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.
Intended Audience
H3Africa 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.
Skill level of training: Beginner
Language: English
Credential awarded: No credential awarded
Type of training: Face-to-face
Venue of the course: International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: H3ABioNet
Participation: The course is open to H3Africa members
Course Sponsors: H3ABioNet Local Classrooms
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.


Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at

Participant applications

Registration for participants opens: Thu, 01/01/1970
Registration for participants closes: Thu, 01/01/1970
Participant registration link:
Syllabus and Tools


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"

Course limitations
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Training material availability

Training materials for this course are not currently available.