Learn Bioinformatics in 6 Days

Kickstart Your Journey to be a Bioinformatician!

Created byIsaac Alfred

Last updated 1/2018

English

English [Auto],

What you'll learn

Integrate biological concepts with information technologies to study the biological system.
Apply the theoretical and computational methodologies relevant to the mining of information from large datasets of biological origin.
Combine theory and practice to solve research problems in bioinformatics, genomics and proteomics.
Manipulate data on computer and understand of the algorithms that underlie the analysis tools that are used for essential research tasks.

Course content

6 sections • 38 lectures • 4h 31m total length

Course Introduction & Content2:32
There are several things that you need to know before you start the course. In this lecture I will explain to you about the course structure and contents as well as the learning outcomes that you will gain from this course.
History of Bioinformatics6:05
We will look into several phases of scientific development and growth until to the advent of Bioinformatics which accelerated the advancement of biotechnology research.
Central Dogma & Protein Structures7:04
This is just a refresher topic for those who are familiar with the central dogma of molecular biology. For those of you are not from the biotechnology background, this could be something new.
Bioinformatics Applications3:25
Learning basic analysis will definitely help you to understand better in doing advanced Bioinformatics works. Here I will briefly explain about the current analysis trends in Bioinformatics.
Test your knowledge

Learning Objectives and Outcomes0:48
Introduction to Database & File Format9:10
In order to fully understand what database is, it is important to know the purpose and the structure of a database. Since it is a computer system that stores information, it is ideal to know why we need a database in scientific research.
Nucleotide Sequence Databases7:28
Here in this section we will look specifically into GenBank and some other nucleotide databases. I will teach you on how to perform a query from GenBank.
Protein Databases6:30
Nucleotide databases are not the only type of databases you will learn. I will also introduce to you on the protein databases. pay a closer attention on this section as we will be covering a specific chapter on Proteomics alone later on.
Guide - Browsing GenBank - Part 113:49
Explore the NCBI GenBank interface to search gene records via keyword queries, navigate left, middle, and right sections, and understand per-page results and record updates.
Guide - Browsing GenBank - Part 215:36
Learn to navigate GenBank on NCBI and build precise queries with and, or, not to retrieve human collagen records. Explore genomic context, chromosomal location, and protein interactions for Homo sapiens.
Guide - Browsing UniProt12:31
Guide - Build a simple database using Microsoft Access11:21
Test your knowledge
Find the gene!

Learning Objectives and Outcomes0:58
Sequence Alignment5:52
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.
Simple Alignment5:33
Let's try to align two nucleotide sequences together and observe how many types of alignment we can get and then decide which one is the best alignment. In this section, I will explain to you on just that alone.
Extra - Sequence Alignment4:28
Gain practical insights into sequence alignment for bioinformatics, learning essential methods and their applications across six days of focused study.
Scoring Matrix & Dynamic Programming Algorithm9:29
There are two methods to perform a sequence alignment - local and global sequence alignments. In this section you will learn how to construct both local and global sequence alignment matrices in order to understand how alignment algorithm works.
Extra - Scoring Matrices4:59
Develop practical bioinformatics skills by working with scoring matrices, guided by a concise, hands-on approach in this extra lecture.
Guide - Multiple Sequence Alignment using ClustalX14:43
Learn how to perform multiple sequence alignment with ClustalX, load and align sequences, realign, build a guide tree, and interpret gaps and similarity profiles.
Test your knowledge
Investigating the correlation between human and rat genes.

Learning Objectives and Outcomes0:50
Explore the learning objectives: homology, similarity, identity; key terms on the class platform; using blocks; interpreting results; running plus programs; and generating sequence alignment and guide tree with glass program.
BLAST Programs13:47
In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences.
A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences
BLAST on NCBI6:13
The BLAST algorithm and the computer program that implements it were developed by Stephen Altschul, Warren Gish, and David Lipman at the U.S. National Center for Biotechnology Information (NCBI), Webb Miller at the Pennsylvania State University, and Gene Myers at the University of Arizona.
Guide - How to perform a BLASTn search9:37
Test your knowledge
Find the mutation!
Find the protein!

Learning Objectives and Outcomes1:18
Identify how molecular variation informs evolution, learn key concepts and terminology, construct and interpret phylogenetic trees with maigre, based on sequence similarity profiles, and assess quality.
Molecular Evolution10:39
Explore molecular evolution by examining natural selection, genetic drift, and mutation as sources of genetic variation, including gene flow and sexual recombination that drive evolutionary change.
Understanding Evolution8:47
Reading Phylogenetics Tree7:53
Building Guide Tree5:45
Learn how to build a guide tree from sequence similarity, prioritizing high-quality multiple sequence alignment, and iteratively generate both alignment and phylogeny to reveal evolutionary relationships.
Which Method to Use8:20
Explore three methods to construct phylogenetic trees from sequence alignments: distance-based, maximum parsimony, and maximum likelihood, chosen by alignment similarity and evolutionary models.
Quality Assessments7:41
Use bootstrapping to assess nodal support in phylogenetic trees by resampling alignment positions to create pseudo replicates and reconstruct a consensus tree.
Guide - Let's Build a Phylogenetic Tree0:17
In this section, I have provided the installer for Mega version 6, a zipped folder containing the FASTA sequence file for Ruminants, and the User Manual on how to perform the phylogenetic tree construction using Mega 6. All you need to do is to follow through the User Manual. The download links are as below. If you have any question, do share with me through the comment box. Thank you.
Test your knowledge
Constructing a phylogenetic tree

