Course overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.

eBioKit is a system for teaching bioinformatics, which is running multiple open source web services on an Apple Mac-mini where all databases are stored locally. This reduces the need for a fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services. 
This course is aimed at familiarizing trainees with the multiple uses of ebiokit. The course will train members who are required to perform bioinformatics analysis of genetic and genomic data generated in the various H3Africa projects but most likely also in other projects in there respective institutions.
The course will be 5 days long and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genetic and genomic data. An emphasis will be placed on allowing participants to develop hands-on experience with analyzing real data using ebiokit.
The course is open to all members of the H3A Bioinformatics Network as well as H3A Researchers who are seeking advanced bioinformatics training.

Course objectives

The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to analyze genetic, genomic and metagenomic data. The course will include some basic linux programming and then offer a comprehensive overview of commonly used bioinformatics tools and databases available on the eBiokit system, such as for example Ensembl and Galaxy, a Web-based platform for data-intensive biomedical research.


Prof. Erik Bongcam-Rudloff, SLU-Global Bioinformatics Centre, Sweden
Dr. Andreas Gisel, Institute for Biomedical Technologies, Italy
Dr. Anne Fischer, ICIPE, Kenya
Dr. Etienne de Villiers, KWTRP, Kenya
Rafael Hernández, Centro de Investigaciones Príncipe Felipe

Course programme


Introduction to Bioinformatics 
How to use the eBioKit
UNIX command line


Introduction to Biological Databases
Basics of Blast search
Constructing your own searchable blast database
MRS: searching with names and keywords
Introduction to Genome Browsers: Ensembl: part 1


Exploring ENSEMBL functionalities: part 2
EMBOSS (the European Molecular Biology Open Software Suite):
Alignments, global, local
Searching with motifs and more
Multiple alignments
Introduction to Phylogenetics 


Introduction to the Galaxy platform
NGS data quality control 
NGS genome mapping/SNP analysis


NGS Metagenomic data analysis
Using a Bioinformatics "Graphic User Interface"


Training Materials Availability:

Training materials for this course are not currently available.