510329 - Laboratory of Advanced Bioinformatics for Omics Sciences
Course Details:
Description
The course provides an in-depth exploration of bioinformatics analysis of omics data. The focus will be on understanding the scope of omics research, specifically genomics and proteomics, and the challenges of omics data analysis, including computational resources, by ensuring reproducible research.
Learning outcomes
At the end of this class, the students are expected to:
- Understand the nature and differences in the biological information delivered by different sequencing technologies (i.e. whole genome, whole exome, transcriptome and proteome sequencing)
- Identify the key factors in designing genomics, transcriptomics and proteomics experiments (number of replicates, library construction, run type, coverage, and depth)
- Understand the computational and statistical requirements of the main bioinformatics applications (computing infrastructures, memory, cores, storage)
- Apply infrastructure knowledge and integrate it with a biological understanding of the experiments to design and executing variant calling, RNA sequencing and proteomics analysis workflows
- Solve a given biological problem by choosing the appropriate tools and workflows, develop and report a hypothesis from the biological interpretations of the results
Course contents
- Use of Nextflow in both HPC and cloud environments
- RNA-seq data analysis: experimental design and differential expression analysis, biological interpretation and execution of standard workflows in a cloud environment
- Whole Genome/Exome sequencing: experimental design and variant calling best practices, annotation, and execution of standard workflows in a cloud environment
- Databases for the interpretation of variant calling and transcriptomics results
- Proteomics data analysis
- Molecular docking
- MD simulation and modelling
- Structure prediction