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.

    Intended Audience: This workshop is aimed at attendees of the 3rd Pharmacogenetics and Precision Medicine Conference in Africa, geneticists, genetic counselling students/researchers, clinicians and healthcare professionals interested in the use of genomic data for personalising treatment.

    Keywords: Genetics, Genomics, Nucleic acids analysis, NGS

    Language: English

    Skill level: Introductory

    Type of training: face-to-face / in person

    Credential awarded: none

    Dates for the workshop: 4th April to 6th April 2016

    Venue of workshop: Health Teaching Labs 1, Basement of Anatomy Building, UCT Medical School, Cape Town, South Africa

    Workshop organisers and sponsors: H3ABioNet, African Pharmacogenomics Research Consortium, CBIO.

    Workshop trainers and support: Amel Ghouila, Gerrit Botha, Colleen Saunders, Luiz Olavo Bonino, Nyarai Soko, Suresh Maslamoney, Sumir Panji, Collet Dandara and Nicola Mulder.

     

    Syllabus and Tools: Participants will learn about the handling of NGS data, identification of genomic variants, curated databases that have genomic information/sequences for use; analysis of sequences to look for mutations; evaluation of the significance of mutations observed, pathogenesis and prediction of the functional significance of these variants.

    Prerequisites: Participants are encouraged to work through the following resources to enable them to gain the most from the workshop:
    https://wiki.galaxyproject.org/Learn/GalaxyNGS101
    https://usegalaxy.org/u/galaxyproject/p/galaxy-variant-101
    https://wiki.galaxyproject.org/Learn/Screencasts
    http://www.1000genomes.org/using-1000-genomes-data 
    http://www.h3abionet.org/tools-and-resources/sops/human-variant-calling
    ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120229_tutorial_docs/G1K_web_based_tutorial_exercises_20120217.pdf 
    ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120229_tutorial_docs/G1K_web_based_tutorial_answers_20120217.pdf 
    https://www.clinicalgenome.org/data-sharing/clinvar/clinvar-multimedia-tools/
    http://www.ensembl.org/info/docs/tools/vep/online/VEP_web_documentation.pdf

    Objectives:

    • Participants will learn how to execute a web based NGS workflows using Galaxy.
    • Participants should come out understanding how to obtain and analyse variants, particularly from NGS data.
    • Participants should come out with knowledge on how to predict the significance of identified mutations, checking for pathogenesis, or whether they affect regulatory regions.
    • Participants should come out with knowledge on the possible clinical significance (pharmacogenomics relevance) of variants.

    Workshop limitations: This workshop will provide a foundation for continued learning in the bioinformatics handling of NGS data, identification, annotation and functional prediction effects of variants. The workshop will not make one an expert on NGS data, filtering, functional predication and annotation of variants.

    Workshop program

    4th April 2016
    Time Topic (Health Teaching Labs 1)
    8:30 am Registration
    9:00 am Welcome address
    9:10 am Participant introductions
    9:30 am Introduction to NGS, file formats and workflows (Talk)
    10:00 am Introduction to the web based Galaxy platform for NGS analysis (Talk)
    10:20 am Register for a Galaxy account (Practical)
    10:30 am Tea break (Student Cafeteria)
    11:00 am Uploading data into Galaxy, tools, histories and workflow sharing (Practical)
    11:20 am Preprocessing and QC of NGS data (Talk)
    11:40 am Examining FASTQ files in Galaxy, pre-processing and quality control of NGS data (Practical)
    12:20 pm Alignment of reads, reference sequence, indel realignment (Talk)
    12:40 pm Submit alignment jobs to Galaxy (Practical)
    1:00 pm Lunch (Mac Club)
    2:00 pm Alignment of reads, post processing, obtaining statistics, visualising alignments (Practical)
    3:00 pm Introduction to variant calling (Talk)
    3:20 pm Submit variant calling jobs to Galaxy (Practical)
    3:30 pm Tea Break (Student Cafeteria)
    4:00 pm Alignment of reads, indel realignment, and variant calling (Practical)
    5:00 pm Workshop End
    5th April 2016
    Time Topic (Health Teaching Labs 1)
    9:00 am Recap of previous days activities and Q and A session
    9:30 am Overview of variant prioritisation and Introduction to genome databases (Talk)
    10:30 am Tea break (Student Cafeteria)
    11:00 am Exploring genome databases (Practical)
    12:00 pm Lunch (IIDMM Cafeteria)
    1:00 pm NGS variant analysis: Annotation and filtering (Talk and practical)
    2:30 pm Tea break (Student Cafeteria)
    3:30 pm

    NGS variant analysis: Exploring links to phenotype and biological function (Talk and practical)

    5:00 pm Workshop End
    6th April 2016
    Time Topic (Health Teaching Labs 1)
    9:00 am Recap of previous days activities and Q and A session
    9:30 am Findable, accessible, interoperable and reusable (FAIR) Data in Life Sciences (Talk)
    10:30 am Tea break (Student Cafeteria)
    11:00 am Gene-disease investigation in integrated datasets (Practical)
    12:30 pm Lunch (IIDMM Cafeteria)
    Venue change to Postgraduate Lecture room 2
    1:30 pm Introduction to pharmacogenomics (Talk)
    1:45 pm Setting up a pharmacogenomics study: important considerations (Talk)
    3:00 pm Tea break (Student Cafeteria)
    3:30 pm Pharmacokinetics and pharmacogenetics of rosuvastatin (Talk)
    4:00 pm Discussion of project ideas (Group discussion led by Prof. Collet Dandara)
    5:00 pm Workshop End

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19129955. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

    ,


    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 scope as the field attempts to process and interpret the growing amount of information being generated. For this workshop, we will adopt a hands-on approach to navigate some of the more popular genome-wide software packages available. A general overview of the topics to be covered is as follows. After a brief introduction on the current state of genetic research, we will begin with a discussion of the key quality assurance and quality control steps that are necessary to any genome-wide analysis. We will then transition to the analysis phase with a focus on genome-wide association using unrelated samples, including an overview of the analysis of gene pathways. Next, we will discuss the use of genome-wide data to estimate heritability, construction of genetic risk scores and pathway analysis. We will conclude with an introduction to family-based analysis and an overview of meta-analytic techniques.

