Course Outlines:
The course will be a modern introduction to statistical physics with biological examples. We will discuss random walks, partial differential equations, markov processes, random matrix theory, entropy and information, Ising model and its applications in Biology and end with a discussion of Scaling and Universality. We will consider biological applications across scales including molecular, cell and population biology.
Course Outcomes:
At the end of the course, the students will be familiar with stochastic processes and how to model them, with examples from population biology. They will have an appreciation for how to model gene regulation, both deterministic and stochastic. They will understand the close relationship between entropy and information theory, and see the application of information theory in various systems including chemotaxis, kinetic proofreading, bacterial persisters and positional information during development. Finally, they will get an appreciation for scaling, universality and emergence in statistical physics. They will have a mathematical understanding of stochastic differential equations, markov processes, maximum entropy, random matrix theory, and scaling analysis.
Instructor: Archishman Raju
Venue: LH-2
Schedule: Monday and Wednesday - 11.30 am to 1.00 pm
- Teacher: Archishman Raju
Description: QuERMA is designed to be an introduction to concepts,
laboratory methods and quantitative analysis to prepare incoming students
to tackle biological questions with an eye for the quantitative, and on
overarching theories. Experimental biology techniques together with advanced
microscopy will be combined with sophisticated image processing and data
analytical tools to explore the broad themes of living systems, centered on
growth, dynamical processes and evolution. The course will seamlessly move
between the classroom, with lectures that provide in-depth theoretical
background, and the laboratory, where experiments are performed and computer
based image/data tools are used for analysis and simulations.
This course is targeted primarily towards the newly inducted graduate students
of the Physics of Life program to serve as an introduction to
experimentation in physical biology and is also open to interested students
coming through the regular GS stream at NCBS, subject to satisfying
the prerequisites for the course.
Course Prerequisites:
• Basic Mathematical Methods
– Fourier Analysis
– Calculus and Differential Equations
– Linear Algebra
– Statistics
• Basic coding/Matlab
Instructor(s) : Shashi Thutupalli, Madan Rao, Shaon Chakrabarti, Tapomoy Bhattacharjee
Time : Friday and
Saturday - 9.00 AM to 6.00 PM
Venu : Raspuri
- Teacher: Tapomoy Bhattacharjee
- Teacher: Shaon Chakrabarti
- Teacher: Asha Joseph
- Teacher: Madan Rao
- Teacher: Shashi Thutupalli
As our data generation capabilities are fast outpacing our ability to analyze and make sense of the data, statistical inference and machine learning methods are becoming invaluable across the realms of science. This is a course on the fundamentals of stastical inference/machine learning/data science. Emphasis will be on learning the methods from first principles as opposed to using them as black boxes. We will use real biological examples as much as possible. Note that this is not really a course on statistics (e.g. hypothesis testing is not covered).
Syllabus :
Basics of probability: axioms, conditional probability, random variables, expectations, standard probability distributions, methods for sampling from a distribution, Introduction to Markov Chains, Monte Carlo sampling, Least squares and Linear regression, Constrained Optimization, Bias-variance tradeoff and variable selection (ridge regression and lasso), Linear Mixed Effects, Maximum Likelihood and Expectation Maximization, Bayesian inference, MCMC and Gibbs sampling, Bayesian model selection, Dimensionality reduction and clustering, supervised learning: SVMs, neural networks, deep networks, genetic algorithms.
Course structure: Lectures + weekly programming/maths assignments. A term project involving implementing one of the methods on a biological example is to be submitted in the last month of the course.
Prerequisites: Basic programming skills in Python or R, mathematics upto class 12.
Evaluation: 6 homework assignments + 1 end-term project.
Course outcome :
Familiarity with basic concepts in statistical inference, able to choose and implement the above sorts of methods for their own research.
Instructor(s) : Shruthi Viswanath, Shaon Chakrabarti
Time : Monday and Wednesday, 2:00 to 3:30 PM
Venue : SAFEDA
- Teacher: Shaon Chakrabarti
- Teacher: Shruthi Viswanath
Course Syllabus :
This course will go through the basics: virus classification and structure, entry into host cells, replication, assembly and release. Host (both cellular and immune) responses to viral infection. Basics of viral infection, spread and therapeutics. Other sampled topics: viral evolution, applications of viruses, etc.
Course Outcomes :
A basic understanding of viruses and their life cycle within host cells.
A basic understanding of host cell and immune response to viruses.
A basic understanding of viral infections, spread, vaccines, etc.
Instructor(s) : Shachi Gosavi
Time : Monday, Wednesday, Friday - 9.00 to 10.00 AM
Venue : SAFEDA
- Teacher: Shachi Gosavi
Syllabus
How does a zygote form an organism? What processes ensure that the anatomy of this organism, its antecedents, its siblings, and its descendants is the same? How does evolution act on these processes? What happens when development goes wrong? This course aims to give you an understanding of how developmental programmes work and how to think across scales to gain insights into these processes.
