Residential Training Programme
Congratulations on your acceptance for the residential training. Here you will find the Residential Training program and a link to the training materials that wil be used for each module.
| Week | Course | Time Allocated (HRS) | Tentative day of the week | Facilitator (s) |
|---|---|---|---|---|
| Kilifi | ||||
| 1 | Version control and collaborative development (Git & Github & Slack) | 6 | Monday 01/07 | Caleb |
| Linux commandline | 1 | Tuesday 02/07 | J.B | |
| Advanced Scripting (including sed, Awk, Regex) | 5 | Tuesday 02/07 | J.B | |
| Gene models and annotation | 6 | Wednesday 03/07 | Caleb & JB | |
| HPC SSH (SLURM scheduler) | 1 | Wednesday 03/07 | J.B | |
| Biological databases and API | 2 | Thursday 04/07 | Caleb & JB | |
| Sequence submission to public databases | 2 | Thursday 04/07 | Caleb & JB | |
| Presentation of mini-projects by the mentors | 2 | Thursday Afternoon 04/07 | All | |
| Assign groups | 0.5 | Thursday Afternoon 04/07 | All | |
| Bash scripting practice | 1 | Friday 05/07 | J.B or Caleb | |
| Scientific writing and presentation skills | 3 | Friday 05/07 | Peter Emmrich | |
| Introduction to Purpose Roadmap--PRM | 3 | Friday 05/07 | Rose Kigathi | |
| Mini-project methods review | Weekend Assignment | Weekend | ||
| 2 | Reproducibility and package management : workflow languages (CWL, Snakemake, Conda) | 5 | Monday 08/07 | Caleb |
| Python | 1 | Monday 08/07 | Caleb | |
| Jupyter Notebooks | 1 | Monday 08/07 | Caleb | |
| Develop mini-project methodology | All day | Tuesday 09/07 | ||
| Meeting with mentors | 1 | Tuesday 09/07 | ||
| Present mini-project group concepts (how they plan to tackle them) | Tuesday 09/07 (end of afternoon) | |||
| Nanopore | 6 | Wednesday 10/07 | George Githinji | |
| Phylogenomics (Visualization and Annotation) + Bayesian phylogenetics | 7 | Thursday 11/07 | J.B | |
| R, R- markdown, Shiny apps (with practicals) | 5 | Friday 12/07 | Oluwaseyi Shorinola & JB | |
| Seminars : Human Health | 1 | Friday 12/07 | ||
| Research consultations | 1 | Friday 12/07 | ||
| 3 | Whole-genome Genomics: Metagenomics (16S and Whole genome shotgun sequencing) + reference mapping + RNA-sequencing (2 days in total) | 14 | Monday 15/07 & Tuesday 16/07 | Etienne de Villiers |
| Introduction to Machine Learning and modeling for big data (fuzzy strings, HMM) | 7 | Wednesday 17/07 | Anthony Etuk | |
| Meeting with mentors | 1 | Wednesday 17/07 | ||
| Introduction to Machine Learning and modeling for big data (fuzzy strings, HMM) | 2 | Thursday 18/07 | Anthony Etuk | |
| Seminar : Genomic technologies and massive data: what does the future look like? | 2 | Thursday 18/07 | Erik Bongcam | |
| KWTRP seminar | 1 | Thursday 18/07 | Anthony Etuk | |
| Seminar: Agricultural sector | 1 | Thursday 18/07 | Trushar Shah | |
| EANBiT Advisory Board meeting (for S.C. members) | All day | Friday 19/07 | ||
| Mini-projects implementation | Through the week | |||
| Nairobi | ||||
| 4 | Practical Proteomics (domain databases, GO) &Pathways , gene regulation networks (KEGG) | 6 | Monday 22/07 | Vincent Owino |
| Tour of selected icipe labs | 3 | Tuesday 21/07 | ||
| Soft skills (Research and Work Ethics) | 6 | Wednesday 24/07 | Rob Skilton | |
| Meeting with mentors | 1 | Wednesday 24/07 | ||
| Seminar: Marine sector | 1 | Thursday 25/07 | Christopher Meyer | |
| Career Development and Funding | 2 | TBC | Laura Polvich | |
| Mini-projects implementation | Through the week | |||
| 5 | EU PATH DB TRAINING | |||
| 6 | Mini-Project report presentations (with GitHub repository + adequate visualization, e.g. through a Shiny App) | Through the week | Monday - Wednesday 05/08-07/08 | |
| MSc. project presentations | Through the week | Thursday 08/08 | ||
| Student presentations on PRM | 2 | Friday 09/08 | ||