Complex Systems Winter School 2015-Tutorials
From Santa Fe Institute Events Wiki
CSWS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.
You can schedule your own tutorial here, they will be held informally during the evening. Please do not schedule during other CSWS Lectures.
Tutorials can be given in the Visitors Hostel Conference Room on level 2.
try to use this template:
- 1 Bare minimum of Fractals
- 2 Social Networks: Understanding aid work through relational ontologies
- 3 Single-cell gene expression analysis and stem cell differentiation
- 4 Turning Concepts Into Networks
- 5 Perspectives on Cancer Evolution and Stem Cell Biology
- 6 Designing an anticipatory systems based on the concepts and tools of complexity theory
- 7 Phylogeny of metabolic networks: A spectral graph theoretical approach
- 8 Network science and video games
Bare minimum of Fractals
Speaker: Sagar Chakraborty
Date & Time & Place:' Friday, 11 Dec at 9:30pm in 1st floor conference room.
Content: Improvising on Chapter-11 of Strogatz's book on non-linear dynamics. .
Motivation: Fractals are mathematical objects with precise definition. Plan is to motivate the need of introducing fractals using not-so-rigorous mathematics.
Prerequisite: Love for maths for maths' sake.
Slides: Chalk/Pen and Board only.
Interested Participants: Katrina, Chakresh, Srashti Goyal, Bhumika Thakur, Promit, Cory, Prateek, Aaron
Social Networks: Understanding aid work through relational ontologies
Speaker: Emily Lynch
Date & Time & Place:' Tuesday, December 15, 20h45 - 21h30 ; 2nd floor conference room.
Content: It is an open question for me how to understand humanitarian aid in terms of complex systems. I've just finished a paper proposing that the network position of the aid worker increases their capacity to influence information exchange between clustering communities. In the paper, I argue that there has been a recent shift of aid workers' network position in a way that is reducing humanitarian space - e.g. making aid work more dangerous. .
Motivation: I'd like to present some of the work I've done, and use this case study/example to brainstorm how what we have learned so far about complex systems could apply to questions in social science, particularly those about power, agency, knowledge production, etc.
Slides: Chalk/Pen and Board only.
Interested: Isabel, Katrina, Chakresh, Bhumika, Saji, Cory, Pam, Prateek, Amanda
Single-cell gene expression analysis and stem cell differentiation
Speaker: Rhishikesh Bargaje, Aaron Taudt
Date & Time & Place: Wednesday, 16 December, 9:00pm, 2nd floor conference room.
Content: I will talk about recent advances in single-cell gene expression analysis. Currently, it's one of the hottest areas of research in biology. There are newer and newer methods/techniques being developed to generate and analyze such datasets. However, we still need advanced methods to derive meaningful, physiologically relevant information from such datasets. I will briefly introduce some of the different types of tools and techniques used in single-cell gene expression analysis. I also see that there is lot of interest in Stem cell research; in case there is enough motivation I can go through some of the basics of stem cell research.
Motivation: Majority of the tools that are being utilized for single-cell gene expression analysis are based on linear models. However, we know that most biological systems are not linear and you all are unique set of people that can bring newer insights to this field. So, I would like to sensitize you all to this new area.
Prerequisite: Beer!! (kidding of course). None.
Slides: I can share it on request.
Interested Participants: Rajesh, Sagar, Cory, Ria, Pam, Bhumika, Ravi, Amanda, Jeff, Ravins, Kiran
Turning Concepts Into Networks
Facilitator: Cory Cox
Date & Time & Place:' FRIDAY, 18 Dec at 9:00pm in 2nd floor conference room
Content: I will demonstrate what we do - at my startup - to help firms improve collaboration and communication. The goal is to show how you can build graphs/networks from purposively collected sociometric data (surveys for example) to measure concepts of interest. Goal is to give you a real world example and then talk about your own work to see how different approaches to data collection / graph construction can be used in your research. I am not the expert, just a facilitator... but together we can share ideas and generate some creative avenues for you to get started.' I also have a cloud solution for data collection and simple analysis that I would be happy to contribute to any collaborations anyone would like to do together. .
Motivation: Defining the network(s) and boundaries is difficult. And specifying exactly what a link between two nodes encodes about interactions or relations is not always intuitive.
