H3ABioNet Courses and Events

H3ABioNet delivers high quality training covering various aspects of bioinformatics

Training

Upcoming and Current Training

H3ABioNet organises a variety of high-quality courses and training events covering various aspects of bioinformatics from general introductory topics to more specialised ones such as Next Generation Sequencing and Genome-Wide Association Studies analyses.
Training proposals on different topics that are pertinent to human health, have synergies with the H3Africa projects and are also in line with H3ABioNet's vision of developing Bioinformatics capacity within Africa, may be submitted here. Please also take note of the H3ABioNet training event policy available here.

Past Courses and Training Events

H3ABioNet has hosted and been involved in a number of training events and courses since it's conception in 2012. For a list of past H3ABioNet courses and training events and to access the applicable training material, please browse through the training categories below:

Bioinformatics Introduction

2024
- UCT Software Carpentry Workshop April 2024
  Course Overview: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one...
- Introduction to Bioinformatics Training 2024
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.
2023
- Online Ensembl Genome Browser Workshop 2023
  Course Overview: This one-day workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser (https://ensembl.org/), but also provides them with the necessary background information. The workshop consists of a series of modules which include a presentation and a demonstration of the...
- Introduction to Bioinformatics Training 2023
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.
2022
- Introduction to Bioinformatics Training 2022
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.
- UCT CBIO Software Carpentry Workshop March 2022
  Course Overview: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover an introduction to The Shell, Python and R. Participants will be encouraged to help one another and to apply what they have learned to their own...
- Virtual Software Carpentry Workshop, NGS Academy 2022
  Course Overview: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one...
2021
- Look Out for IBT 2021 Classroom Call
  Course Overview: H3ABioNet‘s IBT 2021 Classroom Call H3ABioNet‘s Introduction to Bioinformatics course (IBT) provides an introduction to the field of bioinformatics with a focus on important bioinformatics tools and resources. The 2021 iteration will be running soon. Kindly watch out for the call for classrooms by 26th April 2021.
- Ensembl Genome Browser Workshop, April 2021, Cape Town, South Africa
  Course Overview: The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background...
- Introduction to Bioinformatics Training 2021
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources. Intended Audience: The...
2020
- Introduction to Git and Github 30 Nov 2020
  Course Overview: The use of repositories and version control tools such as GitHub and Git for hosting, pulling, installing and collaborative development of code and software in bioinformatics is now commonplace. The “Introduction to Git and Github” course will provide an overview of version control, creating a GitHub account and how to use Git...
- Introduction to Nextflow Workshop 2020
  Course Overview: The use of workflow technologies such as Nextflow is becoming increasingly pervasive in bioinformatics. Workflows automate the execution of various bioinformatics tools and pipelines and reduces the time one spends on running the different steps in a particular pipeline while testing various parameters as well as enabling...
- Introduction to Bioinformatics Training 2020
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.
2019
- Introduction to Bioinformatics Training 2019
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.
- Ensembl Genome Browser Workshop, 20 May 2019, Cape Town, South Africa
  Course Overview: The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background...
2018
- Introductory Python based Software Carpentry_2018
  Course Overview: Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one...
- Introduction to Bioinformatics Training 2018
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources. Intended Audience: The...
2017
- Introduction to Bioinformatics Training 2017
  Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources. Intended Audience: The...
2016
- Ensembl Browser Workshop- University of Cape Town, 6th June 2016
  Course Overview: The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background...
- H3ABioNet Introduction to Bioinformatics online course (IBT_2016)
  Course Overview: The IBT_2016 course is an introduction to the field of Bioinformatics, with a focus on important Bioinformatic tools, algorithms and resources. Over a period of 3 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow participants to gain practical experience in using various...
2015
- Bioinformatics in the tropics Uganda 2015: Introduction to bioinformatics analysis techniques for next generation sequencing data
  Course Overview: The workshop involves theoretical lectures and practical sessions on analysis techniques for dealing with Next Generation Sequencing (NGS) data, including an introduction to programming for the study of large data sets of HIV and other genomic data. It will introduce working in Linux and R statistical programming. Various topics on NGS...
- Introduction to Biostatistics for Genome Wide Association Testing 2015
  Course Overview: The “Introduction to Biostatistics for Genome Wide Association testing” workshop provides an introduction to the basic concepts in biostatistics required for genome wide association studies, e.g. data types, experimental design, statistical tests, probabilities, R, etc. During the second week, basic statistical concepts relevant to...
2014
- H3ABioNet Postgraduate Bioinformatics Workshop 21st April-26th May 2014 Covenant University Bioinformatics Research (CUBRe), Ota Nigeria
  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....
2013
- H3ABioNet Introduction to Bioinformatics using the eBioKit platform 29th of July to 2nd of August 2013 International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
  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...

