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    Course Overview: The Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), together with H3ABioNet will be running a Best practices in Bioinformatics Training workshop in Cape Town from the 16th - 17th of November 2015. The first day will cover aspects of teaching and the second day will be more of a workshop to discuss bioinformatics curricula, course materials, trainer recognition, etc. This “train-the-trainer” course is designed for anyone who currently or plans to teach bioinformatics both in universities as part of degree programs or as short specialized courses. The workshop will be in the Dumo Baqwa room, Barnard Fuller Building, University of Cape Town Medical School, Anzio Road Observatory.

    Intended Audience: “First time” trainers or those with no formal teaching on how to train and bioinformatics trainers

    Keywords: Teaching, Education, Training

    Skill level: Advanced

    Language: English

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


    Aim: Provide practical tips and guidance for delivery and development of bioinformatics training solutions. Discuss ongoing training community efforts for training sustainability, curriculum development and core competencies, and trainer recognition.

    Trainers / facilitators:

    • Gabriella Rustici: University of Cambridge, UK
    • Sarah Morgan: European Bioinformatics Institute, UK
    • Cath Brooksbank: European Bioinformatics Institute, UK
    • Nicky Mulder: University of Cape Town
    • Pedro Fernandes: Instituto Gulbenkian de Ciência Portugal
    • Fran Lewitter: Whitehead Institute, USA
    • Celia van Gelder: ELIXIR Training Program, Netherlands
    • Michelle Brazas: Ontario Institute for Cancer Research
    • Patricia Palagi: Swiss Institute of Bioinformatics

    Workshop curriculum and training materials

     

     

     Best practices in Bioinformatics Training

     Workshop – Day 1: 16th November 2015

    Audience: “First time”  trainers or those with no formal teaching on how to train
       University of Cape Town Medical School, Duma Baqwa room, Barnard Fuller Building
     8:30-9:00
    • Registration
    		 Duma Baqwa room
     9:00-10:30

     Gabriella Rustici, Sarah Morgan
     10:30-11:00    Coffee Break  
     11:00-12:30

     Gabriella Rustici, Sarah Morgan
     12:30-13:30    Lunch Break   Mac Club
     13:30-15:30
    • How do you put together a new teaching session?
    • Challenges in training; focus on how to tackle participants expectations: selection criteria and learning objectives
    • Course format - how is this linked to participants expectations/background? What is different between an introductory and an intermediate course and how content should be influenced by participants background

     Gabriella Rustici, Sarah Morgan
     15:30-16:00    Coffee Break  
     16:00-17:30

     Gabriella Rustici, Sarah Morgan

     

     

    Best practices in Bioinformatics Training, Curriculum & Core competencies

    Workshop – Day 2: 17th November 2015

    Audience: All trainers

       University of Cape Town Medical School, Duma Baqwa room, Barnard Fuller Building
     9:00-10:30
    • What is important to you as a community of trainers? What issues are you facing?
    • Training sustainability - feedback on Train-the-Trainer program
    		  Gabriella Rustici, Sarah Morgan

     10:30-11:00         

       Coffee Break

    		 
     11:00-11:30 Distance learning explanation & discussion  Nicky Mulder, Pedro Fernandes

    Bioinformatics curriculum & core competencies

     11:30-11:40 Why core competencies?

     Cath Brooksbank
     11:40-11:50 Applying core competencies in Africa – the H3BioNet Experience

     Nicola Mulder
     11:50-12:00 Training needs for core facilities  Fran Lewitter
     12:00-12:10 ELIXIR’s training plan  Celia van Gelder
     12:10-12:20 Q & A session  
     12:20-12:30 Introduction to break-out sessions  Cath Brooksbank
     12:30-13:30    Lunch Break  
     13:30-14:30

    Break-out sessions: Core competencies ISCB Matrix

    Bioinformatics users (Celia, Michelle)

    Bioinformatics scientists(Fran, Nicky)

    Bioinformatics engineers(Pedro, Patricia)

    		  Facilitator names in brackets
     14:30-15:00 Groups report back on break-out sessions(4x5mins)  
     15:00-15:30 Discussion and wrap up  All (Chair - Cath Brooksbank)
     15:30-16:00    Coffee Break  
     16:00-17:30

    Trainer recognition mechanisms & criteria

    Discussion

    		  Pedro Fernandes

    Workshop pictures

    IMG 4806

    IMG 4810

    IMG 4813

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19129940. 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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    Training
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    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.

     

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    1. Medical population genetics and GWAS for complex diseases 19th April - 24th April, 2015
    2. H3ABioNet Advanced Systems Administration Workshop - Bioinformatics and Computational Biology Unit, University of Pretoria 2nd to 11th Feb 2015
    3. Computational Metagenomics Workshop University of Mauritius 1st Dec – 5th Dec 2014
    4. NMIMR H3ABioNet Intermediate Bioinformatics Workshop 2014

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