BO4012 Computational Systems Biology Syllabus:
BO4012 Computational Systems Biology Syllabus – Anna University PG Syllabus Regulation 2021
OBJECTIVES
The course aims to,
•Introduce Systems Biology concepts, Graph theory, network models and properties.
•Familiarize with data resources and tools, kinetic modelling and flux balance analysis.
•Understand network motifs, SBML and genome scale modelling.
UNIT I INTRODUCTION TO NETWORKS
Introduction to Systems Biology, Systems level understanding of biological systems. Basic concepts in Systems modeling, Networks and graph theory: Basic properties of Network: Degree, average degree and degree distribution. Adjacency matrix, weighted and unweighted networks, Bipartite network, Paths and distances, Random Networks: Erdos-Renyi model, Small-world effect, clustering coefficient, Scale-free networks: Power laws, Hubs, ultra-small property, degree exponent, The Barabasi-Albert Model. Degree correlations: assortativity and disassortativity.
UNIT II KINETIC MODELING
Kinetic modelling of biochemical reactions, describing dynamics with ODEs, rate equations, deriving a rate equation, incorporating regulation of enzyme activity by effectors, E-cell platform and erythrocyte modeling
UNIT III FLUX BALANCE ANALYSIS
Introduction to Flux balance analysis, Construction of stoichiometric matrices, Constraint based models. Network basics, examples of mathematical reconstruction of transcriptional networks and signal transduction networks.
UNIT IV NETWORK MOTIFS AND MODELS
Network motifs, Feed forward loop network motif. Gene circuits, robustness of models, Chemotaxis model, Integration of data from multiple sources: Building genome scale models.
UNIT V RESOURCES AND SBML
Tools and databases for modeling: Pathway databases KEGG, EMP, Metacyc, Enzyme kinetics database BRENDA, Gene expression databases, Biomodels database, Basics of Systems Biology Markup Language (SBML), SBML editors.
TOTAL: 45 PERIODS
OUTCOMES:
At the end of the course students will be able to,
CO1 Understand Systems Biology concepts, network models and properties from biological networks perspective
CO2 Understand the design of kinetic models, flux balance analysis and interpret results
CO3 Get acquainted with the steps involved in genome scale modeling
REFERENCES
1.Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald,“Systems Biology a Textbook”, Wiley-CH, 2nd Edition,2016
2.Uri Alon, “An introduction to Systems Biology: Design Principles of Biological Circuits”, Chapman and Hall /CRC,2006
3.EddaKlipp, Ralf Herwig, Axelkowald, Christoph Wierling, Hans Lehrach,“Systems Biology in Practice: concepts, implementation and application”,Wiley-VCH,2005
4.Hiroaki Kitano, “Foundations of Systems Biology”, MIT Press,2001
5.Lilia Albhergina, Hans V Westerhoff “Systems Biology: Definitions and perspectives”, Springer Publications, 2008