Module Catalogues, Xi'an Jiaotong-Liverpool University   
Module Code: BIO405
Module Title: Research Methods in Bioinformatics
Module Level: Level 4
Module Credits: 5.00
Academic Year: 2020/21
Semester: SEM1
Originating Department: Biological Sciences
Pre-requisites: N/A
To provide students with training in handling diverse, large-scale, biomolecular datasets and in extracting biologically meaningful information from them
Learning outcomes 
A. Use programming language (such as R, Python, Bash) to perform basic analyses tasks.

B. Apply appropriate bioinformatics tools to conduct a research project in this area.

C. Critically analyse and process high-throughput biomolecular data.

D. Appraise, integrate and present different types of bioinformatic data in appropriate formats.

E. Apply appropriate statistical tools to analyse bioinformatics data.

Method of teaching and learning 
Lectures and computational skills training.
Section 1. Introduction to programming and data analysis, including: introduction to programming, R programming language, graphical visualization with ggplot2, R for bioinformatics analysis, Bioconductor, basic statistical tests, R markdown

Section 2. Linux basics and NGS basics, including Linux operation systems, Bash scripts, history and recent development of sequencing technology, NGS data, NGS data quality assessment, NGS data visualization, Basic of server usage (Putty and WinSCP)

Section 3. Sequencing data analysis, including reads alignment, visualization, genome browser, RNA-seq quantification, differential expression, reference-based transcriptome assembly, ChIP-seq analysis, parallel computation on HPC

Section 4. Other high-throughput data analysis tasks: mutation calling, exome sequencing, cancer variant analysis, Galaxy web tools, Shiny framework for web development, GenomicFeatures R package for advanced analysis of NGS data

Delivery Hours  
Lectures Seminars Tutorials Lab/Prcaticals Fieldwork / Placement Other(Private study) Total
Hours/Semester 12      72    66  150 


Sequence Method % of Final Mark
1 Report 1 10.00
2 Report 2 30.00
3 Report 3 30.00
4 Report 4 30.00

Module Catalogue generated from SITS CUT-OFF: 6/6/2020 10:34:23 PM