Virtual Bioinformatics Short Course Series

Special notice: The revised schedule for the short course  “Transcriptome Data Analysis” is given below. Kindly note that the Course Registration is closed now.

Resource persons:

Dr Shani Amarasinghe, Research Fellow in Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Australia

Ms Thulani Hewavithana, Graduate Teaching Assistant and Postgraduate Candidate, University of Saskatchewan, Canada

Date  Time Course Section Content
Day 01 9th July

From 6.30am

to

9.00am

R crash course Data manipulation and Visualisation using R language: http://bioinformatics-core-shared-training.github.io/r-intermediate/
Day 02 13th July Follow up R crash course Follow up session of R to answer questions
Day 03 16th July Introduction to transcriptomics  Basic concepts in transcriptome analysis
Day 04 23rd July RNA-Seq preprocessing and differential expression analysis (part 1) Introducing RNA-Seq data normalisation, gene filtering, quality control and various QC plots in R; Introducing DE analysis through edgeR$, limma-voom pipeline in R
Day 05 30th July Differential gene expression analysis (part 2) Continue DE analysis through edgeR, limma-voom pipeline in R
Day 06 6th August Downstream functional analysis Various downstream plot generation to visualise the results, geneset testing in R

Target group:

Undergraduate and postgraduate students, researchers and clinicians who wish to make sense of genomic, transcriptomic, and proteomic data to understand the biological systems.

 

Prerequisites:

Participants should have basic knowledge in molecular biology.  Knowledge in programming is not required.

 

Selection of courses

Can enrol to any course depending on your requirement. Although each course is designed independent to each other, beginners are strongly recommended to follow the Foundation Course, prior to registering for more specialised courses.

Course fee

Rs 5000 per course.

 

Registration and closing date

You can pay and register for any number of courses according to your requirement.

Protein bioinformatics                        : 27th February 2022

Phylogenetics                                        : 13th March 2022

Metabarcoding                                      : 27th March 2022

Transcriptome Analysis                       : 21st  April 2022

Register Now!

Course duration

Each course consists of 10 hrs of online lectures and includes hands on training.

Certificate of Participation

A certificate of participation will be awarded for those who successfully complete each course with at least 75% attendance.

Resource Persons

  1. Dr Pasan Fernando, Department of Plant Sciences, Faculty of Science, University of Colombo.
  2. Dr Anushka Wickramasuriya, Department of Plant Sciences, Faculty of Science, University of Colombo.
  3. Dr Hashendra Kathriarachchi, Department of Plant Sciences, Faculty of Science, University of Colombo.
  4. Prof Chandima Dangalla, Department of Zoology and Environment Sciences University of Colombo
  5. Mr Nilaksha Freeson, Bioinformatics Scientist, Human Genetics Unit, Faculty of Medicine, University of Colombo
  6. Dr Roshan Perera, Bioinformatics Scientist,
  7. Miss Bhagya Senadheera, Bioinformatics Scientist, Business Management School (BMS) Sri Lanka

More information

Dr Gayani Galhena– iobslcourses@gmail.com | +94777381668

Course Name: Essentials in Bioinformatics

Dates Time Topics Content
Day 1

Jan 22

5.30 –

8.00 pm

Basic bioinformatics tools Primer designing, Promoter analysis, Restriction mapping, Sanger sequence editing
Day 2

Jan 23

Bioinformatics databases and online resources Introduction to biological databases, Navigating the NCBI and UniProt databases
Day 3

Jan 29

Sequence alignment and database searching NCBI BLAST, Multiple sequence alignment, Phylogenetic tree construction
Day 4 Jan 30 Sequence alignment and database searching NCBI BLAST, Multiple sequence alignment, Phylogenetic tree construction

 

Course Name: Genomic Data Analysis

Dates Time Topics Content
Day 1

Feb 1

6.30-9.00 pm

Introduction to Genetics and Genomics Sequence variation; Functional Genomics
An overview of Next Generation Sequencing (NGS) Different NGS platforms; Chemistry and Library Preparation
Day 2

Feb 3

Quality assurance of NGS data Phred Scale Quality; QC with FASTQC; Adapter trimming with Trimmomatic
Data Preprocessing for variant discovery Read mapping, duplicate reads removal, Indel realignment and SAM->BAM conversion and visualization
Day 3

Feb 8

Introduction to Galaxy web server Utilizing usegalaxy.org to evaluate different bioinformatic tools
Implementing a Germline short variant discovery pipeline with Galaxy Preprocessing and variant calling steps

– mapping, dedupping, base-calling and annotation

Day 4

Feb 10

Variant interpretation, prioritization, and evaluation Case study presentation In silico functional prediction upon mutation, Hyperlipedemia case study for variant prioritization

Course Name: Transcriptome Data Analysis

” See the top of the page for details”

 

Course Name: Protein Bioinformatics

Dates Time Topics Contents
Day 1

March 1

6.30-9.00 pm

Introduction to protein bioinformatics Protein structure: primary, secondary, and tertiary structure; functional importance
Day 2

March 3

Protein sequence databases Sequence databases: UniProt, Pfam, Prosite, STRING database
Day 3

March 8

Protein structure prediction Experimental elucidation; computational prediction: secondary structure prediction using Jpred; Tertiary structure prediction methods
Day 4

March 10

Protein structure visualization and analysis Using PDB to retrieve sequences, visualizing protein structure using PyMol

 

Course Name: Phylogenetics

Dates Time Topics
Day 1

March 15

6.30-9.00 pm

Introduction to phylogenetics
Basic principles and terminology in phylogenetic analysis and trees
Day 2

March 18

Different data and methods in phylogenetic analysis
Distance based tree construction methods
Day 3

March 22

Character based tree construction methods
Day 4

March 24

Evaluating phylogenetic trees
Applications of phylogenetic analysis

 

Course Name: Metagenomics and Metabarcoding

Dates Time Topics Content
Day 1:

March 29

6.30 – 9 PM Introduction to microbial bioinformatics and metabarcoding Importance of microbial bioinformatics; Practical applications; Introduction to meta-barcoding and metagenomics, Metabarcoding data analysis pipeline steps and tools, Microbial composition analysis
Day 2:

March 31

Metabarcoding diversity analysis (1 hour)

Metagenomics (1 and 30 hours)

Alpha diversity and beta diversity analysis

Introduction to metagenomics

Metagenomics types:

Amplicon Sequencing

Shotgun sequencing

Day 3: April 5 Algorithms and tools in metagenomics Algorithms in Metagenomics;  Tools and databases;

Quality control

Day 4: April 7 Metagenomics in Galaxy Introduction to galaxy instances

Workflow

Summary and Q&A