Course Overview: This interactive workshop will provide an overview of data management, analysis and submission for H3Africa projects. It also provides an opportunity for Data Support Working Group members, who represent the H3Africa projects to engage with H3ABioNet and discuss their needs.

Intended Audience: This workshop is aimed at Data Support Working Group members who should be the H3Africa project data managers, data analysts or bioinformaticians. It is important that the attendees have knowledge of the data being generated by their H3Africa projects and information about the project’s data analysis plan.

Keywords: Data handling, Ontologies, Genomics, Nucleic acid analysis

Language: English

Skill level: Intermediate

Type of training: face-to-face / in person

Credential awarded: none

Workshop dates: 12th May 2016

Venue: Ocean Room, Radisson Blu Hotel, Dakar, Senegal

Workshop organisers and sponsors: H3ABioNet, NIH Common Fund

Workshop trainers and support: Nicola Mulder, Sumir Panji, Ayton Meintjes, Scott Hazelhurst, Fourie Joubert, Alia Benkahla and Faisal Fadlemola.


Syllabus: Participants will discuss their current data plans and challenges. Lectures will be given on Clinical data collection & storage, overview of GWAS/NGS/microbiome processing, downstream analysis (Variant annotation, meta-analysis, structure, ancGWAS), Data transfer considerations, security, data processing options, and H3Africa Archive and EGA submission. This will be followed by discussion on developing data management plans (with reference to the article: Michener WK (2015) Ten Simple Rules for Creating a Good Data Management Plan. PLoS Comput Biol 11(10): e1004525), and interactive sessions discussing specific projects.

Prerequisites: Participants should complete the survey at: H3Africa Data Support workshop planning survey - Senegal 2016. One survey needs to be completed per H3Africa project.


  • Participants will learn how to develop a data management plan.
  • Participants will gain basic knowledge on issues around data security & submission.
  • Participants should come out understanding what considerations there are for their own data analysis, storage and compute requirements.
  • Participants will be able to engage with H3ABioNet on their needs and issues.

Workshop limitations: This workshop will provide a foundation for continued learning in the handling of H3Africa project data. It will not make one an expert in specific data  analysis pipelines.

Workshop Program

Time Topic
8:30 am Registration
9:00 am Welcome and Participant introductions (Nicky)
9:10 am Discussion in groups on workshop expectations and report back (All)
9:30 am Clinical data storage (Freedom) & CRF harmonization (Alia)
10:00 am Overview of NGS data analysis pipeline for human genomes & microbiomes (Fourie)
10:30 am Tea break
11:00 am Overview of GWAS data analysis pipelines (Scott)
11:30 am Down stream analysis varian tannotation and analysis (Nicky)
11:50 am Data processing options - Cloud & Galaxy (Scott & Fourie)
12:20 pm Data transfer, storage and security considerations (Ayton)
12:40 pm H3Africa Archive and EGA submission (Ayton)
1:00pm Lunch break
2:00pm Developing a Data Management plan (Sumir,Faisal)
2:20pm Group sessions on data management plans (Break-out sessions)
3:00pm Tea Break
3:30pm Report back on data management sessions (group leads)
4:00pm Group sessionson data analysis requirements(Break-outsessions)
4:40pm Report back on data analysis break-out sessions (group leads)
5:00pm Workshop End


Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.