Course Information: 2011/2012

Introduction to Laboratory Practices [2011 Aug Term]
Instructors: Raghu Padinjat, Deepak Nair, Sandeep Krishna, Madhu Venkadesan
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Scientific Communication [2011 Aug Term]
Instructor: Geoff Hyde
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Physical Biochemistry [2011 Aug Term]
Instructors: MK Mathew, Jayant Udgaonkar
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Cell Biology [2011 Aug Term]
Instructors: Satyajit Mayor and others
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Developmental Biology [2011 Aug Term]
Instructors: K VijayRaghavan and others
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Chemical Biology [2011 Aug Term]
Instructors: Yamuna Krishnan, MM Panicker
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Algorithms [2011 Aug Term]
Instructors: Aswin Sesasayee, Sandeep Krishna
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Biology of Disease [2011 Aug Term]
Instructors; Sudhir Krishna, Seema Nanda (TIFR-CAM)
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Statistics [2011 Aug Term]
Instructor: Vasanth Kumar
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Pre-calculus [2011 Aug Term]
Instructor: Eli Lebow

Credits: 0
Duration: Sep 8, 2011 - approx. Sep 26, 2011
Schedule: TBA
Outline: Algebra pitfalls, exponents, logarithms, and trigonometry.

Login to moodle

Calculus [2011 Aug Term]
Instructor: Eli Lebow

Credits: 3 (Basic)
Duration: approx. Oct 3, 2011 - approx. Dec 17, 2011
Schedule: MW 2:00PM - 4:00PM, LH-2
Outline: Graphs and functions. Limits, derivatives. Maxima and minima.
Basic calculus rules; product rule; chain rule. The integral. Differential
equations.

Login to moodle

2012 Jan Term

Basic Neuroscience [2012 Jan Term]
Instructors: Sumantra Chattarji (coordinator), Upinder Bhalla, Sanjay Sane, Vatsala Tirumalai
Credits: 3
Duration: To be announced
Schedule: MW 11:30 - 13:00; F 9:00 - 10:30; LH2

Outline:
Neuro basic course will consist of 4 modules of around 6 lectures each, plus a couple of labs on electrical models of cells. Each lecture will be around 90 minutes. Two lectures a week, and there will also be a TA-led tutorial session each week.

Module 1: Upi: Cellular biophysics.
Neurons as electrical entities. Passive properties and cable theory. Active properties and Hodgkin-Huxley equations.

Module 2: Shona: Synaptic transmission in invertebrate and vertebrate nervous systems;
Synaptic plasticity in the mammalian brain;
Basic concepts in neuroanatomy

Module 3: Vatsala: Small circuits and neuromodulators
Module 4: Sanjay: Comparative neurobiology and ethology

Login to moodle

Ecology and Evolution [2012 Jan Term]
Instructors: Mahesh Sankaran and others
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Control and Optimization [2012 Jan Term]

Instructor: Madhu Venkadesan

Duration: 30 to 32 lectures, starting on February 6

Timing: M,W,F - 9:00am to 10:00am

Location: GS-01 (ground floor seminar room)

Prerequisites: Linear algebra; calculus; good familiarity with MATLAB or similar scientific computing environment; undergraduate-level control theory would be helpful, but not essential.

Description: This course covers topics on feedback control of dynamical systems, linear and nonlinear least squares optimization, model-based estimation, and optimal trajectory control. Lectures on feedback control will be mostly restricted to linear, time-invariant control systems. Introductory topics on optimal feedback control, particle filtering and bond graph modelling will also be covered. Refresher lectures on some topics such as singular value decomposition, constrained optimization, Lagrange multipliers will be included. Topics covered will include: single-input-single-output (SISO) systems, mutliple-input-multiple-output (MIMO) systems, transfer functions, state-space models, stability analysis, model-based estimation, numerical optimization, optimal control, Kalman filters, linear-Gaussian and general nonlinear methods for optimal estimation.