    Intended Audience: This workshop is aimed at beginning and intermediate level graduate students, postdoctoral researchers and faculty.

    Keywords: Genetics, Genomics, Nucleic acids analysis, GWAS

    Language: English

    Skill level: Intermediate

    Type of training: Face-to-face /  in person

    Credential awarded:  none

    Venue of workshop: Medical Campus, University of Cape Town

    Dates for the workshop: 22nd February to 24th February, 2016

    Workshop organisers: CBIO, Nicola Mulder, Matthew McQueen

    Participation: Open application with selection

    Workshop Sponsors: CBIO

     

    Syllabus and Tools: Participants will learn about quality control and quality assurance steps of genome-wide data, basic GWAS analysis, construction of genetic risk scores, estimation of genome-wide SNP heritability, an introduction to family-based association approaches and an overview of meta-analytic techniques.

    Workshop Trainers: Dr. Matthew McQueen is an Associate Professor and Director of the Public Health Program at the Department of Integrative Physiology at Colorado University, Boulder, USA. His research is focused on a multi-faceted approach to the investigation of genetic determinants underlying complex disease, with a particular interest in psychiatric, behavioral and neurologic disorders. Recent areas of research include the development and application of statistical and epidemiological methods geared towards large-scale genomic analysis in both family-based and population-based samples.

    Prerequisites: Participants are encouraged to work through the following resources to enable them to gain the most from the workshop. We will provide a basic overview of the Linux environment as well as work towards gaining an understanding of R.

    http://www.ee.surrey.ac.uk/Teaching/Unix/

    http://www.r-tutor.com/r-introduction

    Objectives: After this workshop participants should be able to:

    - Understand the steps necessary to assess the quality of genome-wide data

    - Use common software to conduct a basic GWAS analysis

    - Conduct relationship-checks and generate components of ancestry

    - Aggregate genome-wide association data using GCTA and genetic risk scores

    - Understand the features of a family-based association test

    - Understand the different techniques to conduct a meta-analysis of genetic results

    Workshop limitations: This workshop will only provide a foundation for continued learning in genome wide association testing and studies. Further directions for specific genome-wide approaches will need to be tailored towards particular studies.

    Registration: All potential applicants must complete the application form. Incomplete applications will NOTbe reviewed. Successful participants will be notified of their selection for the workshop and will be contacted provide a short biosketch with a recent picture.

    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.

    Workshop Programme:

     

    Time Topic Trainer
    22nd February 2016
    9:00 Registration and Introductions  
    9:30 Lecture 1: Introduction to Genome-Wide Approaches Matthew McQueen
    10:30 Tea break  
    11:00 Tutorial 1: Getting Started (Linux) Matthew McQueen
    12:00 Lunch  
    1:00 Lecture 2: Quality Control Procedures for GWAS Data Matthew McQueen
    2:00 Tea Break  
    2:30 Tutorial 2: Data Cleaning, Relationship Checks and Genetic Ancestry (PLINK, R) Matthew McQueen
    3:30 Workshop End  
    23rd February 2016
    9:30 Lecture 3: Genome-Wide Association Approaches Matthew McQueen
    10:30 Tea Break  
    11:00 Tutorial 3: Genome-Wide Association Analysis (PLINK, R) Matthew McQueen
    12:00 Lunch  
    1:00 Lecture 4: Aggregation of GWAS Information Matthew McQueen
    2:00 Tea Break  
    2:30 Tutorial 4: Heritability (GCTA), Genetic Risk Score ® and Pathway Analysis Matthew McQueen
    3:30 Workshop End  
    24th February 2016
    9:30 Lecture 5: Introduction to Family-Based Approaches Matthew McQueen
    10:30 Tea Break  
    11:00 Tutorial 5: Family-Based Association Test (FBAT) Matthew McQueen
    12:00 Lunch  
    1:00 Lecture 6: Meta-Analysis of Genetic Results Matthew McQueen
    2:00 Tea Break  
    2:30 Tutorial 6: Meta-Analysis (R) Matthew McQueen
    3:30 Workshop End  

     

     

    Training Materials Availability:

    Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://doi.org/10.25375/uct.19130048. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.

     


    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.

    Keywords: Genetics, Genomics, Nucleic acid analysis, Biostatistics

    Langiage: English

    Skill level: Intermediate

    Type of training: face-to-face / in person

    Credential awarded: none

    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

     

    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

     

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19130000. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.


    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.

    Keywords: Genetics, Genomics, Nucleic acid analysis, GWAS

    Language: English

    Skill level of training: Beginner

    Type of training: face-to-face / in person

    Credential awarded: none

    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

     

    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

     

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19129964. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.


    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.

    Keywords: System administration, Data handling, Bioinformatics

    Skill level of training: Advanced

    Language: English

    Credential awarded:  no credential awarded

    Type of training: face-to-face / in person

    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.

    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.

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19106870. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

     

     


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