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Course 2: Comprehensive Bioinformatics for Advanced Microbial Genomics
Course 2: Comprehensive Bioinformatics for Advanced Microbial Genomics
Overview
Overview
Mode of Communication: Bangla
Duration: 10 Weeks (2.5 months)
Frequency: Once a week
Live Session Time:
Lecture (2-3 hours):
Bangladesh Time: Friday 9:00 AM ~ 11:30 AM
USA Pacific Time (CA/OR/WA): Thursday 8:00 PM ~ 10:30 PM
UK Time: Friday 3:00 AM ~ 5:30 AM
Total Classes: ~30 hours of live lectures and support
Assignments: Weekly Problem Solving exercise
Community Coding Support: Through Google Classroom
Projects: We will reproduce published journal articles. Comprehensive group projects with Github-based reproducibility
Contact: oxfordbiodiscoveryventures@gmail.com
Prerequisites: None. This course is tailored for complete beginners
Certificates will be provided after successful completion of the course
Certificates will be provided after successful completion of the course
Module 1
Module 1
Python for Bioinformatics
Python for Bioinformatics
Week 1: Programming Fundamentals with Python
VSCode setup, Variables, data-structures, loops, conditionals, Scripting for automating repetitive tasks, Simulation: Mutation in DNA and why we need substitution models.
Exercise
Week 2: Introduction to BioPython
Functions: Introduction to Functional Programming. Class: the big picture, Parsing FASTA and GenBank files. Sequence analysis and feature extraction. Importance of commenting, docstrings and other good practices in programming
Assignments (Rosalind)
Week 3: Essential Modules for Numeric Analysis
Jupyter Notebooks NumPy, Pandas, Matplotlib Plotting data with Seaborn
Module 1 project overview: Biochemical properties for TSS site prediction
Week 4: From scripting to writing tools
Writing a CLI Class: Introduction to OOP Version control with GitHub. Managing environments with Conda. Importance of understanding Bioinformatics Algorithms Self-paced Rosalind problem solving challenge
Module 1 Project due
Module 2
Module 2
Microbial Genomics: Sequencing to Annotation
Microbial Genomics: Sequencing to Annotation
Week 5: Sequencing, Assembly, Annotation
Introduction to Sequencing, Genome Assembly, Genome Annotation, Public Data Utilization
Module 2 project overview: Reproduce results from a bioinformatics paper.
Week 6: Phylogenetic Analysis
Phylogenetic Methods Tree Visualization, Community Structure Analysis, Additional Tools, Temporal Analysis
Week 7: Ortholog and Pan-Genome Analysis
Ortholog Detection, Pan-Genome Analysis, Microbial GWAS analysis, Phylogenomics
Week 8: Mobilome Analysis
Identification and functional annotation of Plasmids and ICEs, Genomic Comparisons, Phylogenetic Networks
Week 9: Variant Calling
SNP Calling Pipelines Visualizing Variants Automating Analysis using Snakemake
Module 2 project GitHub repo due
Week 10: Evolutionary Analysis
Statistical Metrics: Fst, Tajima's D, and other population-genetic statistics. Selection Analysis with PAML, HyPhy
Student Group Presentations
Week 11: Reserve Day
Discussion on bioinformatics careers, additional tools (Python, Linux), future learning
Instructor
Instructor
Arafat Rahman, Ph.D.
Post-doctoral fellow,
Oregon State University, OR
Ph.D. in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA
Address
Address
Oxford, Oxfordshire,
United Kingdom
Email
Email
oxfordbiodiscoveryventures@gmail.com
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