Grading: Your grade in the course will depend on your involvement in the course as seen from your homework (30%), the midterm exam (10%), the final exam (10%), and the optional final project (50%). The score distribution in the absence of the optional project will be homework (30%), midterm exam (35%), final exam (35%).

Population Genetics and Molecular Evolution [2012 Jan Term] - Postponed to 2012 Aug Term
Instructor: Uma Ramakrishnan
Credits:
Duration:
Schedule:
Outline:

Login to moodle

Essentials of Glycobiology [2012 Jan Term]
Instructor: Ajit Varki [UCSD]

Credits: 2

Duration: Feb 1 - 7, 2012

Schedule: Lectures: 10 am - 12 noon [Teaching Lab]; Discussions: 2 pm - 3pm [Teaching Lab]

Prerequisites: Students should have graduate level exposure to molecular and cellular biology.

Outline: Every living cell in nature displays a dense and complex array of cell surface and secreted glycan chains, as well as intracellular glycosylation. Historical and technical factors caused these essential components of life to be left out of consideration during the initial revolution in molecular and cellular biology. With the advent of improved technologies and a flood of new information, the myriad functional role of glycans in biology and pathology can now be fully integrated into our understanding of life. This course will use the textbook "Essentials of Glycobiology" to provide an overview of the entire field.

Grading: Grades will be based on participation during the discussion sessions.

Signalling [2012 Jan Term]
Instructor: Raghu Padinjat
Credits: 3
Duration: Feb 7, 2012 -
Schedule: TF 9:00 – 10:12, LH2
Outline: This course will cover topics in cell signalling, ranging from molecules to cell biology.

Login to moodle

Genome biology and technologies [2012 Jan Term]
Instructors: A Sesasayee, Dasarathi [inStem]
Credits:
Duration:
Schedule:
Outline: The course will cover biology of genomes starting from genome content (from single reference genomes to comparative genomics), transcription and its control, epigenetic control of transcription (methylation and chromatin modification), post-transcriptional regulation (ncRNA) and post-translational signalling networks. The course will be supported by discussions of microarray and deep sequencing technologies and methods for analysis of data they produce. There will be a few guest lectures covering mass-spectrometry-based proteomics and metabolomics.

Introduction to Experimental Statistics [2012 Jan Term]
Instructor: Vasanth Kumar

Credits: 3
Duration: Jan 18, 2012 – Apr 2012
Schedule: MW 2:00PM - 4:00PM, LH-2
Outline: Experimental design, statistical inference

Prerequisites: Students should have taken and cleared Basic Statistics

Genome Biology [2012 Jan Term]
Instructors: Aswin Sesasayee, Dasaradhi
Duration: Feb 1 2012 -
Schedule: W 8:45 - 10:15, R 10:30 - 12:00, C-CAMP Seminar Hall

Prerequisites:
undergraduate-level exposure to molecular biology or the physical sciences

Outline:
The course will include a set of lectures and student presentations and discussions. Several guest faculty will be involved. The following topics will be covered: History of genomics; Comparative genomics; Gene expression; Post-transcriptional biology; Proteins, small-molecules and networks

Mathematics: Population models [2012 Jan Term]

Instructor: Eli Lebow

Credits: 3 (Basic or Advanced)
Duration: Feb 10, 2012 -- May 4, 2012
Schedule: T 10:15AM -- 12:30PM, F 4:00PM -- 5:00PM, LH3

Outline: Difference equations, exponential growth. Some nonlinear equations, and what they model. Systems of difference equations, and what they model. Review of matrix algebra, determinants, etc. Eigenvalues and eigenvectors. Using eigenvalues and eigenvectors to solve systems of difference equations. Dominant eigenvalues, stability. Programming for use in simulating population models. Equilibria and linearising nonlinear difference equations. Complex eigenvalues. Differential equations, and analysing them--eigenvalues, eigenvectors, stability, equilibria, linearising, and drawing vector fields.