Course Outcomes :Understand the cellular and molecules mechanisms of the generation of complexity
Connect multiple scales of biology to understand how cells are organised into tissues
Identify and understand key findings in developmental biology
Synthesise literature and communicate in a written format
Instructor(s) : Raj Ladher and Tina
Time : Monday, Wednesday, Friday - 10.00 to 11.30 AM
Venue : SAFEDA
- Teacher: Palak Chugh
- Teacher: Raj Ladher
- Teacher: Tina Mukherjee
- Teacher: Shivangi Pandey
Course outline:
Section 1: Introduction (1 class)
Course structure:
Common and diverse features in cell (biology): Pro- and Eu-karyotes
Section 2: Molecular basis of cellular organisations (9 classes)
Different Types of compartments:
Compartmentalisation and Membrane:
Cytoskeleton:
Central dogma of information flow:
Macromolecular machines and their functions:
Physicist view of cellular forms:
Chemist view of cellular forms:
Selected Papers Discussion:
Section 3: Cells as replicating units (9 classes)
Introduction to the concepts of cell cycle: Pro- and Eu-karyotes
Preparation for prokaryotic cell division:
Preparation for eukaryotic cell division:
Mechanisms of prokaryotic cell division:
Mechanisms of eukaryotic cell division (mitosis):
Mechanisms of eukaryotic cell division (meiosis):
Wrap up class:
Selected Papers Discussion:
Examination & Discussion of answers: (2 classes)
Course Outcomes :
Students comprehend the molecular basis of common/diverse cellular forms
Students comprehend how cells act as self-replicating units
They will also understand why cellular structures/conditions need to be robust
They will also discuss what happens when they deviate from those nature defined rules
Instructor(s) : Swadhin Chandra Jana and Sudarshan Gadadhar
Time : Tuesday, Thursday - 11.30 to 1.00 PM
Venue : SAFEDA
- Teacher: Sudarshan Gadadhar
- Teacher: SWADHIN C JANA
Course details: This course is aimed as a refresher for students to learn (or recall) about biochemistry of the cell and runs parallel with fundamentals of molecular biology, covering some of the seminal discoveries that laid foundation of modern biology and provide a platform for advance courses in the next semester.
Topics:
Biological periodic table: why life uses only certain elements
Biological Spectroscopy
Proteins and their structure
Protein Structure - specificity and selectivity
DNA/RNA discovery/type
RNA structure
Methods to study RNA
Lipids, membranes and selectivity
What is an enzyme and how they work
Allostery
Basic Energetics
Biochemical and Biophysical techniques
Classic papers – key landmarks in biochemistry (examples – Pauling’s articles, Ramachandran plot, Anfinsen hypothesis, Kornberg’s polymerase …)
Reference Books: Basic Biochemistry books like Leininger and Stryer but largely from the original articles in each topic discussed.
Course Outcomes :
Understand how chemistry is indispensable in biology.
Basic understanding of protein structure, spectroscopy techniques, nucleic acid biology
Enzymology and Bioenergetics
Read classis papers in Biochemistry
Instructor(s) : Vinothkumar, K.R. and Sunil Laxman
Time : Tuesday, Thursday - 09:00 to 10:00 AM
Venue : SAFEDA
- Teacher: Vinothkumar Kutti Ragunath
- Teacher: Sunil Laxman
Course Syllabus:
This course will focus on the causes and impacts of different global change
drivers (altered climate, anthropogenic nutrient deposition and land-use
change) on the biosphere. We will cover
a whole range of topics including
a) Changes in atmospheric chemistry and climate from deep time to the present;
b) Fire in the earth system- from deep time to the present
c) The water, carbon, nitrogen and phosphorous cycles and how they are closely linked with and respond to changes in atmospheric chemistry and climate
d) The roles of climate, fire and nutrient availability in shaping life on earth
e) Anthropogenic land-use change in historical time and the genesis of the Anthropocene, with its implications for shaping life on earth today.
f) Impacts of different global change drivers on patterns of species distribution and richness
g) Impacts of different global change drivers on physiological and behavioural responses of species
h) Ecological and evolutionary responses of species, communities and ecosystems to changing anthropogenic drivers.
Teaching methods: The course will be delivered as a series of classroom lectures and scientific paper discussions. Expert guest lectures will be invited on special topics.
Assessment: Grading for the course will be based on a presentation (30%), a final term paper (60%) and class participation (10%)
Course Outcomes:
Understand the deep time history and current day dynamics of Earth’s climate and biogeochemistry
Have a broad knowledge of major themes that emerge in the responses of species and ecosystems to ongoing and predicted global change
Be able to critically read and evaluate the burgeoning literature in this field
Have a strong knowledge-base of the literature and knowledge gaps in the above topics for the Indian subcontinent
Instructor(s) : Jayashree Ratnam and Mahesh Sankaran
Time : Tuesday, Thursday, Friday - 2.00 to 3.30 PM
Venue : LH-2
- Teacher: Jayashree Ratnam
- Teacher: Mahesh Sankaran
Course Syllabus
We are surrounded by a fascinating array of species that live in varied habitats. How has this biodiversity come to be? What processes lead to the formation of species? How do animals adapt to their environments? Why do some parts of the world have more diversity than others? How do species change over time? How has the diversity of life changed over time? These are some of the questions we will seek to answer through this basic course. We will explore the basics (and some more advanced concepts) of evolution through lectures and guest research talks. Broadly, we will study paleontology and the past, evolutionary processes like adaptation, natural selection, sexual selection, speciation and phylogenies, microevolution and population genetics, biogeography and human evolution. Finally, we will try to understand why you, as budding biology researcher should care about the study of evolution.
Lectures are ninety minutes each, the research talks are an hour each with 30 minutes for interactions and questions. You will also visit the NCBS collections facility. Evaluations will be through homework, quizzes and other assessments and a fun project at the end.
Course Outcome:Think about biological phenomena from an evolutionary perspective
Understand population genetics and how to quantify evolutionary change
Understand phylogenies and how to represent evolutionary hypotheses through them
Get a perspective on research in evolutionary biology
Time : Monday, Wednesday, Friday - 11.30 to 1.00 PM
Venue : SAFEDA
Rough Course Schedule:
- Teacher: Uma Ramakrishnan