Pan African Bioinformatics Network for H3Africa

H3ABioNet Technical Training Course (University of Pretoria, South Africa): 3 - 14 June 2013.

Workshop training materials are available at: http://training.h3abionet.org/technical_workshop_2013/

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.

In order to prepare for the large amount of data that will be generated by the various projects, the initial requirement is to set up the required computational infrastructure and resources to store, manage the data. To address this requirement, the H3ABioNet will be hosting a technical training course for H3ABioNet-funded staff and students.

Course objectives

The objective of the two-week training course is to equip H3ABioNet technical staff and students at the partner sites with the skills required to set up and maintain the necessary computational infrastructure and resources. The course will be both theoretical and practical, with an emphasis placed on hands-on experience in setting up and maintaining these resources. The course is aimed at individuals with a computational science background.

Course outline

Linux installation and system administration

Galaxy installation, configuration and optimisation

High performance computing, optimisation for genomic applications

Security and data stewardship, firewalls, intrusion detection, data backups and archives, encryption, data privacy

Data management, GridFTP, Globus Online, database design, web interfaces

Genome databases, CHADO and BioMart,

Data Visualisation, genome browsers, trackster and DAS

Cloud computing, basic concepts, cloud services, creating virtual machines, deploying software environments, CloudMan, genome browsers

Course prerequisites

The course will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences. The minimum requirement is a computer science/IT background with some Unix and programming experience.

How to apply

To apply to attend the course please complete the application form found here:


Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached. The deadline for applications is the 10th May 2013