GA-027 - Redes de Computadores - 2012.3

Last modified on Tuesday, September 11th 2012 at 7:03 PM.

Professor:

• Artur Ziviani (LNCC/MCTI)

Contatos: ziviani@lncc.br / Sala 2C-12

Participantes:

• Daniel Abrunhosa Fernandes
• Daniel Gaspar Gonçalves de Souza
• Fernanda Alves de Freitas Guedes
• Thiago Costa Dourado (*)

(*) ouvinte(s).

Livro básico:

• Computer Networking: A Top-Down Approach Featuring the Internet, James F. Kurose and Keith W. Ross, Addison Wesley

Outros livros:

• Computer Networks, Andrew S. Tanenbaum, Prentice Hall

• Computer Networks: A Systems Approach, Larry L. Peterson and Bruce S. Davie, Morgan Kaufmann

• Interconnecting with TCP/IP, Volume I: Principles, Protocols, and Architecture, Douglas E. Comer, Prentice Hall

Critérios de avaliação:

A anunciar.

Estrutura e material de aula:

Parte 0: Informes gerais (Slides)

Parte 1: Introdução (Slides)

Parte 2: Camada de Aplicação - Visão geral (Slides)

Parte 2.a: Teoria de redes complexas - básico (Slides)

Parte 2.b: Teoria de redes complexas - modelos de rede (Slides)

Parte 2.c: Teoria de redes complexas - exemplos de aplicação (Slides)

Leitura complementar:

Surveys da áreas de análise e modelagem de redes complexas

Statistical mechanics of complex networks, Réka Albert and Albert-László Barabási, Rev. Mod. Phys. 74, 47–97 (2002). (LINK)

The Structure and Function of Complex Networks, M. E. J. Newman, SIAM Rev. 45, pp. 167-256 (2003). (LINK)

Characterization of complex networks: A survey of measurements, Luciano da F. Costa, Francisco A. Rodrigues, Gonzalo Travieso, P. R. Villas Boas, Advances in Physics, Volume 56, pages 167 - 242, Issue 1 (2007). (LINK)

Artigos sugeridos para os temas a estudar atribuídos

1) Daniel Abrunhosa Fernandes

Brain Networks

The Small World of the Cerebral Cortex, Olaf Sporns and Jonathan D. Zwi, Neuroinformatics, vol. 2, no. 2, pp. 145-162, 2004. (LINK)

Complex brain networks: graph theoretical analysis of structural and functional systems, Ed Bullmore and Olaf Sporns, Nature Reviews Neuroscience 10, pp. 186-198 (March 2009). (LINK)

From gene networks to brain networks, Bota M, Dong HW, Swanson LW, Nature Neurosciences 2003 Aug;6(8):795-9. (LINK)

2) Daniel Gaspar Gonçalves de Souza

Nanonetworks

Nanonetworks: A New frontier in communications, Ian F. Akyildiz, Josep Miquel Jornet, and Massimiliano Pierobon, Communications of the ACM, vol. 54, no. 11, pp. 84-89, November 2011. (LINK)

Quantum Networking and Internetworking, Rodney Van Meter, IEEE Newtork, pp. 59-64, July/August 2012. (LINK)

NanoNS: A nanoscale network simulator framework for molecular communications, Ertan Gul, Baris Atakan, Ozgur B. Akan, Nano Communication Networks, Elsevier, vol. 1, no. 2, June 2010, Pages 138–156. (LINK)

3) Fernanda Alves de Freitas Guedes

Protein Networks (dica: procurar também pelo termo "System Biology" para avaliar se há ligação)

Comparative Analysis of Protein Networks: Hard Problems, Practical Solutions, Nir Atias and Roded Sharan, Communications of the ACM, vol. 55, no. 5, pp. 88-97, August 2012. (LINK)

Modular Biological Complexity, Christof Koch, Science, vol. 337, pp. 531-532, August 2012. (LINK)

Lethality and centrality in protein networks, H. Jeong, S. P. Mason, A.-L. Barabási, Z. N. Oltvai, Nature, vol. 411, pp. 41-42, May 2001. (LINK)

Evolution and dynamics of protein interactions and networks, E. D. Levy and J. B. Pereira-Leal, Current Opinion in Structural Biology, vol. 18, no. 3, pp. 349-357, July 2008. (LINK)

Network biology: understanding the cell’s functional organization, A.-L. Barabási, Z. N. Oltvai, Nature 427, 839-843 (2004), (LINK)

4) Thiago Costa Dourado

Community Detection

Detecting community structure in networks, M. E. J. Newman, Eur. Phys. J. B 38, 321–330 (2004). (LINK)

Community detection in graphs, Santo Fortunato, Physics Reports, vol. 486, nos 3–5, Pages 75–174, February 2010. (LINK)

Fast unfolding of communities in large networks, Vincent D. Blondel, Jean-Loup Guillaume, Renaud Lambiotte, and Etienne Lefebvre, Journal of Statistical Mechanics: Theory and Experiment, no. 10, October 2008. (LINK)

Modularity and community structure in networks, M. E. J. Newman, PNAS, PNAS, vol. 103 no. 23, June 2006. (LINK)

Repositórios de datasets

Stanford Large Network Dataset Collection (LINK)

Complex Network Resources (LINK)

Brain Connectivity Datasets (LINK)

Biological Networks - Datasets (LINK)

BioGRID - Biological General Repository for Interaction Datasets (LINK)

DIP - Database of Interacting Proteins (LINK)

Ferramentas de análise e/ou visualização

NetworkX - Python package (LINK)

igraph (LINK)

Boost graph library - C++ (LINK)

math-bgl - A graph library for Matlab based on the boost graph library (LINK)

Gephi - visualization tool (LINK)

Cytoscape - tool for analysis and visualization (LINK)

Tulip - visualization tool (LINK)

MCL-Edge (LINK)

Caret - package for structural and functional analyses of the cerebral and cerebellar cortex (LINK)

Brain Connectivity Toolbox (LINK)