Cloud Infrastructure for Bioinformatics

This course equips students with the skills and knowledge to leverage cloud computing resources for bioinformatics research and data analysis, focusing on AWS cloud systems and running bioinformatics resources, workflows, containers, scripts, and pipelines on AWS.

Course abbreviation: CIB

Instructor: Eng. Omar Mostafa

Senior Solution Architect

Workload: 12 lectures, 3 hours each. Total workload: 36 hours of lectures and tutorials.

Entrance requirements: None

Used media: Jupyter Notebook, PDF slides

Objectives

• Understand the basics and fundamentals of cloud computing and its benefits for bioinformatics engineers
• Gain hands-on experience working on AWS
• Manage, store, and analyze large-scale biological datasets on cloud platforms
• Optimize cloud-based bioinformatics workflows for scalability, cost-effectiveness, and data security

Competences to be Developed

• Basic cloud computing skills
• Version control tools for bioinformatics projects: Bitbucket and GitHub
• AWS core, supporting, and machine learning services
• Running bioinformatics scripts and pipelines on AWS
• Container engines: Singularity and Docker
• Nextflow and Snakemake workflow systems
• Web app development using Streamlit on AWS

Assessment

• Complete specified exercises during each lecture
• Successfully complete and present the capstone project