Course Overview
One of H3ABioNet’s deliverables is to investigate the use of Cloud computing for H3Africa data analysis. It was recently agreed that important pipelines should be made available as Docker containers that can be deployed on public or private clouds. The Wits’ Node has made a start by “containerizing” the Wits GWAS pipeline, and a Cloud Computing Task Force has recently been established in H3ABioNet to examine and implement the use of cloud based technologies for bioinformatics pipelines relevant to H3Africa researchers. In order to further the work of this task force we will be holding a Cloud computing hackathon.
Intended Audience
H3ABioNet staff and students with working knowledge of Cloud computing and developing containers International collaborators with expertise in developing Docker containers
Skill level of training: Advanced
Language: English
Credential awarded: No credential awarded
Type of training: Face-to-face
Venue of the course: University of Pretoria, South Africa
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: Scott Hazelhurst, Fourie Joubert, Sumir Panji and Nicola Mulder
Participation: -
Course Sponsors: H3ABioNet
Course objectives

To bring together H3ABioNet staff and students who have some working knowledge of Cloud computing and enable them to interact with international partners with experience in  Docker pipelines

  • To assess existing Docker containers for relevant pipelines
  • To develop Docker containers for specific pipelines of relevance to H3Africa
  • To work on interoperability between containers and portability
  • To document the pipelines and make them available from the H3ABioNet website and/or GitHub
  • To document the available public and private clouds with the appropriate infrastructure for these pipelines to be run on

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

The selection will be partly through an open call for applications and part invitation. As this will be a working meeting, participants are expected to have good programming ability (Python is likely to be the working language) and some knowledge of some of the following areas bioinformatics, cloud computing, Docker, pipeline construction (we don’t expect everyone to know everything and will have multi-skilled teams).

Course limitations
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Training material availability