Table 2 2019 EANBiT-RT program designed with four tracks: technical training, seminars, daily coding, and mini projects. The key modules are in bold
From: Designing and delivering bioinformatics project-based learning in East Africa
Week | Course | Allocated (HRS) |
|---|---|---|
1 | Technical: Version control and collaborative development (Git & GitHub & Slack) | 6 |
Technical: Advanced Scripting | 5 | |
Coding: Linux command line | 1 | |
Technical: Gene models and annotation | 6 | |
Coding: HPC SSH (SLURM scheduler) | 1 | |
Technical: Biological databases and API | 2 | |
Technical: Submission to public databases | 2 | |
Project: Presentation of mini projects | 2.5 | |
Assign groups | 1 | |
Coding: Bash (sed, Awk, Regex) | 1 | |
Soft skills: Scientific Writing and Presentation Skills | 3 | |
Project: Review of mini project methods | Weekend | |
2 | Technical: Reproducibility: package management and workflow languages (Nextflow, Snakemake) | 3 |
Coding: Python | 1 | |
Coding: Jupyter Notebooks | 1 | |
Technical: Specialized databases (VectorBase, EupathDB) and APIs | 1 | |
Technical: Practical proteomics (domain databases, GO) | 2 | |
Technical: Pathways, Gene Regulation Networks (KEGG) | 2 | |
Project: Develop a mini project methodology | 1 | |
Meetings with mentors | 1 | |
Technical: Phylogenomic (Visualization and Annotation) | 3 | |
Project: Present mini project group concepts | 0.5 | |
Seminars: Human health | 1 | |
Project: Research Consultations | 1 | |
3 | Technical: Metagenomics (16S and whole genome shotgun sequencing) | 3 |
Coding: Practice R | 1 | |
Coding: R-markdown | 1 | |
Technical: Machine Learning and Modeling for Big Data (fuzzy strings, HMM) | 5 | |
Coding: Shiny Apps | 1 | |
Project: Meetings with mentors | 1 | |
Seminar: Marine Sector | 1 | |
Project: Implementation of mini projects | 7 | |
4 | Project: Implementation of mini projects | 7 |
Seminar: Agricultural sector | 1 | |
Project: Meetings with mentors | 1 | |
Soft skills: Introduction to the Purpose Roadmap-PRM | 2 | |
5 | EU PATH DB TRAINING | |
Project: Implementation of mini projects | Four days | |
6 | Project: Presentations of mini project reports | One day |
Project: M.Sc. project presentations | Throughout the week | |
Soft skills: Student presentations on PRM | 2 |