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OE60247: Modeling and Analysis of Biological Complex Systems

Summer 2013 @ Indian Institute of Technology Jodhpur.

Duration: 9 weeks (13 May 2013 -- 9 July 2013 )

Credits: 4 (Four)

Students: 14 (BTech-1st year[1], BTech-2nd year[3], BTech-3rd year[2], MTech 1st year [2], MTech 2nd year [4], PhD [2]).

Broad topics covered in the course:

  • Notion of a systems, complex system, complexity of biological systems.

  • Introduction to graph theory

  • Topological properties of a graph/network

  • Small-world networks

  • Watts and Strogatz model

  • Scale-free networks

  • Barabasi-Albert strategy for evolution of scale-free networks

  • Error and Attack tolerance of scale-free networks

  • Proteins: Structure, function and folding

  • Residue Interaction Graph (RIG) models of protein structures

  • Long-range Interaction (LIN) models of protein structures

  • Properties of RIG and LIN models

  • Protein-Protein Interaction Networks (PINs)

  • Topological properties of PINs

  • Gene Coexpression Networks (GCN)

  • Gene Regulatory Networks (GRN)

  • Anatomical Networks

  • Neuronal connectivity and functional models of brain

  • Ecological Networks (Food webs and Landscape networks)

  • Prevalence of regulatory motifs in various networks

  • Algorithms for generating generic features of RIGs and GRNs

Reference book:

"The structure of complex networks" by Ernesto Estrada

Reading materials:

  • "Collective dynamics of ‘small-world’ networks", Duncan J. Watts and Steven H. Strogatz, Nature, 393, 1998.

  • "Scale-Free Networks", A-L Barabasi and Eric Bonabeau, Scientific American, May 2003, pp 50-59.

  • PDB-101: Molecular Machinery: A Tour of the Protein Data Bank

  • PDB-101: What is a protein?

Illustrative research papers discussed in the class:

  • "Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks", Javier De Las Rivas and Celia Fontanillo, PLoS Computational Biology, 6(6), e1000807 (2010)

  • "A Protein–Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje Cell Degeneration", J Lim et al., Cell 125, 801–814 (2006).

Educational videos (TED-talks) referred in the class:

  • "A map of the brain" by Allan Jones

  • "The real reasons of the brain" by Daniel Wolpert

  • "How complexity leads to simplicity" by Eric Burlow