Virtual Bioinformatics Short Course Series

Special notice: The new dates of the short course  “Transcriptome Data Analysis” are  April 26, 28 and May  5 and 10 (Tuesdays and Thursdays)  from 6.30 PM-9.00 PM

The new deadlines for registration are as follows

Protein bioinformatics                        : 27th February 2022

Phylogenetics                                        : 13th March 2022

Metabarcoding                                      : 27th March 2022

Transcriptome Analysis                      : 21st  April 2022

 

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

                        Dates Time Topic Content/ Sub-topics
Day 1

Feb 15

 

 

 

 

 

 

 

 

 

6.30-9.00 pm

Introduction to Next Generation Sequencing (NGS) and RNA Sequencing Gene Expression; RNA Sequencing; Advantages of RNA Seq over Microarray; Different NGS platforms; Chemistry and Library Preparation for RNA Sequencing
Day 2

Feb 17

Quality assurance of NGS data Phred Scale Quality; QC with FASTQC; Adapter trimming with Trimmomatic
Overview of the RNA Sequencing analysis pipeline Differences in Genomic data preprocessing and RNA Seq data preprocessing; Adopting New Tuxedo protocol
Gene Expression Analysis Expression estimation for known genes and transcripts (FPKM); Differential expression analysis
Day 3

Feb 22

Introduction to Galaxy web server Utilizing usegalaxy.org to evaluate different bioinformatic tools
Implementing the RNA Seq Analysis pipeline with Galaxy New tuxedo protocol implementation with HISAT2, bamtools, stringtie and Ballgown
Day 4

Feb 24

Gene Enrichment Analysis Differentially expressed gene enrichment with DAVID

 

 

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