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
- Dr Pasan Fernando, Department of Plant Sciences, Faculty of Science, University of Colombo.
- Dr Anushka Wickramasuriya, Department of Plant Sciences, Faculty of Science, University of Colombo.
- Dr Hashendra Kathriarachchi, Department of Plant Sciences, Faculty of Science, University of Colombo.
- Prof Chandima Dangalla, Department of Zoology and Environment Sciences University of Colombo
- Mr Nilaksha Freeson, Bioinformatics Scientist, Human Genetics Unit, Faculty of Medicine, University of Colombo
- Dr Roshan Perera, Bioinformatics Scientist,
- Miss Bhagya Senadheera, Bioinformatics Scientist, Business Management School (BMS) Sri Lanka
More information
Dr Gayani Galhena– [email protected] | +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 |
