| Home | Complex Networks | Structural Bioinformatics | Network Medicine | Network Biology |
| Transportation Systems | Notebooks | Publications | Bookshelf |
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