Past overseas courses
2013
Genomics and Epidemiological Surveillance of Bacterial Pathogens, San José, Costa Rica 3-8 February 2013
The aim of this course is to forge a strong link between traditional methods of epidemiological surveillance, the latest molecular sub-typing techniques and the ability to use, analyse and interpret whole genome sequence data for the same purpose. The course is targeted at clinical molecular biologists and microbiologists working in resource-limited countries in Latin America and the Caribbean and will focus on human, animal and food-borne bacterial diseases.
This new course is a collaboration between Wellcome Trust Advanced Courses, The Wellcome Trust Sanger Institute Pathogen Genomics Group, The PulseNet Latin America & Caribbean Network, The University of Costa Rica and Universidad Nacional of Costa Rica.
2012
Working with Pathogen Genomes, Bangkok, Thailand 20-24 February 2012
This five-day workshop aims to give molecular microbiologists a working knowledge of genomic analysis, which will cover the handling and processing of DNA sequence and transcriptomic data produced by ‘second generation’ sequencers. The workshop will be taught by members of the Wellcome Trust Sanger Institute Pathogen Genomics team and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Modules will be introduced with a short talk, followed by 'hands on' worked examples using bacterial and small eukaryotic pathogens.
The workshop begins with training in the use of genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute for genome exploration and comparative genomics. It then goes onto cover the mapping of Illumina sequence data and calling and recording SNPs and other sequence variation data. The course also features a module that aims to teach the basics of using genome/gene sequences to plot phylogenetic relationships between microbes, as well as an introduction to Perl programming for basic processing and mining of data.
Working with the Human Genome Sequence Montevideo, Uruguay 16-19 April 2012
This 4-day workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will have access to a desk-top PC for the duration of the course.The course is limited to 20 participants and will be held in English.
Topics
Sequence formats and retrieval
Genome browsing
De novo analysis of sequence
Exploring function and disease
Sequence variation
Comparative sequence analysis
Genomic Epidemiology in Africa, Blantyre, Malawi, 6-11 May 2012
Large-scale genetic studies have become a powerful tool for understanding resistance and susceptibility to disease. There is growing interest among medical researchers in Africa in applying these new methodologies to gain a better understanding of common diseases that affect African populations. This course aims to describe the key aspects of population genetics and genome wide association studies (GWAS); participants will be able to perform analyses on their own data. We will cover both theoretical and practical issues of genetic epidemiology via association analysis, illustrating particular concepts with examples from recent studies in Type 2 Diabetes, sickle cell disease and Malaria.
Course Organisers
Muntaser Ibrahim (University of Khartoum, Sudan)
Manj Sandhu (Wellcome Trust Sanger Institute, UK)
Inês Barroso (Wellcome Trust Sanger Institute, UK)
Jeff Barrett (Wellcome Trust Sanger Institute, UK)
Chris Spencer (Wellcome Trust Centre for Human Genetics, Oxford, UK)
Kirk Rockett (Wellcome Trust Centre for Human Genetics, Oxford, UK)
Working with the Human Genome Sequence, Ho Chi Minh City, Vietnam, 3-6 December 2012
This 4-day workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will have access to a desk-top PC for the duration of the course. The course is limited to 20 participants and will be held in English.
Topics
Sequence formats and retrieval
Genome browsing
De novo analysis of sequence
Exploring function and disease
Sequence variation
Comparative sequence analysis
2011
Working with Pathogen Genomes, New Delhi, India 16-21 January 2011
This five-day workshop aims to give microbiologists with a working knowledge of computational sequence analysis, a firm grounding in the use of the latest genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute Pathogen Sequencing Unit (PSU).
Artemis is a powerful annotation tool and DNA viewer that allows the user to analyse sequence data generated in house as well as being able to upload and re-analyse data taken from databases such as EMBL or Genbank. ACT is a comparative genomic tool that allows direct, and interactive, comparisons of multiple genomes/sequences. This enables the user to exploit the growing number of genomes from closely related organisms to look at genome architecture and evolution.
The course will be taught by members of the PSU and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Each module will be introduced with a short talk followed by 'hands on' worked examples using many of the organisms sequenced by the PSU (bacterial pathogens e.g. Salmonella and Chlamydia), as well as small eukaryotic pathogens (such as Plasmodium and Trypanosomes) to illustrate points in whole genome analysis.
Working with the Human Genome Sequence Dubai, United Arab Emirates 19-21 March 2011
The workshop is being held as a post-meeting event to the HGM2011 conference, Dubai. This three-day workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will need to bring their own laptop computer to use for the duration of the course. This course is limited to 30 participants and will be held in English.
