H3ABioNet Microbiome & Precision Medicine Portals Design Hackathon 12 -18 April 2019

This Hackathon aims to develop two H3ABioNet Databases and Resources Work Package Portals:

1. 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 and resources in order to support precision medicine initiatives within Africa.
2. African Microbiome Portal (AMP) - a web based portal to collate, curate and provide primary references for African specific microbiome metadata and resources for African based microbiome research.

The hackathon participants will be divided into three streams: Stream A for the African Precision Medicine web portal development, Stream B for the African Microbiome web portal development and Stream C for testing the portals. An additional team for writing and drafting a manuscript about the hackathon will also be formed. Stream A and B will consist of technical programming members as well as portal content experts. Stream C consists local undergraduate students who should be recruited from IPT for testing the two portals.

This hands-on course is a 2-day intensive overview of Fragment Analysis (i.e. Microsatellite). Course topics include application workflow setup and optimization; an overview of instrument hardware, operation and maintenance; use of data collection software; preparation and running of samples and standards; analysis software tutorials, and troubleshooting discussions. Students will run, analyze and troubleshoot sequencing samples as well as fragment analysis samples. Applied Biosystems 3500 instruments will be used for lab practicals.

Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 24-25 March 2019

This hands-on course is a 2-day intensive overview of DNA sequencing. Course topics include application workflow setup and optimization; an overview of instrument hardware, operation and maintenance; use of data collection software; preparation and running of samples and standards; analysis software tutorials, and troubleshooting discussions. Students will run, analyze and troubleshoot sequencing samples as well as fragment analysis samples. Applied Biosystems 3500 instruments will be used for lab practicals.

NMIMR H3ABioNet Intermediate Bioinformatics Workshop (7^th-11^th July, 2014 at the NMIMR Conference Room, Legon Accra, Ghana)
This Intermediate Bioinformatics Workshop will strengthen and expand on some relevant tools in Bioinformatics and Computational Biology. It will also serve as a refresher for trainees of the previous workshop enabling a better integration of Bioinformatics into their on-going research and teaching. This workshop will prepare participants adequately to enrol in the last (advanced) workshop of the series in the current year. The modules for the Intermediate Workshop, like the previous modules, will be based on freely available software suites, Biocomputing platforms and data from public databases. Each module will consist of lectures, demonstrations and hands-on tutorials.

No advanced general bioinformatics courses have been run to date.

INDA Hands-on NGS-Statistics course (3^rd-14^th October 2016, Institut Pasteur, Senegal)
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.

Bioinformatics analysis and annotation of variants in NGS data (4^th-6^th April 2016, Cape Town, South Africa)
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.

Bioinformatics in the tropics Uganda 2015: Introduction to bioinformatics analysis techniques for next generation sequencing data (6^th-10^th July 2015, Entebbe, Uganda)
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 analysis e.g. de novo genome assembly, annotation, SNP calling, HIV-1 drug resistance mutation genotyping, population genetics/phylogenetics etc will be covered. Tools for data visualization and analysis e.g. Galaxy, e-Biokit among others will also be introduced. Usage of open source technologies will be encouraged. 

H3ABioNet Advanced Systems Administration Workshop (2nd - 11th February, 2015, Bioinformatics and Computational Biology Unit, University of Pretoria)
The aim of the workshop is to train newly hired System Administrators and/or their representatives on systems administration of Unix type servers/infrastructure relevant for data management and storage for H3Africa affiliated projects and subsequent bioinformatics research.

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