Command-line Series Advanced Linux Scripting For Bioinformatics

admin

About This Course

Advanced Linux Scripting For Bioinformatics Allows You To Develop Advanced Level Scripting Skills In Linux

Linux/Unix operating systems have the ability to string commands and utilities together in unlimited ways to achieve more complicated tasks. In Bioinformatics, the researchers have to work through a huge set of textual data in the form of CSV files, genomic data, tabular data, etc.

Such data analysis can be quickly and easily done using the command line or terminal interface of Linux or Unix operating systems. Moreover, it takes a few minutes to complete a task on Linux OS which you cannot even think of performing on the Windows or any other operating system.

About 90% of the Bioinformatics programs, scripts, or packages are built for Linux computers rather than other operating systems. Linux makes the 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 to process the datasets.

In this course you’ll learn advanced biological programming on Linux terminal to efficiently process, pre-process, retrieve, manipulate and analyze bioinformatics genomic datasets. Along with, learn how to develop expertise in molecular dynamics simulations to predict the most suitable in vivo conformations of biological macromolecules for designing novel drugs. You’ll also be learning complete end-to-end Linux (BASH) for Bioinformatics.

Joining and learning from the Advanced Linux Scripting for Bioinformatics can enhance your biological career by learning through various useful & informative pre-recorded lectures on Linux(BASH) scripting.

Learning Objectives

Getting Familiar With Linux
Piping and Control Data Flow
Processing and Analysis of
Biological Datasets
Molecular Dynamics
Simulations: GROMACS

Target Audience

  • The target audience for the Advanced Linux Scripting for Bioinformatics are biologists, beginner or intermediate Bioinformaticians or data analysts with no or little experience in applications of computational bioinformatics and analysis.
  • However, a superficial understanding of molecular biology and logic development for coding is expected from you before you join the course.
  • Bioinformatics is quite easy to get started in, even if you lack a proper understanding of the underlying concepts of Bioinformatics databases, servers, tools and the algorithms working behind them.

Curriculum

38 Lessons16h 25m

Linux

Introduction to Linux for Bioinformatics22:32
PWD – Print Working Directory00:01:26
Exercise
CD – Changing Directories00:05:03
Exercise
MKDIR – Making Directories00:08:13
Exercise
MV – Moving Files, Directories and Data00:05:11
Exercise
Which & Whereis – Find Programs You Installed00:03:43
Exercise
RM – Deleting Files and Directories00:01:24
Exercise
Find – Finding User Created Files00:03:39
Exercise
LS – Listing Files and Directories on Linux00:06:46
Exercise
Piping and Redirection of Data00:06:35
Exercise
Cat – Visualization and Inspection of Text Data00:03:56
Exercise
Head – Reading Specified Number of Lines from Top00:03:50
Exercise
Tail- Reading Specified Number of Lines from Bottom00:02:23
Exercise
Touch – Modifying File Statistics and Creating Files00:07:04
Exercise
Stat – Statistics of File & Directories00:02:43
Exercise
Wget – Retrieval of Genome Assemblies00:06:48
Exercise
Curl – Retrieval of Bioinformatics Files00:02:25
Exercise
Vim – Create and Edit Text Files00:05:59
Exercise
Diff – Find Sequence Differences in Files00:02:35
Exercise
GZIP – Compress and Archive Files Efficiently00:06:05
Exercise
GUNZIP – Extract Compressed Content00:02:14
Exercise
Tar – Create Archives of Genome Data00:04:19
Exercise
Grep – Finding Uncharacterized Proteins in Human Genome8:55
Exercise
Cut – Subsetting Required Textual Data from Text Files00:05:49
Exercise
Sort – Sorting Data00:04:23
Exercise
WC – Statistics of the Data Within File00:02:46
Exercise
CP – Copying Files and Files Contents00:03:43
Exercise
Column – Proper Visualizations of Delimited Datasets00:04:38
Exercise
pdb2gmx – Construction of Topology File for Simulation00:09:01
Exercise
Getting Started With Molecular Dynamics Simulation – Preprocessing of Protein Structure and Removal of Unnecessary Structural Features00:12:34
Exercise
Defining a Solvant Box for Simulation00:04:14
Exercise
Solvation – Adding Water Molecules in Solvant Box00:05:31
Exercise
Generating Input Run File Replacement of Water Molecules With Ions00:06:55
Exercise
Energy Minimization – Relaxing and Fixing the Structure for Simulation00:11:25
Exercise
GRACE – Visualization and Analysis of Minimized Structure00:04:12
Exercise
Equibiliration of Protein Structure NVT ENSEMBLE Phase 100:08:38
Exercise
Equibiliration of Protein Structure NPT ENSEMBLE Phase 200:08:10
Exercise
mdrun – Executing Simulation Analysis00:03:47
Exercise
Exercise

Evaluation

Write a review

$90.99$129.99

30% off
Level
Intermediate
Duration 16.4 hours
Lectures
38 lectures
Language
English

Enrolment validity: 365 days

Select the fields to be shown. Others will be hidden. Drag and drop to rearrange the order.
  • Image
  • SKU
  • Rating
  • Price
  • Stock
  • Availability
  • Add to cart
  • Description
  • Content
  • Weight
  • Dimensions
  • Additional information
  • Attributes
  • Custom attributes
  • Custom fields
Click outside to hide the compare bar
Compare
Wishlist 0
Open wishlist page Continue shopping