Bioinformatics Intermediary

2022
- post-GWAS Intermediate Bioinformatics Training Course
  Several projects within the H3Africa consortium are conducting Genome Wide Association Studies on different traits and phenotypes. H3ABioNet has run several workshops on the analysis of GWAS data, however, much of the focus has been on the quality control and running of the association analysis. H3ABioNet would therefore like to run a Post-GWAS...
2021
- Introduction to Hands-on Bioconductor Workshop
  Course Overview: The introduction to hands-on Bioconductor workshop is a virtual two-half-day training to provide an overview of leveraging open-source Bioconductor resources for research studies. There will be two courses offered by the BioConductor community: Introduction to Bioconductor Annotation Resources (Thursday, 29th April) Epidemiology...
2020
- 16SrRNA Microbiome Intermediate Bioinformatics Training_2020
  Course Overview: The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools. The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a...
- 16S rRNA Microbiome Intermediate Bioinformatics Training 2021
  Course Overview: The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools. The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a...
2019
- 16SrRNA Microbiome Intermediate Bioinformatics Training
  Course Overview: The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools. The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a...
2017
- Analysing the Microbiome 29th to 31st March 2017
  Workshop Overview: The development of next generation sequence technology has led to rapid advances in microbiome study. The Sydney Brenner Institute for Molecular Bioscience with support from the Pan-African Bioinformatics Network for H3Africa will be offering a short-course on the bioinformatics of analysing the microbiome. The course will give...
- EMBO Practical Course on Computational analysis of protein-protein interactions: From sequences to networks
  EMBO Practical Course on Computational analysis of protein-protein interactions: From sequences to networks.
- H3ABioNet NABDA Metagenomics Data Analytics Workshop July 21 - 25, 2014, Ibadan, Nigeria
  Course Overview: Metagenomics uses advanced DNA sequencing technologies to generate data on the collection of genomes and genes from the assemblage of microorganisms present in a defined environment. The microbiome is the entire habitat, including the microorganisms, their genomes and the surrounding environmental conditions. Advances in...
- NMIMR H3ABioNet Intermediate Bioinformatics Workshop 2014
  Workshop Overview: The H3Africa Consortium aims to study the genomic and environmental determinants of diseases in Africa. It also strives to build genomic expertise among scientific investigators in Africa as well as encourage collaborations between them through infrastructure development and research support. The H3ABioNet, a Pan African...
- Computational Metagenomics Workshop University of Mauritius 1st Dec – 5th Dec 2014
  Workshop Overview: The Computational Metagenomics Workshop at the University of Mauritius will provide a week-long series of training seminars, practical demonstrations, hands-on tutorials and research talks on the use of software tools to analyze and interpret metagenomics data. The scope is quite broad and offers an overview of cutting-edge...

Bioinformatics Advanced

Data Management

H3ABioNet Data Management Workshop June 3 - 6, 2014, Cape Town
Course Overview: The goal of the H3ABioNet Data Management workshop is to prepare H3Africa researchers for management of their data, including knowing what data to collect, what file formats, etc. to use. The course will present options for setting up and storing patient data, discuss the EGA requirements to ensure the researchers collect all the necessary...
H3ABioNet Data Support Workshop - 8th H3Africa Meeting
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...
Bioschemas Workshop_Cape Town_May_2019
Course Overview: Various data intensive initiatives are taking place in South Africa that will involve in the storing and describing of genomics data in various platforms. The utility of data for research and reuse is how well structured and described the data and meta-data records are as this contributes towards making data FAIR. Bioschemas (...
Research Data Management Short Course June 2021
Course Overview: The Research Data Management (RDM) short course will introduce the principles and practices of RDM and provide practical advice for implementing these practices in an African research context. Topics covered will include data discovery and re-use, data documentation and organization, data standards and Ontology, data storage and...
H3ABioNet Research Data Management (RDM) Short Course 2022
Course Overview: The Research Data Management (RDM) short course introduces the principles and practices of RDM and practical advice for implementing these practices in African research context. Topics covered include data discovery and re-use, data documentation and organization, data standards and Ontology, data storage and security,...
H3ABioNet Research Data Management (RDM) Short Course 2023
Course Overview: The Research Data Management (RDM) short course introduces the principles and practices of RDM and practical advice for implementing these practices in African research context. Topics covered include data discovery and re-use, data documentation and organization, data standards and Ontology, data storage and security,...

