Schedule.md

Planning a Reproducible Genomics Project Workshop

Here's the roadmap for the Reproducibility in genomics Workshop:

Date: June 10, 9:00AM - 5:00PM

Venue: IT Training Room (Carol Wilson)

9:00AM - 9:30AM: Welcome and registration (Caleb and Careen)

• Registration
• Welcome
• Introductions
• set-up
• Filling Bioinformatics Needs Assessment Survey (If you haven't)

9:30AM - 10:30AM: Introduction (Caleb and Ouso)

• Presentation on Open Science (20 minutes) -- Gilbert and Careen
• Bioinformatics capacity and resources at icipe (20 minutes)
• Introduction to genomics and Bioinformatics (20 minutes) -- Jacob
• Organizing a genomic project workspace (Genomic Data Management Plan) (20 minutes) -- Ouso

10:30AM - 10:45AM

• Tea Break (Provided)

10:45 - 11:30AM: Commandline (Careen and Gilbert)

• Basic Linux commandline introduction
• Slides

11:30 - 1:00: Introduction to Git and GitHub (Caleb and Gilbert)

• Introduction to version Contol
• Setting up GitHub account
• GitHub terminologies
• Markdown syntax
• Markdown editors

1:00PM - 1:45PM

• LUNCH (Not Provided)

1:45 - 2:30: Genomic Data Management Plan (Ouso and Jacob)

• Inroduction to FAIR data
• What is a data management plan?
• How do you design a data management plan?
• DMP design framework
• Genomic DMP Example

2:30PM - 3:30PM: Hands-on GitHub (Caleb and Kennedy)

• Creating a Git repository
• Adding changes to stage
• Committing changes
• Pushing changes to GitHub

3:30AM - 3:45PM

• Tea Break (Provided)

3:30 - 4:15PM: Reproducible Bioinformatics Research (Caleb and Jacob)

• What makes a genomics project reprodcible?
• Tools for planning and executing a reprodicible project
• Research notebook in Bioinformatics (Jacob)

4:00PM - 5:00PM: Interactive Sessions (Careen and Pauline?)

• Group discussions and interactions (We can use Amels cards here)
• Hands-on Group activities on Open Science and Data Management Plan

5:00PM - 5:30PM

• Q&A and Wrap Up for the Day