Internship_Curriculum.md

A training curriculum for the Internship program at ICIPE.

Week 1

• Day 1 - Onboarding and general overview of MBBU and Introduction to collaborative documents - Slack
• Day 2 - Purpose roadmap, objectives and goals
• Day 3 - Introduction to GitHub
• Day 4 - Data management and reproducible tools
• Day 5 - Intro to Bioinformatics

Week 2

• Day 1 - Intro to NGS: Sequencing and file formats
• Day 2 - Introduction to Unix and Personality & Motivation
• Day 3 - Shell Scripting
• Day 4 - Shell Scripting
• Day 5 - Shell exercices and Leadership/Leadeship attributes/LeadershipStyles

Week 3

• Day 1 - Git on the commandline
• Day 2 - Phylogenetics
• Day 3 - Introduction to HPC and Introduction to Python and Reproducible research tools (Miniconda, Jupyter and Rmarkdown)
• Day 4 - Python scripting
• Day 5 - More python and Leadership Styles and diversity

Week 4

• Day 1 - Intro to R and Communication and presentation skills
• Day 2 - Nextflow, Singularity & Docker and Feedback and conflict resolution
• Day 3 - Nextflow & Docker and Career planning and peer mentoring
• Day 4 - Nextflow & Docker and Interns presentation on a topic of interest
• Day 5 - Nextflow & Docker

Week 5

• Day 1 - Introduction to Data Science and Machine Learning
• Day 2 - Introduction to Data Science and Machine Learning
• Day 3 - Introduction to Data Science and Machine Learning
• Day 4 - Introduction to Data Science and Machine Learning
• Day 5 - Soft Skills:
  • Cover letter (motivation) and CV writing: make a mock application to EANBiT
  • Presentation skills
  • Mock interview

Week 6 & Week 7

Work on reproducing a paper

Week 8 onwards,

The interns will be assigned to a range of mini projects which the will work on to build on different skills acquired from week 1 to week 7.

Add:

• A stronger focus on Pipelines, Workflows and Containers
• Follow up Book a day for Lab tour or even wet lab practicals
• Shadow someone in the lab
• A focus on research results interpretation
• Information literacy workshop

Notes

1. The interns will be expected to attend other adhoc trainings organized by MBBU or other organization which are deemed important for their growth.
2. The interns will self organize every day stand up meeting and make a presentation of a new concept learned within the Bioinformatics space.
3. The interns will be expected to participate in journal club and Monday morning meetings.
4. There shall be a code/progress review every Friday of the week.
5. The interns will be expected to write a mid-internship and end of intership reports documenting their journey.

Evaluation

• Pre Internship Survey
• Post Internship Survey