The demand for well-trained Bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialisation in Bioinformatics. The graduates are not aware of the career opportunities in Bioinformatics, and those who do lack mentors to help choose a specialisation. icipe has been instrumental in bridging this gap through short-term training and workshops, but this has not been sufficient. Those who receive the training lack support to continue learning and apply the skills gained in research projects. Additionally, this approach is unsustainable; there is low retention of Bioinformatics skills gained. The EANBiT program is a step in the right direction towards filling the training and retention gap, but it is not enough.

The purpose of the internship is to impart the following competencies:

1. Knowledge and Skills: Details of the scientific discovery process and the role of bioinformatics in it.
2. Knowledge: Data management
3. Knowledge and Skills: Bioinformatics tools and resources and their usage
4. Knowledge and skills: Fundamentals of computer science systems
5. Knowledge and Skills: Scripting and programming appropriate to the discipline.

In this incubation program, we will follow a curriculum that identifies students with diverse interests in the program.

1. Introduction to Collaborative tools (1 day)

   • Git and GitHub
   • Slack for communications

2. Introduction to genomics (3 days)

   • Project organisation
   • Introduction to Linux
     • The unix shell
     • Intro to linux
   • Introduction to HPC and cloud computing

3. Open Science (1-day workshop)

   • Reproducible genomic data analysis
   • Genomics Data Management Plan

4. Introduction to Bioinformatics (for this part, we will use the H3ABioNet programs) —One Week Self-paced Quick Introduction to these concepts.

   • Introduction to Biological Databases
   • Introduction to sequence alignment
   • Introduction to genomics
   • Introduction to Phylogenetics

5. Mini-project

   • After the quick introduction, which should take less than a month, we'll assign a mini-project that will utilise some of the core skills

Learning Roadmap:

• Each of you will be expected to develop a learning RoadMap guided by your trainers. Here you are expected to create a pathway you'd like to take, create a timeline for acquiring various skills, and the resources you will use.
• Your learning pathway will be based on your knowledge gaps and interest, and the mini-projects will be designed to maximise skills acquisition

• Linux/Unix/Bash

  • IntroductoryLinux-2019
  • BASH-Intro-2018
  • The unix shell
  • Intro to linux
  • Guide for beginners

• Python

  • Python4Bioinformatics2019
  • Programming with Python
  • Plotting and Programming in Python

• R

  • R tutor
  • Intro to R
  • Programming with R
  • R for Reproducible Scientific Analysis

• All-round resources

  • Happy Belly Bioinformatics
  • Bioinformatics Workbook
  • Training in Bioinformatics
  • Data science and the commandline