Course Content

Day 1 – Linux for Biologist

 

 What is Linux

 

 Explaining different components of Linux OS

 

 Linux commands for data processing

 

 Linux commands for process management

 

Day 2

 

 File handling in Linux

 

 Vi Editor

 

 Shell scripting basics

 

Day 3- Python

 

 What is Python, a brief history

 

 Installing and Setting Python

 

 Basics of Programming

 

 Hello World!

 

 Variables and Types

 

Day 4

 

 Operators

 

 Conditions and Loops

 

 String Functions

 

Day 5

 

 Lists

 

 Hashes

 

 Regular Expressions

 

Day 6

 

 File I/O

 

 Functions

 

 Exception handling in Python

 

Day 7

 

 Object oriented programming concepts

 

 Classes and Objects

 

 Concept of inheritance

 

 Concept of accessibility

 

Day 8

 

 Modules in Python

 

 Python and MySQL - demo

 

 Python and WebService- demo

 

 Best Practices in Programming

 

Day 9 - BioPython

 

 Introduction to BioPython

 

 Sneak Peak of BioPython

 

 Installing and Setting on System

 

 BioPython important module, and how to read about them

 

Day 10

 

 Sequence Object

 

 Sequence I/O Object

 

 Different sequence formats available

 

Day 11

 

 Handling of fasta file.

 

 How to find sequence from the fasta file.

 

 Performing various operations on fasta file sequence.

 

 Parsing files, FASTA, Genbank

 

Day 12- NGS Data Case study

 

 Introduction to Big Data

 

 Introduction to NGS Data

 

 Why NGS Data, and complexities of it

 

 FASTQ format

 

 Demo handling NGS data with Linux commands

 

 Demo handling NGS data with a Big data software