Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.

    Intended Audience: The course is aimed at individuals from a molecular biology background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.

    Logistics 

    Venue of workshop: Local classrooms ( usually 30 physical sites across Africa) and online

    Dates for the workshop:10 July – 15 October; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

    Workshop organisers: Kim GurwitzShaun Aron, Sumir Panji and Nicola Mulder

    Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical classroom, if one has been set up at a local institution, provided they have been selected via the selection process.

    Workshop Sponsors: H3ABioNet

     

    Course Curriculum:

    Syllabus and Tools:

    The course curriculum will cover the following main themes (subject to slight changes):

    • Bioinformatics resources and databases
      • Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
    • Linux
      • Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
    • Sequence alignment theory and applications
      • Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
    • Multiple sequence alignment (MSA)
      • MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
    • Genomics
      • Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
    • Molecular evolution and phylogenetics
      • Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)

     **All modules make use of ONLY web-based tools such as NCBI, Ensembl, etc.

    Prerequisites: A basic background/understanding of of biochemistry and/or genetics.

    Objectives: After this workshop participants should be able to:

    • Explain the use of bioinformatics
    • Name the key bioinformatics techniques and tools
    • Locate important biological databases and retrieve data
    • Use selected tools effectively to run specific bioinformatics analyses
    • Understand the strengths and limitations of the various techniques

    Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

     

    See course website here: https://training.h3abionet.org/IBT_2017/


    Venue of workshop: University of Cape Town – venue (TBA)


    Dates for the workshop: 30th October – 31st October 2018: Face to face practical workshop (bring your own laptop)

    Workshop organisers: Ziyaad Parker, Suresh Maslamoney, Sumir Panji, Nicola Mulder

    Application opens: 26th September 2018

    Application for the workshop closes: 11th October 2018

    Notification or acceptance date for the workshop: 12th October 2018

    Link to application form: https://tinyurl.com/cbio-sfc

    Course Overview Participation: The workshop is open to anybody who is interested in learning the Introduction to Python programming using the
    principles of Software Carpentry.

    Workshop Sponsor: UCT Computational Biology Division (CBIO) and H3ABioNet

    Intended Audience: Students and Staff who would like to learn more about the basics of Python programming.

    Tools: Python, Jypter Notebook, GitHub, Git, Numpy, Pandas, Linux/Mac/Windows

    Objectives: After this workshop participants should:

    • Be familiar Git and GitHub as well as using it
    • Be familiar with Jupyter Notebook
    • Be familiar with Python and executing scripts
    • Understand the different Python packages
    • Be familiar with steps and procedures involved in working with Python

    Workshop limitations: The workshop is set for two days. This course will teach the foundations of Python programming Linux and Git.

    Prerequisites: The participants must have their own laptop and install software below before the workshop:

    • Python 3
    • Numpy and Pandas Python package,
    • Git
      and
    • Jupyter Notebook

    Without the above installed participants will not be able to complete the course. Follow these instructions on this link to install: https://swcarpentry.github.io/python-novice-gapminder/setup/

    Contact Person:

     

    Link to course website: https://h3abionet.github.io/2018-10-30-SWC-course/ 


    Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.

    Intended Audience: The course is aimed at individuals from a molecular biology background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.

    Logistics 

    Venue of workshop: Local classrooms ( usually 30 physical sites across Africa) and online

    Dates for the workshop: 11 September – 13 December; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

    Workshop organisers: Paballo Chauke, Verena Ras, Shaun Aron, Sumir Panji and Nicola Mulder

    Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical classroom, if one has been set up at a local institution, provided they have been selected via the selection process.

    Workshop Sponsors: H3ABioNet

    Classroom applications:

    Registration for classrooms opens:  07 June 2018

    Registration for classrooms closes: 07 July 2018

    Link to classroom application form: applications are now closed

    Notification date for successful classrooms: 10 July 2018

    Participant applications:

    Registration for participants opens:  15 July 2018

    Registration for participants closes: 10 August 2018

    Link to participant application form: https://is.gd/IBT_participant_registration

    Notification date for successful participants: 20 August 2018

    Course Curriculum:

    Syllabus and Tools:

    The course curriculum will cover the following main themes (subject to slight changes):

    • Bioinformatics resources and databases
      • Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
    • Linux
      • Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
    • Sequence alignment theory and applications
      • Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
    • Multiple sequence alignment (MSA)
      • MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
    • Genomics
      • Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
    • Molecular evolution and phylogenetics
      • Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)

     **All modules make use of ONLY web-based tools such as NCBI, Ensembl, etc.

    Prerequisites: A basic background/understanding of of biochemistry and/or genetics.

    Objectives: After this workshop participants should be able to:

    • Explain the use of bioinformatics
    • Name the key bioinformatics techniques and tools
    • Locate important biological databases and retrieve data
    • Use selected tools effectively to run specific bioinformatics analyses
    • Understand the strengths and limitations of the various techniques

    Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

     

    For more information on IBT, please visit: https://www.h3abionet.org/training/ibt

    IBT Youtube channel: https://www.youtube.com/playlist?list=PLcQ0XMykNhCQXNXiv6jtEo8WnOMlT7XeS 


    Venue  of  workshop:  Online  workshop  for  4  weeks  (2-­‐3  hours  per  week),  and  face  to  face workshop at the University of Cape Town for 5 days.

