answers to Dan Rockmore's questions:<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=Rob_Mills&diff=13088Rob Mills2008-05-07T21:57:11Z<p>RobMills: </p>
<hr />
<div>[[Image:rmm-kai-iwi.jpg |right]]<br />
<br />
I'm a graduate student in the Natural Systems research group at the University of Southampton, in the UK. I'll say some more about myself very soon, but for now I'll just post my answers to Dan Rockmore's questions:<br />
<br />
'''1. what are your main interests? Feel free to include a "pie in the sky" big idea!'''<br />
<br />
My thesis research aims to understand evolutionary processes and how we can exploit these in a computational problem-solving sense. More specifically, I am interested in modelling macro-evolutionary trends such as the major transitions in evolution through symbiotic (and ultimately symbiogenic) relationships. Understanding under what conditions symbiotic associations will form, and what selective advantages exist for the composite entities formed in this manner are key questions in my work. Considering these same ideas from an engineering perspective, I am looking at how the combination of pre-adapted genetic material in collaborative groups can provide a bottom-up approach to automatic problem decomposition. <br />
<br />
One of my long-term aims for this research is to develop general methods that can identify & reveal decompositions automatically in a broader class of systems, including those where a solution is not trivial even when a decomposition is known. Indeed a strong motivator is from engineering a solution to a medical application, where I believe the very simplistic decomposition used could be significantly improved upon.<br />
<br />
My thesis aside, I am interested in almost any evolutionary process; the evolutionary biology that I have been exposed to fascinates me.<br />
<br />
'''2. What sorts of expertise can you bring to the group?'''<br />
<br />
I have working knowledge of evolutionary algorithms, and artificial life modelling. My understanding in evolutionary biology is limited to processes, rather than knowledge of any biological systems in particular. Whilst not obviously relevant, I have had some exposure to silicon chip design and testing. The systems-level design and general design methodology does influence the way that I approach a problem. On a very technical front, I can program in a few languages (c, matlab, perl).<br />
<br />
'''3. What do you hope to get out of the CSSS?'''<br />
<br />
I look forward to developing my knowledge in the theory of networks and non-linear dynamics, and in more general I'd like to improve the rigour of the approach I take to understanding complex systems.<br />
<br />
I hope to be exposed to complex systems study from disciplines outside my own: I'd like to find out what else I could get involved in later in my career (not much later!), using the skills and understanding that I have developed through my thesis research.<br />
<br />
'''4. Do you have any possible projects in mind for the CSSS?'''<br />
<br />
I am drawing close to the end of my doctoral research, and I'd really like to use the opportunity of working with researchers from the broad set of disciplines that complexity brings together to explore questions that I am not intimately familiar with. For instance, I'd be very keen to pursue a project that asks questions in ecology, financial markets, or climate modelling.</div>RobMillshttps://wiki.santafe.edu/index.php?title=File:Rmm-kai-iwi.JPG&diff=13086File:Rmm-kai-iwi.JPG2008-05-07T21:52:26Z<p>RobMills: Rob Mills profile pic</p>
<hr />
<div>Rob Mills profile pic</div>RobMills