Embedded Files
Professor: Sergi Valverde (Institut de Biologia Evolutiva, CSIC-UPF).
Complex Networks Tools
Netlab Lite (link): This is a compact, on-line version of the Netlab platform that I have developed over the years. Netlab allows students to code (using the programming language Wren ) their own network models and analysis tools. Netlab lite works directly from the web browser (it requires WebGL, Firefox is recommended), and without additional installations.
Network Attacks (link): Learn about network fragmentation and the concept of percolation with this interactive website. How many nodes would you have to remove to break up an urban network?
Path Length (link): Interactive visualization of shortest path lengths.
Random Graph (link): Random graphs are used as null models when assessing the significance of network patterns. The Erdös-Renyi model creates random graphing with a given number of nodes and a fixed link probability.
Small Worlds (link): Add 10 shortcuts in order to minimise the average path length in the urban network.
Preferential Attachment (link): Generates a scale-free graph by a process of "preferential attachment", in which new nodes prefer to make a connection to the more popular existing nodes.
Network Modularity (link): Generates a random modular network and computes its modularity values.
Vaccination Game (link): Fight against the spreading of infectious diseases in different types of networks. After distributing a limited number of vaccines, the infectious outbreak spreads and the player quarantines individuals at the risk of becoming infected.
The above models have been all developed by Sergi Valverde with the Netlab system. They require a WebGL-compliant web browser.
Some References
Mark Newman (2010) Networks: an introduction, Oxford University Press. http://www-personal.umich.edu/~mejn/
Melanie Mitchell (2009) Complexity: a guided tour, Oxford University Press. http://web.cecs.pdx.edu/~mm/
Steven H. Strogatz (2001) Nonlinear dynamics and chaos: with applications to physics, biology, chemistry and engineering (studies in nonlinearity), Westview Press. http://www.stevenstrogatz.com
Ricard V. Solé (2009) Redes complejas: del genoma a internet, Tusquets (Metatemas). http://complex.upf.es/~ricard
Ricard V. Solé (2011) Phase transitions, Princeton University Press.
Albert-Laszlo Barabasi and Reka Albert (1999) Emergence of scaling in random networks, Science 286 (5439). https://arxiv.org/pdf/cond-mat/9910332.pdf
Duncan J. Watts and Steven H. Strogatz (1998) Collective dynamics of ‘small-world’ networks, Nature 393 (6684). http://worrydream.com/refs/Watts-CollectiveDynamicsOfSmallWorldNetworks.pdf https://en.wikipedia.org/wiki/Watts_and_Strogatz_model
Geoffrey West (1999) The origin of universal scaling laws in biology, Physica A. http://www.cs.cornell.edu/~ginsparg/physics/Phys446-546/gbwscl99.pdf
Sergi Valverde and Jordi Garcia-Ojalvo (2016) Hacia una teoría unificada de la criticalidad biológica. Investigación y Ciencia, Marzo 2016 (N. 474). http://www.investigacionyciencia.es/revistas/investigacion-y-ciencia/numero/474/hacia-una-teora-unificada-de-la-criticalidad-biolgica-13970
Spatial Networks
Citation: J. Buhl, J. Gautrais, N. Reeves, R. V. Solé, S. Valverde, P. Kuntz, G. Theraulaz "Topological patterns in street networks of self-organized urban settlements" (2006) European Physical Journal B - Condensed Matter and Complex Systems 49(4): 513-522 (Journal, PDF, Scholar).
Social Networks
Jazz musicians network (Gephi): List of edges of the network of Jazz musicians.
Citation: P. Gleiser and L. Danon, (2003) Advances in Complex Systems 6, 565 (Journal, PDF, Scholar).
Software Networks
Citation: S. Valverde, R. Ferrer-Cancho, R. V. Solé "Scale-free networks from optimal design" (2002) Europhysics Letters 60 (4), 512 (Journal, PDF, Scholar).
Citation: S. Valverde, R. V. Solé "Logarithmic growth dynamics in software networks" (2005) Europhysics Letters 72 (5), 858 (Journal, PDF, Scholar).
Netlogo Models
Erdös-Renyi (NetLogo): Generates a random graph by adding an edge between each pair of nodes with given probability. This model was adapted by L. Adamic from the U. Wilensky's Giant Component model in NetLogo's models library.
Erdös-Renyi + Average Shortest Path (NetLogo): Generates a random graph and computes the average shortest path between all pairs of nodes in the largest connected component. This model was adapted from the Erdös-Renyi code.
Preferential Attachment + Fitting Exponent (NetLogo): Generates a scale-free graph by a process of "preferential attachment", in which new nodes prefer to make a connection to the more popular existing nodes. This model was adapted from the U. Wilensky's Preferential Attachment in NetLogo's models library.
Tinkering model + Fitting Exponent (NetLogo): Generates a scale-free network by a process of duplication of rewiring, in which new nodes inherit connections of randomly chosen targets. This model by Sergi Valverde was adapted from the U. Wilensky's Preferential Attachment in NetLogo's models library. Citation: R. V. Solé and S. Valverde "Spontaneous Emergence of Modularity in Cellular Networks" (2008) J. R. Soc. Interface, 129-133 (Journal, PDF, Scholar).
Links
Sergi Valverde (Twitter, Scholar)
Evolution of Technology Lab (Web)
Institut de Biologia Evolutiva (IBE) (Web)
Institut de Biologia Integrativa de Sistemes (I2SysBio) (Web)
Complexitat.cat (Web)
Gephi (Web, Yosemite Instructions)
Netlogo (Web)
Complex Networks Resources (Web)
Google Sites
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