BIT1031 SYSTEM BIOLOGY L T P J C

3 0 0 0 3
Pre-requisite BIT 2001 / BIT 2004 Syllabus version
V.1.0
Course Objectives:
 It aims at system-level understanding of biology, and to understand biological systems as a
system. This means an examination of the structure and dynamics of cellular and organism
function, rather than the characteristics of isolated parts of a cell or organism.

Expected Course Outcome:

 Gives a holistic approach to decipher the complexity of biological systems by understanding
the interaction networks
 Provides an ability to predict how these systems change over time and under varying
conditions, and to develop solutions to health issues
 Provides an ability to design predictive, multiscale models that enables our scientists to
discover new biomarkers for disease, stratify patients based on unique genetic profiles,
and target drugs and other treatments

Student Learning Outcomes (SLO): 2, 4

Module:1 System-level Understanding of Biological 6 hours SLO: 2,4

Systems
Introduction - system level understanding of biological systems - Biological systems: Example.
Advanced measurement systems - cell lineage and its application

Module:2 Modeling the Activity of Single Genes 6 hours SLO: 2

Modeling the activity of single genes - Chemical reactions- Physical chemistry, The Basics of
Transcription, a probabilistic model of a prokaryotic gene and its regulation

Module:3 Modeling biochemical networks 7 hours SLO: 2

Atomic - level simulation and modeling of bio-macromolecules - molecular dynamics – the force field,
molecular dynamics methods – Monte Carlo methods

Module:4 Kinetic Models 7 hours SLO: 2

Kinetic models of excitable membranes and synaptic interactions - Kinetic models of ion channels –
Voltage-dependent Ion channels – Ligand gated synaptic ion channels

Module:5 Stochastic Models 6 hours SLO: 4

Stochastic simulation of cell signaling pathways – Limitations of deterministic models. A novel
stochastic simulator, Multistate molecules, signalling complex and allostery

Module:6 Virtual Biology Laboratory 6 hours SLO: 4

Modeling large biological systems from functional genomic data: Parameter estimation, cellular
simulation, towards a virtual biology laboratory, computational cell biology, the stochastic
approach.

Module:7 Simulation of the Whole Cell 5 hours SLO: 4

Computer simulation of the whole cell, computer simulation of the cell, human erythrocyte model
and its application, software for modeling and simulation, E-cell, and V-cell.

Module:8 Contemporary issues: 2 hours

Lecture by Industrial Expert

Total Lecture hours: 45 hours

Text Book(s)
1. Uri Alon, 2016 An Introduction to Systems Biology: Design Principles of Biological Circuits, 1st
Edition, Chapman & Hall/CRC publishers
Reference Books
1. Systems Biology: A Textbook- Axel Kowald, Christoph Wierling, Edda Klipp, and Wolfram
Liebermeister, 2016

2. Eberhard O. Voit, 2012, A First Course in Systems Biology, 1st Edition, Garland Science

Recommended by Board of Studies 03-08-2017

Approved by Academic Council No.47 Date 05.10.2017