ELL 707, I semester 2015-16
This is the the webpage for ELL 707, I semester 2015-16
Systems Biology
Instructor
Shaunak Sen
E-mail: shaunak.sen@ee.iitd.ac.in
Lectures: MW 11:00-11:50am, Th 12:00-12:50pm
Room: Block IIA - 201
Announcements
23.11.2015: MAJOR TEST scheduled from 6PM-8PM on Mon, 23.11.2015 in II-LT1. Please check Exam Schedule for up-to-date information.
07.10.2015: HW2 posted.
07.10.2015: MINOR TEST 2 scheduled from 4-5PM on Sun, 11.10.2015 in II-LT1. Please check Exam Schedule for up-to-date information.
28.08.2014: MINOR TEST 1 scheduled from 4-5PM on Wed, 02.09.2015 in II-LT1. Please check Exam Schedule for up-to-date information.
18.08.2015: HW1 posted.
23.07.2015: Webpage online.
Lectures
| S. No. | Date | Topic | Advised Reading | Homework |
| 1 | Week 1
(Jul 23) | Overview
Biological Systems | | |
| 2 | Week 2
(Jul 27, 29, 30) | Biology as a System
Feedback, Dynamics, Models | del Vecchio & Murray Ch. 1 | |
| 3 | Week 3
(Aug 3, 5, 6, 7) | Models
Law of Mass Action
Signaling Systems
Protein Production-Degradation
Repression | del Vecchio & Murray Ch. 2 | |
| 4 | Week 4
(Aug 10) | Negative Feedback | del Vecchio & Murray Ex. 2.2 | |
| 5 | Week 5
(Aug 19, 20) | Positive Feedback
Probabilistic Modelling | | HW1 |
| 6 | Week 6
(Aug 24, 26, 27) | Chemical Master Equation
Discussion: Separation of Timescales | del Vecchio & Murray Ch. 4 | |
| 7 | Week 7
(Sep 2 - MINOR TEST 1, 3) | Dynamics
Effect of Feedback on Speed of Response | del Vecchio & Murray Sec 5.2
Lecture Notes | |
| 8 | Week 8
(Sep 7, 9, 10) | Linearization
Equilibrium Point = Steady-State = Fixed Point
Projects | del Vecchio & Murray Sec. 3.1 | |
| 9 | Week 9
(Sep 14, 17) | Multiple Steady-States
Stability
Effect of Positive Feedback
Examples | Examples | |
| 10 | Week 10
(Sep 21, 23, 24) | Toggle Switch
Pulsed Responses
Example
Projects | del Vecchio & Murray 5.3
Handout
Lecture | |
| 11 | Week 11
(Sep 28, 30, Oct 1) | Oscillations
Negative Feedback + Delay
Negative Feedback + Positive Feedback | Handout
Code
del Vecchio & Murray 3.3, 5.4, 5.5
B. Novak & J. J. Tyson, 'Design Principles of Biochemical Oscillators’, Nat. Rev. Mol. Cell. Biol., 9(12), 2008. | |
| 12 | Week 12
(Oct 5, 7, 11 - MINOR TEST 2) | Examples
Projects | Lecture | HW2 |
| 13 | Week 13
(Oct 12, 14, 15) | Projects
Control
Robustness to Perturbations
Concentration Robustness | del Vecchio & Murray Sec. 1.3 | |
| 14 | Week 14
(Mid-Semester Break) | | | |
| 15 | Week 15
(Oct 26, 29) | Chemotaxis in E. coli | Lecture
del Vecchio & Muray 5.7 | |
| 16 | Week 16
(Nov 2, 4, 5) | Projects
Feedforward Loops | del Vecchio & Murray 5.6 | |
| 17 | Week 17
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| 18 | Week 18
(Nov 18) | Fold-Change Detection | Lecture |
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References
D. del Vecchio & R. M. Murray, Biomolecular Feedback Systems, Princeton University Press, 2014 (available online).
S. Strogatz, Nonlinear Dynamics and Chaos, Westview Press, 2001.
J. D. Murray, Mathematical Biology parts I & II, Springer 3rd edition, 2007.
U. Alon, An Introduction to Systems Biology, Chapman & Hall/ CRC Mathematical and Computational Biology, 2006.
E. Klipp et al., Systems Biology, Wiley-Blackwell, 2009.
N. G. van Kampen, Stochastic Processes in Physics and Chemistry, North-Holland 3rd edition, 2007.
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