Education

2022
- Train-the-Trainer: Course Design and Delivery for Bioinformatics Trainers
  Course Overview: H3ABioNet, Wellcome Connecting Science and the European Bioinformatics Institute are hosting a Train-the-Trainer workshop. The aim of the workshop is to empower trainers and educators focused on bioinformatics and data science to design, develop, and deliver effective training in their field of expertise. Trainers will learn how to...
2020
- Bioinformatics Instructional Design Online Course: Oct - Nov 2020
  Course Overview: The societal challenge of the 2019 Coronavirus Disease (COVID-19) pandemic increases the global needed for technology-facilitated learning. Additionally, there is a growing need for experts who can design and deliver technology-facilitated courses that enable course participants to successfully apply course knowledge content and...
2018
- GOBLET Bioinformatics Training Best Practices Workshop
  Course Overview: The Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), together with H3ABioNet will be running a Best practices in Bioinformatics Training workshop in Cape Town from the 16th - 17th of November 2015. The first day will cover aspects of teaching and the second day will be more of a workshop to...
2017
- H3ABioNet University of Botswana Bioinformatics Curriculum Development Workshop 2014
  Course Overview: The goal of the H3ABioNet and University of Botswana curriculum development workshop is to present success stories of Masters programmes that have been developed elsewhere and then discuss the challenges in starting such a programme at African universities who don’t yet offer them, and how to overcome these challenges. The...
2013
- H3ABioNet Train-the-Trainer Bioinformatics Course 8th – 26th July 2013 International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
  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. The...
- H3ABioNet NABDA Node Training Course on Visual Analytics of Human Genome Variation Datasets
  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....

African Genomic Medicine Training Initiative (AGMT)

African Genomic Medicine Training Initiative (AGMT) 2017, 2019, 2022 & 2023

The African Genomic Medicine Training Initiative (AGMT) was launched in May 2016, in Senegal, by a group of stakeholders from the Human Heredity and Health in Africa (H3Africa) Consortium and the African Society of Human Genetics (AfSHG). The work was initiated by a working group made up of volunteers from across the globe which was made up of experts and supported by consultants. In addition, there was an advisory board. The different working group members volunteered for specific tasks such as developing competencies and curricula for healthcare professionals, to be trainers, facilitators, and a workshop task team. This initiative started as a response to the lack of Genetics and Genomics training for healthcare professionals in Africa.

The first and second iterations ran in 2017 and 2019 respectively and targeted Nurses as the first group of healthcare workers to be trained. This is because Nurses are pivotal to the realization of Genomic Medicine in Africa as they are frontline workers in most healthcare facilities in Africa and have access to in-depth knowledge of the patients, families, and communities.

However, due to the demand for Genomic Medicine training from Medical Doctors, Pathologists, Medical Laboratory Scientists and Medical Laboratory Technicians and considering that they are also likely to have an impact on Genomic Medicine, the curriculum was reviewed and adjusted to suit these groups. As a result, the third and fourth iterations which ran in 2022 and 2023 respectively included a curriculum for Medical Doctors, Pathologists, Medical Laboratory Scientists and Medical Laboratory Technicians in addition to the initially implemented curriculum for Nurses.

The course was sponsored by the Pan African Bioinformatics Network for H3Africa (H3ABioNet) and classroom infrastructure was provided and sponsored by the host classrooms. Participants attended the course free of charge and all staff (core team, trainers, classroom hosts, facilitators and systems administrators) were working on a voluntary basis.

