Attendees of the Establishing Capacity for Pathogen Genomics 2023
About the course
This workshop was by the Ethiopian Public Health Insitute in Addis Ababa, Ethiopia and took place on 7-12 May 2023. The in-person workshop consisted of lectures, workshops, knowledge exchange and networking, case studies, world café, individual and group projects and action settings. Over 30 research and healthcare professionals based in 26 African countries attended the workshop.
Topics
This workshop included the following topics:
- Practical approaches to establishing genomics and data infrastructure
- Data workflows, analysis and interpretation
- Pathogen genomics application in local and global contexts
- Data collection, linkage and integration
- Communication of data and public health decision-making
- Effective methods, tools, and resources for training others in pathogen genomics
- Building a sustainable model for sequencing capacity and data science
- Establishing workforce capacity for pathogen genomics
- Frameworks for genomic surveillance for research and public health practice skills training
- Consortium, network establishment and mentorship
Training team
Instructors and facilitators:
Amadou Diallo, Institut Pasteur de Dakar, Senegal
Aquilla Kanzi, African Society for Laboratory Medicine, Ethiopia
Brenda Kwambana, Malawi Liverpool Wellcome Trust, Malawi
Fatma Guerfali, Institut Pasteur de Tunis, Tunisia
Fatuma Guleid, Kenya Medical Research Institute, Kenya
Francis Chikuse, Africa Centre for Disease Control and Prevention, Namibia
George Githinji, Kenya Medical Research Institute, Kenya
Harris Onywera, Africa CDC Insitute of Pathogen Genomics, Ethiopia
John Tembo, HerpeZ, Zambia
Jonathan Emmanuel Chukwuemeka, Institute of Human Virology, Nigeria
Kareemah Suleiman, Institute of Human Virology, Nigeria
Kirsty Lee Garson, University of Cape Town, South Africa
Linzy Elton, University College London, United Kingdom
Luria Leslie Founou, CEDBCAM-RI, Cameroon
Sam Oyola, International Livestock Research Institute, Kenya
Stanford Kwenda, National Institute for Communicable Diseases, South Africa
Tapfumanei Mashe, National Microbiology Research Laboratory, Zimbabwe
Honorable guest speakers:
Alan Christofels, Public Health Alliance for Genomic Epidemiology, South Africa
Dawit Wolday, Ethiopian Public Health Institute, Ethiopia
Getachew Tollera, Ethiopian Public Health Institute, Ethiopia
Mebratu Messebo, Ethiopian Public Health Institute, Ethiopia
Messay Hailu, Ethiopian Public Health Institute, Ethiopia
Mohammed Rameto, Ethiopian Public Health Institute, Ethiopia
Naod Wendrad, Ministry of Health, Ethiopia
Saro Abdella, Ethiopian Public Health Institute, Ethiopia
Organisers:
Abebe Asefa, Ethiopian Public Health Insitute, Ethiopia
Alice Matimba, Wellcome Connecting Science, United Kingdom
Jorge Batista da Rocha, Wellcome Connecting Science, United Kingdom
Leigh Jackson, University of Exeter, United Kingdom
Liã Bárbara Arruda, Wellcome Connecting Science, United Kingdom
Melanie Sharpe, Wellcome Connecting Science, United Kingdom
Shavanthi Rajatileka, Wellcome Sanger Insitute, United Kingdom
Treasa Creavin, Wellcome Connecting Science, United Kingdom
Decodified Bioinformatics: the beginner’s journey into pathogen genomics
This is a learning-by-doing bilingual pilot approach in collaboration with Instituto Gonçalo Moniz FIOCRUZ-BA. In this initiative, the hosts and instructors work with the COG-Train education developers to deliver a bioinformatics course for beginners course in Portuguese.
In this approach, administrative and organisational documentation is provided in both English and Portuguese, while the course is delivered in the native language of the Brazilian audience.
Topics
The course will include the following topics:
- Basic concepts in pathogen genomics
- Command line logic
- Basic concepts of statistics for bioinformatics
- How to obtain high-quality data and why it is important
- Applications of bioinformatics in pathogen genomics
- Critical assessment of available analysis tools and resources
Training team
Instructors and facilitators
Andrêza Leite, Universidade Federal de Pernambuco, Brazil
Laise de Moraes, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Brazil
Luciane Amorim, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz e Escola Bahiana de Medicina e Saúde Pública, Brazil
Ricardo Khouri, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Brazil
Robson de Souza, Universidade de São Paulo, Brazil
Túlio Campos, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Brazil
Education developers and advisers
Liã Bárbara Arruda, Wellcome Connecting Science, United Kingdom
Jorge Batista da Rocha, Wellcome Connecting Science, United Kingdom