Topics
Sequence formats and retrieval
Genome browsing
'De novo' analysis of sequence
Exploring function and disease
Sequence variation
Comparative sequence analysis
Working with Pathogen Genomes Montevideo, Uruguay 20-25 March 2011
This five-day workshop aims to give microbiologists with a working knowledge of computational sequence analysis, a firm grounding in the use of the latest genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute Pathogen Sequencing Unit (PSU).
Artemis is a powerful annotation tool and DNA viewer that allows the user to analyse sequence data generated in house as well as being able to upload and re-analyse data taken from databases such as EMBL or Genbank. ACT is a comparative genomic tool that allows direct, and interactive, comparisons of multiple genomes/sequences. This enables the user to exploit the growing number of genomes from closely related organisms to look at genome architecture and evolution.
The course will be taught by members of the PSU and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Each module will be introduced with a short talk followed by 'hands on' worked examples using many of the organisms sequenced by the PSU (bacterial pathogens e.g. 'Salmonella' and 'Chlamydia'), as well as small eukaryotic pathogens (such as Plasmodium and Trypanosomes) to illustrate points in whole genome analysis.
Molecular Approaches to Clinical Microbiology in Africa, Blantyre, Malawi 10-16 September 2011
This practical, laboratory-based course aims to introduce clinical microbiologists and laboratory scientists working in Africa to genome-based molecular techniques for the diagnosis and characterisation of, and research into, bacterial pathogens.These techniques shall be: (i) currently applicable in African laboratories; (ii) likely to be applicable in Africa in the foreseeable future; or (iii) of value to participants in interpreting the literature and assessing the likely utility of new technologies as they are developed.
An important objective is to provide a foundation-level of understanding of the philosophy, methods and vocabulary of molecular techniques for those primarily trained in culture-based microbiology.
Working with the Human Genome Sequence, Kilifi, Kenya 31 October-2 November 2011
This three-day workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will have access to a desk-top PC to use for the duration of the course. This course is limited to 30 participants and will be held in English.
Topics
Sequence formats and retrieval
Genome browsing
'De novo' analysis of sequence
Exploring function and disease
Sequence variation
Comparative sequence analysis
2010
Working with Pathogen Genomes, Ho Chi Minh City, Vietnam 28 February-6 March 2010
This five-day workshop aims to give microbiologists with a working knowledge of computational sequence analysis, a firm grounding in the use of the latest genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute Pathogen Sequencing Unit (PSU). This workshop is free to attend for non-commercial applicants and bursaries are available to cover travel and accommodation (see below for details).
Artemis is a powerful annotation tool and DNA viewer that allows the user to analyse sequence data generated in house as well as being able to upload and re-analyse data taken from databases such as EMBL or Genbank. ACT is a comparative genomic tool that allows direct, and interactive, comparisons of multiple genomes/sequences. This enables the user to exploit the growing number of genomes from closely related organisms to look at genome architecture and evolution.
The course will be taught by members of the PSU and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Each module will be introduced with a short talk followed by 'hands on' worked examples using many of the organisms sequenced by the PSU (bacterial pathogens e.g. 'Salmonella' and 'Chlamydia'), as well as small eukaryotic pathogens (such as Plasmodium and Trypanosomes) to illustrate points in whole genome analysis.
Working with the Human Genome Sequence, Montevideo, Uruguay 9–12 March 2010
This workshop is being held as a pre-meeting event to the ISCB Latin America 2010 conference, Montevideo. The 4-day programme provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be available on the web, and students will have the opportunity to ask questions of the instructors as they apply what they have learned. Each student will have access to a desk-top PC for the duration of the course.
Topics
Sequence formats and retrieval Genome browsing
De novo analysis of sequence
Exploring function and disease
Sequence variation
Comparative sequence analysis
Genomic Epidemiology in Africa, Kilifi, Kenya 28 November-3 December 2010
Genome wide association studies (GWAS) have become a powerful tool for obtaining clues to the genetics of resistance and susceptibility to disease. There is growing interest among medical researchers in Africa in applying these new methodologies to gain a better understanding of common diseases that affect African populations. This course aims to describe the key aspects of GWAS to enable participants to perform analyses in their own research. To do so, we will cover both theoretical and practical issues of genetic epidemiology via association analysis, illustrating particular concepts with examples from recent studies in Type 2 Diabetes, Malaria and Obesity.
Course Instructors
Dominic Kwiatkowski (Wellcome Trust Sanger Institute/ University of Oxford, UK)
Tom Williams (Kenya Medical Research Institute (KEMRI)/ University of Oxford, UK)
Muntaser Ibrahim (University of Khartoum, Sudan)
Manj Sandhu (Wellcome Trust Sanger Institute, UK)
Inês Barroso (Wellcome Trust Sanger Institute, UK)
Jeff Barrett (Wellcome Trust Sanger Institute, UK)
Ele Zeggini (Wellcome Trust Sanger Institute, UK)
Chris Spencer (Wellcome Trust Centre for Human Genetics, Oxford, UK)