GWAS

Introduction to Biostatistics for Genome Wide Association Testing 2015
Course Overview: The “Introduction to Biostatistics for Genome Wide Association testing” workshop provides an introduction to the basic concepts in biostatistics required for genome wide association studies, e.g. data types, experimental design, statistical tests, probabilities, R, etc. During the second week, basic statistical concepts relevant to...
Medical population genetics and GWAS for complex diseases 19th April - 24th April, 2015
Course Overview: The workshop will be split into two tracks: An introductory track that will cover fundamental assumptions, showcase recent successes and discuss limitations of current GWAS approaches in the field of complex diseases, particularly in the case of African populations with known low linkage disequilibrium (LD). It will also provide...
Covenant University GWAS workshop for complex diseases 2015
Course Overview: This workshop provides an overview on medical population genetics, PLINK and basic statistics and practicals in order to build a foundational knowledgebase for genome wide association testing. The workshop will consist of a series of theory lectures and a “hands on” practical lab session at the end.
Genome Wide Association Studies, Quality Control and Family based analysis
Course Overview: The post-genomic era has been characterized by the rapid advance of genotyping technology resulting in a wealth of new, high-quality data that may hold promise for the further elucidation of genetic factors underlying complex disease. Without the proper tools and methods, the ultimate utility of such rich data may be limited in...
Introduction to Genome-Wide Association Studies (GWAS) for complex diseases
Course Overview: The African Institute for Mathematical Sciences (AIMS) Ghana and the H3ABioNet Node of the Noguchi Memorial Institute for Medical Research (NMIMR) University of Ghana, are organizing a five-day intensive workshop on GWAS for complex diseases.
H3Africa Genotyping Chip Data Analysis and GWAS workshop, 2018
Course Overview: The H3Africa chip is being used by the H3Africa projects to generate data that will need to be analysed. The course will consist of two components; a series of online lectures provided by experts in that specific domain. These are to introduce the main concepts and theory behind population genetics and GWAS. The second part of...
post-GWAS Intermediate Bioinformatics Training Course
Several projects within the H3Africa consortium are conducting Genome Wide Association Studies on different traits and phenotypes. H3ABioNet has run several workshops on the analysis of GWAS data, however, much of the focus has been on the quality control and running of the association analysis. H3ABioNet would therefore like to run a Post-GWAS...

NGS

Bioinformatics in the tropics Uganda 2015: Introduction to bioinformatics analysis techniques for next generation sequencing data
Course Overview: The workshop involves theoretical lectures and practical sessions on analysis techniques for dealing with Next Generation Sequencing (NGS) data, including an introduction to programming for the study of large data sets of HIV and other genomic data. It will introduce working in Linux and R statistical programming. Various topics on NGS...
INDA Hands-on NGS-Statistics course - October 3rd to 14th 2016
Course Overview: This theoretical and practical course is aimed at researchers that would like to get the most out of their Next Generation Sequencing datasets. We will tackle several topics, encompassing theoretical NGS approaches and statistical analysis of NGS data. The first week of this course (Oct 3rd – 7th) will be devoted to theory and...
Bioinformatics analysis and annotation of variants in NGS data
Course Overview: This workshop provides an introduction to the computational analyses of NGS data from pre-processing to the identification and annotation of genomic variants and the functional effects of those variants, as well as the use of pharmocogenomic databases.
Next Generation Sequencing Bioinformatics Course 2021
Course Overview: Next generation sequencing (NGS) has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by next generation sequencers. This course will equip participants with the essential...
Next Generation Sequencing Bioinformatics Course 2022
Course Overview: Next generation sequencing (NGS) has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by next generation sequencers. This course will equip participants with the essential...

Research Skills

SysAdmin and Technical

H3ABioNet Technical Training Course (University of Pretoria, South Africa)
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 Advanced Systems Administration Workshop - Bioinformatics and Computational Biology Unit, University of Pretoria 2nd to 11th Feb 2015
Course Overview: In keeping with the H3ABioNet Consortium's mandate to build and develop bioinformatics capacity in Africa, the Infrastructure Working Group (ISWG) is organizing an H3ABioNet-Funded Technical-Training workshop for System Administrators of the various Nodes and H3Africa projects. This is a follow up to the initial systems...
H3ABioNet Cloud computing hackathon
Hackathon 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...
H3ABioNet Microbiome & Precision Medicine Portals Design Hackathon
Hackathon Overview: This Hackathon aims to develop two H3ABioNet Databases and Resources Work Package Portals: African Precision Medicine Portal (APMP) - a web based portal to collate and curate pharmacogenomics and other genomic medicine metadata specific to African populations, as well as links to existing precision medicine implementation tools...

Scientific Communication