Command-line Series Fundamentals of Linux for Bioinformatics

Being a Bioinformatician means you’ve to deal with huge biological datasets which includes retrieval of such datasets, processing & pre-processing of such datasets on a daily basis. Dealing with huge genomic and proteomic-level data, requires an operating system having the caliber to efficiently retrieve, pre-process and process the biological data. Linux/Unix operating systems are always the first choice of Bioinformaticists to handle and analyze huge biological datasets in a much easier and efficient manner.

BioCode is offering a Fundamentals of Linux Scripting for Bioinformatics course so that you can learn from the basics of biological programming on Linux terminal to efficiently retrieve, manipulate and analyze bioinformatics genomic datasets. Along with this, you’ll learn how to get started with Linux, pre-process biological data and create pipelines to process the datasets. Linux allows you to develop and utilize command line tools for easier and efficient data analysis of biological nature utilizing the command-line interface of Linux/Unix operating systems.

This course is for absolute beginners in bioinformatics scripting and you don’t require any prior knowledge of Linux or even bioinformatics to get started with this course. In Bioinformatics, researchers have to work through a huge set of textual data in the form of CSV files, genomic data, tabular data, etc. Therefore, such biological data analysis can be quickly and easily done using the command line or terminal interface of Linux or Unix operating systems. Moreover, Linux makes automated biological analysis easy by providing the ability to create various pipelines so that you don’t have to write the code again and again.

Performing on Windows or any other operating system.

This course will include the following sections:

Section 1: Getting Familiar With Linux

Description: This section will focus on making sure that the students gain an understanding of the Linux operating system and the basic functions that are performed using Linux.

Learning Outcomes:  Upon completion of this section, students will be able to:

1. Discuss Linux Operating System.
2. Print Working Directory in Linux.
3. Make Directories in Linux.
4. Change Directories in Linux.
5. Move Files, Directories, and Data.
6. Delete Files and Directories in Linux.
7. Find the Programs Installed by the User.
8. Find the Files Created by the User.
9. List Files and Directories on Linux.

Section 2: Pre-processing Biological Datasets

Description: This section will focus on making sure that the students learn about the different functions and commands that can be used to pre-process and manipulate biological data using Linux.

Learning Outcomes:  Upon completion of this section, students will be able to:

1. Visualize and Inspect Text Data.
2. Read the Specified Number of Lines from the Top.
3. Read the Specified Number of Lines from the Bottom.
4. Modify File Statistics and Create Files.
5. See the Statistics of Files & Directories.
6. Retrieve Genome Assemblies.
7. Retrieve Bioinformatics Files.
8. Create and Edit Text Files.
9. Find Sequence Differences in Files.

Your first steps in Linux, using biological data

This is the shortest way into the command line — about 3 hours 15 minutes across two sections, aimed at someone who has never opened a terminal. It teaches the commands through biological files rather than abstract examples, so the practice is the work.

What you learn

• Getting familiar with Linux — the filesystem, moving around, creating and inspecting files, permissions, and the handful of commands that do most of the work.
• Pre-processing biological datasets — applying those commands to real sequencing files: inspecting, filtering, counting and reformatting.

Where this sits in the Command-line Series

• Fundamentals (this course) — 3 hours. Absolute beginner to competent navigation and basic file handling.
• Introductory Linux — around 9 hours. Adds piping, data flow control and genuine dataset processing.
• Advanced Linux Scripting — automating multi-step analyses into reproducible scripts.

If you already know how to move around a terminal, start at Introductory instead.

Why this is the blocker worth clearing

Nearly every bioinformatics tutorial assumes you can use a terminal. People who skip this step spend their time fighting the environment instead of learning the analysis, and often conclude they are bad at bioinformatics when they are simply missing three hours of foundation.

What you can do afterwards

Log into a server or cluster, find your way around, inspect and manipulate sequencing files without opening them in an editor, and follow a command-line tutorial without getting stuck on the first instruction.

Who it suits

Complete beginners. Wet-lab biologists, students starting a bioinformatics module, and anyone who has been handed server access and left to work it out.