Prerequisite: You are here... that's enough :)
Slides: I will post soon or after.
Interested Participants: Sagar, Chakresh, Bhumika, Rajesh, Aditya, Snehal,Srashti, Ben, Saji, Pam, Prateek, Ravi
Perspectives on Cancer Evolution and Stem Cell Biology
Speaker: Jeffrey Gerold, Rhishikesh Bargaje
Date & Time & Place: Friday, Dec. 18, 7pm in the second floor conference room
Content: Jeff will give a (very) brief overview of cancer research with a focus on open problems. In particular, cancer as a patient-specific and evolving disease of the genome will be the central theme. Time permitting, recent developments in therapy directions and biotechnology tools will be discussed to give some sense of what the future of cancer research might hold. Rhishi will cover the basics of stem cell research, describe pluripotency and how differentiated adult cells can be turned back into stem cells (called induced pluripotent stem cells).
Motivation: Cancer progression and stem cell differentiation occur through distinct but related pathways. We want to introduce these complex systems in an accessible way.
Prerequisite: Familiarity with biology recommended
Slides: Available on request
Interested: Rajesh, Pam, Cory, Kiran, Amanda, Chakresh
Designing an anticipatory systems based on the concepts and tools of complexity theory
Speaker: Ali Zackery (University of Tehran)
Date & Time & Place: Saturday, Dec. 19, 9:15 pm on the second floor conference room
Content: Imagine you are on a boat docked in a calm harbor and you want to quickly carry a brim-full cup of water across a stateroom without spilling. Now imagine the same situation but with the boat in rough seas. In harbor, the solution is simple: just walk quickly, but not so quickly that the water spills. At sea, speed is a secondary concern; now the real challenge is to maintain balance on an abruptly pitching floor. The solution now is to find secure handholds and footholds and to flex your knees to absorb the roll of the boat. In harbor, the solution is a simple optimization problem (walk as fast as possible but not too fast); at sea the solution requires you to enhance your ability to absorb disturbance— that is, enhance your resilience against the waves. The second metaphor is our society. How can complexity sciences help us improve decision making? Join so we can discuss!
Motivation: The most complicated systems are human decision making systems.
Prerequisite: Ability to participate in a late-night tutorial after a long day!
Slides: Available on request
Interested: Chakresh, Emily, Bhumika, Ben
Phylogeny of metabolic networks: A spectral graph theoretical approach
Speaker: Krishanu Deyasi (IISER Kolkata)
Date & Time & Place: Saturday, Dec. 19, 9:00pm - 9:15 pm on the second floor conference room
Content: Many methods have been developed for finding the commonalities between different organisms in order to study their phylogeny. The structure of metabolic networks also reveals valuable insights into metabolic capacity of species as well as into the habitats where they have evolved. We constructed metabolic networks of 79 fully sequenced organisms and compared their architectures. We used spectral density of normalized Laplacian matrix for comparing the structure of networks. The eigenvalues of this matrix reflect not only the global architecture of a network but also the local topologies that are produced by different graph evolutionary processes like motif duplication or joining. A divergence measure on spectral densities is used to quantify the distances between various metabolic networks, and a split network is constructed to analyse the phylogeny from these distances. In our analysis, we focused on the species that belong to different classes, but appear more related to each other in the phylogeny. We tried to explore whether they have evolved under similar environmental conditions or have similar life histories. With this focus, we have obtained interesting insights into the phylogenetic commonality between different organisms.
Prerequisite: None - It will be simple
Interested: Rajesh,Manisha, Ravins
Network science and video games
Speaker: Amanda Winburn
Date & Time & Place: Sunday, Dec. 20, 10pm-10:30pm in the second floor conference room
Content: I'm going to briefly discuss a couple of exciting articles that have applied network techniques to video games, including Mason and Clauset's work with Halo players (2013), and I'm going to give a short introduction to a project that I'm currently working on with Foldit (https://fold.it/portal/). I'm sure everyone is exhausted from the many lectures this week, so my talk will be informal. I'm going to bring green, rooibos, and ginger tea; if you would like some, please bring a mug and a bottle of water.
Motivation: Everyone loves talking about video games.
Prerequisite: None - this will be beginner-friendly. Social scientists especially welcome.
Interested: Ben, Aditya, Cory
Cory: here is something on video games my advisor wrote: