Venue of workshop: ICT Building, Covenant University, Ota, Ogun state, Nigeria

    Dates for the workshop: 29th June to 1st July, 2015

    Workshop organisers:Covenant University Bioinformatics Research Unit

    Registration opens: 15th June, 2015

    Registration closes: 23rd June, 2015

    Notification date: 27th June, 2015

    Link to workshop:http://cubre.covenantuniversity.edu.ng/index.php/covenant-university-gwas-workshop-for-complex-diseases-2015/

    Participation: Successful applicants will be contacted on how to participate.

    Workshop Sponsors:Covenant University Bioinformatics Research Unit

    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.

    Intended Audience: This workshop is aimed at H3Africa project members who will be involved in the design and analyses of population data and genome wide association testing and will be able to attend from the West African region within a virtual environment.

    Syllabus and Tools: Participants will learn about PLINK, Quality Control and association testing.

    Prerequisites: Participants are encouraged to work through the following resources to enable them to gain the most from the workshop:
    •    http://www.ee.surrey.ac.uk/Teaching/Unix/
    •    http://www.r-tutor.com/r-introduction
    •    http://onlinestatbook.com/2/introduction/introduction.html
    •    http://pngu.mgh.harvard.edu/~purcell/plink/


    Objectives: After this workshop participants should be able to:
    - Conduct genotype calling and association testing
    - Conduct population structure and correct for population structure 
    - Have a good familiarity with PLINK and conducting whole genome data analysis within PLINK
    - Have a good background on the theory behind medical population genetics
    - Be able to conduct a variety of population genetics statistical tests

    Workshop limitations: This workshop will only provide a foundation for continued learning in GWAS study design and medical population genetics and will not make you an expert in medical population genetics and genome wide association testing and studies.

    Registration: All potential applicants should send an email attaching a motivation letter and CV to and Cc  , with heading "YOUR NAME + admission-CU-GWAS workshop for complex diseases”. Once being successfully chosen for the workshop, participants will be contacted with details on how to access and attend the workshop.

    Workshop Curriculum

     

    Time

    Topic

    Trainer

    29thJune 2015

    9:00

    Introduction to GWAS/Designing a GWAS (Lecture)

    Segun Fatumo

    10:30

    Tea break

     

    11:00

    Genotype calling and array QC (Lecture)

    Shaun Aron

    12:00

    Lunch

     

    1:00

    Genotype calling and array QC (Practical)

    Shaun Aron

    2:30

    Introduction to PLINK (Practical)

    Scott Hazelhurst

    5:00

    Workshop End

     

    30thJune 2015

    9:00

    SNP and Sample QC (Lecture)

    Shaun Aron

    10:00

    Tea Break

     

    10:30

    SNP and sample QC (Practical)

    Shaun Aron

    12:30

    Lunch

     

    1:30

    Population Structure (Lecture + Practical)

    Scott Hazelhurst

    5:00

    Workshop End

     

    1stJuly 2015

    9:00

    Association Testing (Lecture)

    Segun Fatumo and Victor Osamor

    10:30

    Tea Break

     

    11:00

    Imputation (Lecture)

    Segun Fatumo

    12:00

    Lunch

     

    1:00

    Visualisation and post GWAS analysis (Lecture)

    Segun Fatumo

    2:00

    Fine Mapping (Lecture)

    Segun Fatumo

    3:00

    Complete GWAS practical exercise (Practical)

    Shaun Aron

    5:00

    Workshop End

     


    Venue of workshop: Uganda Virus Research Institute, Entebbe Uganda

    Dates for the workshop: 6th to 10th July 2015.

    Workshop organisers:  MUIITHRiVEAfrica Centre for Health and Population Studies Wellcome Trust ProgramsH3ABioNet , MRC/UVRI Uganda Research Unit on AIDS, and the Uganda Virus Research Institute

    Registration opens:  8th May, 2015

    Registration closes: 8th June, 2015

    Notification date: 12th June, 2015

    Link to application form: http://www.muii.org.ug

    Participation: Application open to in-country H3Africa/H3ABioNet consortium and UVRI-Node research partners with selection, giving priority to those with demonstrated need for this training. A total of 25 participants from all the applications received will be selected.

    Workshop SponsorsMUII and THRiVE

    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 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.

    Intended Audience: Designed for Scientists, graduate students, postdoctoral research fellows, and exceptional undergraduates in the region to become familiar with NGS data handling and analysis techniques.

    Syllabus and Tools: Participants will learn about Linux, R programming, NGS assembly, annotation, and population genetics of genomes using various data visualization and analysis tools.

    Trainers and support staff: 
    Deo Ssemwanga, (MRC/UVRI, Entebbe, Uganda)
    Jonathan Kayondo, (UVRI, Entebbe, Uganda)
    Fred Lyagoba, (UVRI, Entebbe, Uganda)
    Benard Kulohoma, (ICIPE, Nairobi, Kenya)
    Justen Manasa, (WT Africa Centre for Health and Population Studies, South Africa)
    Anne Derache, (WT Africa Centre for Health and Population Studies, South Africa) 
    Etienne Villiers, (KEMRI/ Wellcome Trust, Kilifi, Kenya)
    Miguel Quinones-Mateu,( Case Western Reserve University, Cleveland , USA)
    Pontiano Kaleebu, (MRC/UVRI, Entebbe, Uganda)
    Tulio de Oliveira (WT Africa Centre for Health and Population Studies, South Africa)

    Prerequisites:  Participants will need to work through the following resources to enable them to gain the most from the workshop:
    http://www.ee.surrey.ac.uk/Teaching/Unix/
    http://www.r-tutor.com/r-introduction

    Objectives:  The objective is to introduce bioinformatics analysis techniques for dealing with Next Generation Sequencing (NGS) data. After this workshop participants should be able to:
    - Attempt using Linux based platforms for analysis
    - Have a good familiarity with R and conducting statistical tests within R
    - Assemble and analyze NGS genome data 
    - Perform HIV-1 drug resistance mutation genotyping
    - Perform various phylogentics analysis for viral transmission, evolution and other studies
    - Use the e-Biokit and other resources for bioinformatics analysis

    Workshop limitations: This workshop will only provide a foundation for continued learning in NGS bioinformatics and will not make you an expert in bioinformatics or NGS analysis.

    Registration: All potential applicants must complete the application form and obtain and attach a motivation letter from their supervisor / Head of Department and submit the application form according to the instructions contained within it. Incomplete applications will NOT be reviewed. The successful applicants for the workshop will be contacted to complete a short biosketch with a recent picture and Participants will also be requested to come to the workshop with a poster describing their research.

    Questions: If you may have any further queries, please contact Dr. Jonathan Kayondo

    ,

    Workshop training materials are available at: http://training.h3abionet.org/technical_workshop_2015/

    Venue of workshop: Bioinformatics and Computational Biology Unit, University of Pretoria

    Dates for the workshop: 2nd February to 11th February, 2015

    Workshop organisers: H3ABioNet and the Bioinformatics and Computational Biology Units, Universities of Pretoria and the Witwatersrand H3ABioNet Nodes

    Link to registration form:http://surveys.h3abionet.org/sysadmincourse2/

    Participation: Participation is by nomination of individuals from their H3ABioNet Node or H3Africa projects’ Principal Investigators.

    Workshop Sponsors: H3ABioNet.

    Workshop 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 administration workshop run in Pretoria, 2013 to enhance the capacity of newly hired personnel.
    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.

    Intended Audience: Newly hired System Administrators and previous attendees of the systems administration workshop in Pretoria who work on systems administration of UNIX type servers and infrastructure relevant for data management and storage for H3ABioNet Nodes and H3Africa affiliated projects engaged in bioinformatics research.

    Syllabus and Tools: Participants will learn about the command line, Linux file management, basic process management, network fundamentals, program installation, job scheduling, backups, encryption, virtualisation, server management and automation using Puppet and Server Configuration, scripts for configuration of multiple machines, setting up compute clusters.

    Trainers: Professor Fourie Joubert (University of Pretoria), Professor Scott Hazelhurst (University of the Witwatersrand), Mohamed Alibi (Institut Pasteur de Tunis), Peter van Huesden (South African National Bioinformatics Institute), Ayton Mentjies (University of Cape Town).
     
    Prerequisites: Remote access and administer privileges to install software programmes on a serve in your Institute is a must. Good working knowledge of Unix, provision of systems administration support within your Institution. Those unfamiliar with Unix are encouraged to work through the following resources to enable them to gain the most from the workshop:
    H3ABioNet Systems Administration Documentation Level 1 and Level 2 and http://www.washington.edu/R870/

    Objectives: After this workshop participants should be able to:

    • Install Linux on a server from scratch,
    • Create basic and advanced bash shell scripts
    • Implement basic Linux file management and manage physical storage partitions,
    • Perform user and group management, and use standard Linux permissions
    • Perform basic network and firewall configuration,
    • Use standard encryption and compression techniques
    • Install software from source and using a package management
    • Remotely access systems and perform large-scale data transfer
    • Automate system setup and configuration
    • Set up compute clusters
    • Follow H3ABioNet Standard Operating Procedures

    Workshop limitations: This workshop will provide an introduction and foundation for continued learning within a user group of your peers who will attend the H3ABioNet Advanced Systems Administration Workshop and participation within the H3ABioNet Infrastructure Working Group.

    Workshop costs: H3ABioNet will cover the costs of the a return economy air ticket to South Africa, accommodation from the night before the portion of the workshop you are attending starts (either the 1st of February or the 5th of February 2015) till the night the workshop ends on 11th of February at the Brooklyn Guesthouse (http://www.brooklynguesthouses.co.za).

    H3ABioNet will not cover the costs of the meal for the first evening of your arrival on the 1st of February 2015, vaccinations, visa fees or airport transfers from your local area which will be borne by your home Institution.

    Please note if a participant is unable to attend this workshop after acceptance due to a last minute cancellation, the costs of the air tickets, accommodation and catering will be borne by their home Institution.

     

    WORKSHOP PROGRAM

     

    Attachments:
    Download this file (L1_Linux _Getting Started HowTo Guide_19Aug2014.pdf)L1_Linux _Getting Started HowTo Guide_19Aug2014.pdf [ ] 5449 Kb

    Venue of workshop:The African Institute for Mathematical Sciences (AIMS),Cape Town, South Africa.

    Dates for the workshop: 20th-22nd April, 2015, followed by a symposium from the 23rd-24th April, 2015

    Workshop organisers: H3ABioNet, the African Institute for Mathematical Sciences (AIMS) and the CPGR node of H3ABioNet

    Registration opens: 14th January, 2015

    Registration closes: 20th February, 2015

    Notification date: March, 2015

    Link to application form:https://bioweb.cpgr.org.za/redcap/surveys/?s=4L3ANT998T

    Workshop Sponsors: H3ABioNet and the African Institute for Mathematical Sciences

    Workshop Overview: The workshop will be split into two tracks:

    1. 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 a ‘hands-on’ experience of data analysis and a stage for shaping the next generation of GWAS scientists/researchers.
    2. An advanced track which will draw upon the audience’s interdisciplinary expertise in mathematics, simulation studies, statistics and machine learning to overcome present challenges and identify the most promising avenues of future research for effective phenotype–genotype association.

    Intended Audience: The target audience includes H3Africa project members who will be involved in the design and analyses of population genetics data and genome wide association testing, technicians, graduate students, postdocs and established and young investigators entering the field of complex trait genetics from a variety of backgrounds such as biological, bioinformatics, statistics, mathematics and computer science.

    Participation: Open application with selection for H3Africa consortium members, African Institute for Mathematical Sciences (AIMS) students and interested participants. The selection procedure will give priority to those with demonstrated need for this training, particularly those with data available or soon to be available. A total of 50 participants will be selected.

    Syllabus and Tools: Participants will learn about the design and analyses of population data and genome wide association testing. On the second day, participants will be split into two groups

    1. Hands on data processing, analysis and the interpretation of results
    2. Advanced mathematical population genetics and disease scoring statistics

    Objectives: This workshop aims to introduce an interdisciplinary audience to the potential of GWAS and to key strategic considerations in designing and performing Genome-wide Association studies, as well as to bring all participants up to speed on the basic principles of human genetic variation, genotyping and disease scoring statistics. In addition, this workshop aims to bridge the gap between statistics, bioinformatics and genetics. We envisage that researchers in machine learning and statistics who have an interest in genetic architecture of complex diseases, as well as statistical geneticists looking for using or improved tools for GWAS will benefit from participating in this workshop.

    Workshop limitations: This workshop will provide a foundation for continued learning in medical genetics and GWAS studies for the introductory track and will not make one an expert in medical population genetics and genome wide association testing and studies. The advanced track will provide the cover current mathematical and statistical models and simulations methods used in population genetics and GWAS and will not make one an expert in simulations, mathematical and statistical modelling and methodology development for population genetics and GWAS studies.

    Trainers and support staff:

    1. Organizers: Prof. Nicola Mulder, Dr. Emile Chimusa, Dr. Judit Kumuthini and Dr. Gaston Kuzamunu
    2. Trainers: Prof. Scott Hazelhurst, Dr. Noah Zaitlen, Dr. Bogdan Pasaniuc, Dr. Bjarni Vilhjalmsson and Shaun Aron

    Prerequisites: Selected participants will need to work through the following resources to enable them to gain the most from the workshop:
    http://www.ee.surrey.ac.uk/Teaching/Unix/
    http://www.r-tutor.com/r-introduction
    https://www.python.org/
    http://onlinestatbook.com/2/ 
    A pre-workshop course on an Introduction to Linux/R/python will take place on the 19th April 2015.

    Registration: All interested applicants must complete the application form and upload a motivation letter from their supervisor. Incomplete applications will NOT be reviewed. The successful applicants for the workshop, will be contacted to complete an airline ticket booking form, a short biosketch with a recent picture and the H3ABioNet workshop policy. The workshop will be followed by a symposium which workshop participants will automatically attend and are encouraged to submit an abstract for either oral or poster presentations.

    H3ABioNet will cover the costs of a return economy air ticket to Cape Town. AIMS will cover the cost of accommodation from the night of the 19th of April till the 24th of April (departing on the 25th) 2015 and meals from the 19th of April to the morning of the 25th of April 2015. H3ABioNet and AIMS will NOT cover the costs of visa fees, vaccinations, airport transfers from your local area or any other costs.

    Please note, if a participant is unable to attend this workshop after acceptance, their place will be passed onto to applicants on the waiting list and not to other recommended members from their Institution or Research project.

    If you would like any additional information, please do not hesitate to contact the symposium and workshop organizers: 

    GWAS data analysis and results interpretation workshop

    Lecturers:

    • Bogdan Pasaniuc (UCLA)
    • Noah Zaitlen (UCSF)
    • Bjarni Vilhjalmsson (HSPH)
    • Shaun Aron (Wits)
    • Scott Hazelhurst (Wits)

     

    Mon 20th April

    Time

    Subject

    Lecturer

    8:00

    Registrations and welcome

     

    9:00

    Overview on medical population genetics: LD, Population Structure

    Bogdan Pasaniuc

    10:30

    Tea/coffee

     

    11:00

    GWAS study design:GWAS versus linkage mapping and power calculations

    Noah Zaitlen

     

    Genotype calling and array QC

    Shaun Aron

     

    SNP and sample QC

    Shaun Aron

    13:00

    Lunch

     

    14:00

    Population structure

    Scott Hazelhurst

     

    Association testing

    Scott Hazelhurst

     

    Imputation

    Noah Zaitlen

    15:30

    Tea/coffee

     

    16:00

    Fine mapping

    Bogdan Pasaniuc

     

    Visualisation and post GWAS analysis

    Shaun Aron

    Tues 21st April

    Time

    Subject

    Lecturer

    9:00

    Introduction to PLINK – data formats, loading, manipulation

    Scott Hazelhurst

    10:30

    Tea/coffee

     

    11:00

    Genotype calling QC

    Shaun Aron

     

    SNP and sample QC

    Shaun Aron

    13:00

    Lunch

     

    14:00

    PCA and population structure

    Scott Hazelhurst

    15:30

    Tea/coffee

     

    16:00

    Preprocessing: imputation, quality control

    Bogdan Pasaniuc

    Wed 22nd April

    Time

    Subject

    Lecturer

    9:00

    Introduction to basic statistics, p-values, multiple-testing correction

    Bogdan Pasaniuc

    10:30

    Tea/coffee

     

    11:00

    Association testing: Example GWAS using linear models. Comparison of F-test and alternatives.

    Bogdan Pasaniuc

     

    Evaluation of linear fits, pitfalls due to overfitting

    Shaun Aron/Scott Hazelhurst

    13:00

    Lunch

     

    14:00

    Empirical evaluation of the importance of population structure correction

    Scott Hazelhurst

     

    Introduction to Meta-analysis and Fine mapping with R

    Scott Hazelhurst

    15:30

    Tea/coffee

     

    16:00

    Visualisation and post GWAS analysis

    Shaun Aron

     

    Complete GWAS practical exercise from QC to association results

    Shaun Aron/Scott Hazelhurst

    Thurs 23rd April

    Time

    Subject

    Lecturer

    9:00

    Finish exercises

    Shaun Aron/Scott Hazelhurst

    11:00

    Wrap-up and finish

     
      GWAS Symposium starts at 11:30am on Thursday 23rd April at False Bay College Muizenberg campus

    Advanced GWAS Modelling Workshop Program

    Lecturers:

    • Bogdan Pasaniuc (UCLA)
    • Noah Zaitlen (UCSF)
    • Bjarni Vilhjalmsson (HSPH)
    • Shaun Aron (Wits)
    • Scott Hazelhurst (Wits)

     

    Mon 20th April

    Time

    Subject

    Lecturer

    8:00

    Registrations and welcome

     

    9:00

    Overview on medical population genetics: LD, Population Structure

    Bogdan Pasaniuc

    10:30

    Tea/coffee

     

    11:00

    GWAS study design:GWAS versus linkage mapping and power calculations

    Noah Zaitlen

     

    Genotype calling and array QC

    Shaun Aron

     

    SNP and sample QC

    Shaun Aron

    13:00

    Lunch

     

    14:00

    Population structure

    Scott Hazelhurst

     

    Association testing

    Scott Hazelhurst

     

    Imputation

    Noah Zaitlen

    15:30

    Tea/coffee

     

    16:00

    Fine mapping

    Bogdan Pasaniuc

     

    Visualisation and post GWAS analysis

    Shaun Aron

    Tues 21st April

    Time

    Subject

    Lecturer

    9:00

    Using simulations to assess power and false-discovery rate

    Noah Zaitlen

    10:30

    Tea/coffee

     

    11:00

    Computational hidden Markov model to infer ancestry

    Bogdan Pasaniuc

    13:00

    Lunch

     

    14:00

    Parameter inference in linear models

    Bjarni Vilhjalmsson

     

    Statistical testing with linear models

    Bjarni Vilhjalmsson

    15:30

    Tea/coffee

     

    16:00

    Linear mixed models to correct for confounding variation

    Bjarni Vilhjalmsson

    Wed 22nd April

    Time

    Subject

    Lecturer

    9:00

    Computational MCMC methods: Gibbs sampling, Metropolis-Hastings for GWAS

    Bjarni Vilhjalmsson

    10:30

    Tea/coffee

     

    11:00

    Computational GWAS mixed Models: from genome architecture to environmental influences

    Bjarni Vilhjalmsson

    13:00

    Lunch

     

    14:00

    Accounting for hidden confounding in high-dimensional studies

    Bjarni Vilhjalmsson

     

    Segment test and Joint testing of multiple related traits at once

    Bjarni Vilhjalmsson

    15:30

    Tea/coffee

     

    16:00

    Computing Meta-analysis

    Noah Zaitlen

    Thurs 23rd April

    Time

    Subject

    Lecturer

    9:00

    Publication or discussion session

    Noah, Bjarni, Bogdan

    11:00

    Wrap-up and finish

     

    GWAS Symposium starts at 11:30am on Thursday 23rd April at False Bay College Muizenberg campus

     

    Workshop Materials:

    https://training.h3abionet.org/aims_gwas_2015/


    Subcategories

    Page 3 of 4

    © 2019 H3ABioNet.org
    Terms - Privacy - Policy & Safety - Helpdesk
    The H3ABioNet website content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health
    Image
    © University of Cape Town 2020. All rights reserved.