    Dates for the workshop: 20th August – 12th September 2018: Online lectures on Monday and Wednesday afternoon. 8th October – 12th October 2018: Face to face practical workshop (bring your own data)

    Workshop organizers: Verena Ras, Paballo Chauke, Mamana Mbiyavanga, Ayton Meintjes, Suresh Maslamoney, Gerrit Botha, Shaun Aron, Sumir Panji, Scott Hazelhurst, Nicola Mulder

    Application opens (online and face to face workshops): 30th July 2018

    Application for the practical workshop closes: 13th August 2018

    Notification date for the practical workshop: 20th August 2018 (attendance requires participation in online course) 

    Link to application form: https://is.gd/H3Africa_Chip_Workshop

    Participation: The online lecture series is open to anyone who is interested in learning more about how to analyse genotyping chip data. The practical workshop is via competitive selection and limited to H3Africa consortium members who have or will soon receive H3Africa genotyping chip data they would like to analyse, and have attended all the online lectures.

    Workshop Sponsor: H3ABioNet 

    Course Overview: The H3Africa chip is being used by the H3Africa projects to generate data that will need to be analysed. 

    The course will consist of two components; a series of online lectures provided by experts in that specific domain. These are to introduce the main concepts and theory behind population genetics and GWAS. The second part of the course for selected participants will be a practical Bring Your Own Data (BYOD) workshop on the analysis of H3Africa genotyping data using the H3ABioNet GWAS and Imputation workflows.

    Intended Audience: People who would like to learn more about genotyping, calling, QC and running a GWAS study for the online lectures. H3Africa project members who will be undertaking the analysis of the genotype data from the H3Africa chip, and will have data available for the practical course.

    Syllabus and Tools: The online lecture series will provide an overview of GWAS studies, genotype calling, quality control of data, population structure, importance of imputation, association testing, fine mapping and further analysis. The hands on workshop will provide practical guidance on the topics above, information on the H3Africa chip, the use of the H3ABioNet GWAS and imputation workflows, Nextflow, GitHub, Plink and Genesis. Participants should work on their own array data where possible. The final day will include tools for further interpretation of GWAS results.

    Prerequisites: Some basic knowledge in genetics, population genetics and GWAS for the online lectures. For the practical workshop: attendance at all the online lectures; belonging to an H3Africa project; have H3Africa genotyping data and will be undertaking analysis for the H3Africa project. Knowledge of Unix / Linux and tools used for GWAS studies such as Plink is essential, for those with no Unix experience, links to online courses will be provided to be completed prior to the workshop.

    *In order to for an application to be considered to attend the hands on workshop, the potential applicants must attend all the online lectures.

    Objectives: After this workshop participants should:

    • Be familiar with the steps to follow when doing a GWAS association study from getting their raw dataset, genotype calling to association testing
    • Be familiar with the use of the H3ABioNet GWAS workflow
    • Be familiar with the various steps and procedures involved in imputation
    • Be able to undertake the downstream interpretation of their results
    • Be familiar with the computational infrastructure needed to undertake a GWAS analysis 

    Workshop limitations: The online lecture series will provide a foundation for conducting a GWAS study and analysing genotype array data. The practical bring your own data workshop will provide skills to analyse one’s data using the H3ABioNet GWAS and Imputation workflows based on the methods and tools used. 

    Online lecture series curriculum: 

    Lecture focus

    List of topics to be covered in the online lectures

    Computational requirements for the H3ABioNet GWAS containerized workflow

    ●          Installing and using Nextflow

    ●          Installing and using Github

    ●          Use of containers for packaging and running tools

    ●          Pulling the GWAS pipeline from Github and running it locally

    Introduction to Genome Wide Association Studies (GWAS) and tests

    ●          An overview on GWAS studies

    ●          Why GWAS studies are conducted

    ●          Types of GWAS study designs

    ●          Taking samples and running on a genotyping chip

    Genotype calling from an .idat file

    ●          What files are generated from a genotype chip (Illumina)

    ●          How genotypes are called

    ●          What clusters are and mean

    ●          How to tell is the calling has gone well, metrics etc

     

    Lecture focus

    List of topics to be covered in the online lectures

     

    ●     The use of manifest files, its definition and purpose

    ●     Tools used and examples

    Quality control

    ●     Why is QC important

    ●     Going through the called files, what are they and what they look like

    ●     How to assess good quality calls and poor quality calls

    ●     What one looks to QC for with examples

    ●     What tools are used for QC

    ●     What a good quality QC files look like vs poor quality QC files

    Population structure

    ●     Why population structure is important

    ●     Types of population structure (terms, concepts and definitions       e.g  cryptic, relatedness)

    ●     How to investigate population structure, PCA plots -­‐     GENESIS

    ●     Correcting for population structure

    ●     Tools used for population structure

    ●     Possible confounding effects on population structure

    ●     Files, format and outputs for population structure

    Imputation and its importance

    ●     What is imputation

    ●     What is a reference panel

    ●     Why is imputation used

    ●     Why different reference panels matter

    ●     Tools to do imputation

    ●     Files, formats and outputs for imputation

    Association testing (GWAS)

    ●     Types of GWAS studies (brief recap as covered in talk 1)

    ●     Types of association testing models and their use

    ●     Covariates and testing / correcting for

    ●     P values and correcting for multiple testing

    ●     Manhattan plots and other visualizations

    ●     Tools used for GWAS testing

    ●     Files, formats and outputs for GWAS testing

     

     Link to YouTube channel housing videos: https://www.youtube.com/playlist?list=PLcQ0XMykNhCQJPz0amnbz9BPM4Bu0Nkgf 

     


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