Learning Objectives and Outcomes0:49
Introduction to Genomics7:48
Sequencing Technologies Overview15:08
Genome Assembly9:38
Learn how SNB genome assembly reconstructs full-length sequences by aligning and merging reads in de novo sequencing and backbone mapping, with coverage guiding scaffold formation.
Genome Annotation6:53
Learn genome annotation by predicting genes and manually curating their location, structure, and function, locating start and stop codons with ab initio and homology methods and transcript and protein data.
Comparing Genomes6:51
Describe comparative genomics by comparing genomes through whole-genome and gene-centric analyses to identify conserved sequences, variants, and evolutionary relationships, informing disease and phenotype insights.
Test your knowledge
Online Tutorials on UGENE0:35

Requirements

An interest in learning Bioinformatics and maintaining the same interest constantly throughout the period of study.
A knowledge in molecular biology, basic genetics and other life science related courses would be an advantage but not necessary.
Some chapters require you to donwload and install certain softwares for the analysis tutorial. You need to have at least a personal laptop or a desktop with a minimum 4GiB RAM and enough storage capasity for data storing.
Good qualitative (semantic) and quantitative (mathemathics/statistics) reasoning.

Description

It's WORTH your money! This program runs through 6 chapters. This is a self-paced course that suits to your own daily busy schedules. Self-paced gives you the freedom to complete each topic based on your own available time before proceeding to the next chapter without hurry. Basically, I will teach about 6 fundamental topics in Bioinformatics to you. Just to let you know, I don't intend to cover a basic programming class here. Udemy has a lot of great programming courses that can be applied in a Bioinformatics settings. So please well equip yourself with at least Python, Perl, PHP, Java, SQL and R programming. That will really help you to take off faster as a Bioinformatician in the near future. In 6 days you will learn through video lectures and tutorials about:

Day 1 - Introduction to Bioinformatics

We will start this course with a brief definition of Bioinformatics - what exactly it constitutes of, and the importance of this field in the scientific world. Also, I will share with you the history of how Bioinformatics came into being - the reason why it was coined.

Day 2 - Bioinformatics Databases

One of the reasons why Bioinformatics exists is due to the increased amount of biological datasets. These are huge scientific research outputs that need to be managed. In this chapter you will learn first of all how data is stored and manipulated. Subsequently I will begin to introduce to you about nucleotide databases. Bioinformatics is all about managing data and providing scientific knowledge. In this chapter we will also focus on protein databases. These two types of databases compliment each other and both are important for your studies. An example of database that we will be covering here is UniProt.

Day 3 - Sequence Alignment

This is one of my favorite chapters. Have you ever wonder how two sequences are being compared using two different sequence alignment algorithms? Think about aligning 100 DNA sequences at one time - is there a way to perform the multiple sequence alignment? In this chapter I will teach you how to perform Global and Local sequence alignments - it's all about basic concepts of scoring matrices. Let's get serious with Bioinformatics from here onward!

Day 4 - BLAST programs

Yeaps! Also my favorite! I will teach you how to perform a Local sequence alignment using a Bioinformatics tool known as BLAST (Basic Local Alignment Search Tool). We will look into both nucleotide and protein sequence BLAST programs and learn how to read and interpret BLAST results in-details.

Day 5 - Molecular Phylogenetics

Let's get straight to the point. You are uniquely different and special! If you are a big fan of X-Men and other Sci-Fi Hollywood movies talking about aliens, superhuman, man with extraordinary powers, or even just about how diversified we are - this is the time to pay attention to this module. I will teach you about how species is identified and classified using genetic data. To do that we will also be looking into several types of phylogeny analysis algorithms and construct a tree of life from a specific set of sequences. Don't skip this session!

Day 6 - Genome Analysis

In this module you will learn about a genome. We will look closely into both structural and comparative genomics. The detail parts begin with the sequencing technologies and followed with genome assembly and annotation.

I have prepared several sets of quizzes and assignments for you to solve. Based on previous experiences with other students, I am aware that some of you might need a one-to-one discussion therefore you are welcome to request for an online meeting / discussion session with me. Just to help you progress in this course. By the way, the first chapter is F.O.C. for preview! Register now to start learning about what Bioinformatics can do to help you, be it in research routines or for career development or simply just for personal interest. You have a lifetime access to this course and the course materials will be updated periodically. Do check for updates from time to time.

Who this course is for:

Anyone who wants to learn Bioinformatics.

Learn Bioinformatics in 6 Days

What you'll learn

Explore related topics

Course content

Course Introduction & Content4 lectures • 19min

Day 2 - Bioinformatics Databases8 lectures • 1hr 17min

Day 3 - Sequence Alignment7 lectures • 46min

Day 4 - BLAST programs4 lectures • 30min

Day 5 - Molecular Phylogenetics8 lectures • 51min

Day 6 - Genomics7 lectures • 48min

Requirements

Description

Who this course is for: