Course Overview: This interactive workshop will provide an overview of data management, analysis and submission for H3Africa projects. It also provides an opportunity for Data Support Working Group members, who represent the H3Africa projects to engage with H3ABioNet and discuss their needs.

    Intended Audience: This workshop is aimed at Data Support Working Group members who should be the H3Africa project data managers, data analysts or bioinformaticians. It is important that the attendees have knowledge of the data being generated by their H3Africa projects and information about the project’s data analysis plan.

    Keywords: Data handling, Ontologies, Genomics, Nucleic acid analysis

    Language: English

    Skill level: Intermediate

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

    Credential awarded: none

    Workshop dates: 12th May 2016

    Venue: Ocean Room, Radisson Blu Hotel, Dakar, Senegal

    Workshop organisers and sponsors: H3ABioNet, NIH Common Fund

    Workshop trainers and support: Nicola Mulder, Sumir Panji, Ayton Meintjes, Scott Hazelhurst, Fourie Joubert, Alia Benkahla and Faisal Fadlemola.

     

    Syllabus: Participants will discuss their current data plans and challenges. Lectures will be given on Clinical data collection & storage, overview of GWAS/NGS/microbiome processing, downstream analysis (Variant annotation, meta-analysis, structure, ancGWAS), Data transfer considerations, security, data processing options, and H3Africa Archive and EGA submission. This will be followed by discussion on developing data management plans (with reference to the article: Michener WK (2015) Ten Simple Rules for Creating a Good Data Management Plan. PLoS Comput Biol 11(10): e1004525), and interactive sessions discussing specific projects.

    Prerequisites: Participants should complete the survey at: H3Africa Data Support workshop planning survey - Senegal 2016. One survey needs to be completed per H3Africa project.

    Objectives:

    • Participants will learn how to develop a data management plan.
    • Participants will gain basic knowledge on issues around data security & submission.
    • Participants should come out understanding what considerations there are for their own data analysis, storage and compute requirements.
    • Participants will be able to engage with H3ABioNet on their needs and issues.

    Workshop limitations: This workshop will provide a foundation for continued learning in the handling of H3Africa project data. It will not make one an expert in specific data  analysis pipelines.

    Workshop Program

    Time Topic
    8:30 am Registration
    9:00 am Welcome and Participant introductions (Nicky)
    9:10 am Discussion in groups on workshop expectations and report back (All)
    9:30 am Clinical data storage (Freedom) & CRF harmonization (Alia)
    10:00 am Overview of NGS data analysis pipeline for human genomes & microbiomes (Fourie)
    10:30 am Tea break
    11:00 am Overview of GWAS data analysis pipelines (Scott)
    11:30 am Down stream analysis varian tannotation and analysis (Nicky)
    11:50 am Data processing options - Cloud & Galaxy (Scott & Fourie)
    12:20 pm Data transfer, storage and security considerations (Ayton)
    12:40 pm H3Africa Archive and EGA submission (Ayton)
    1:00pm Lunch break
    2:00pm Developing a Data Management plan (Sumir,Faisal)
    2:20pm Group sessions on data management plans (Break-out sessions)
    3:00pm Tea Break
    3:30pm Report back on data management sessions (group leads)
    4:00pm Group sessionson data analysis requirements(Break-outsessions)
    4:40pm Report back on data analysis break-out sessions (group leads)
    5:00pm Workshop End

     

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19130012. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.



    Workshop dates: Sunday, 8 October 2017 [post doc/ early career scientist stream] (08:30-17:15); Monday, 9 October 2017 [student stream] (08:30-17:00)

    Venue: Ocean Room, Radisson Blu Hotel, Dakar, Senegal

    Workshop organisers and sponsors: H3ABioNet, NIH Common Fund

    Workshop trainers and support: Nicola Mulder, Sumir Panji, Ayton Meintjes, Scott Hazelhurst, Fourie Joubert, Alia Benkahla and Faisal Fadlemola.

    Course Overview: This interactive workshop will provide an overview of data management, analysis and submission for H3Africa projects. It also provides an opportunity for Data Support Working Group members, who represent the H3Africa projects to engage with H3ABioNet and discuss their needs.

    Intended Audience: This workshop is aimed at Data Support Working Group members who should be the H3Africa project data managers, data analysts or bioinformaticians. It is important that the attendees have knowledge of the data being generated by their H3Africa projects and information about the project’s data analysis plan.

    Syllabus: Participants will discuss their current data plans and challenges. Lectures will be given on Clinical data collection & storage, overview of GWAS/NGS/microbiome processing, downstream analysis (Variant annotation, meta-analysis, structure, ancGWAS), Data transfer considerations, security, data processing options, and H3Africa Archive and EGA submission. This will be followed by discussion on developing data management plans (with reference to the article: Michener WK (2015) Ten Simple Rules for Creating a Good Data Management Plan. PLoS Comput Biol 11(10): e1004525), and interactive sessions discussing specific projects.

    Prerequisites: Participants should complete the survey at: H3Africa Data Support workshop planning survey - Senegal 2016. One survey needs to be completed per H3Africa project.

    Objectives:

    • Participants will learn how to develop a data management plan.
    • Participants will gain basic knowledge on issues around data security & submission.
    • Participants should come out understanding what considerations there are for their own data analysis, storage and compute requirements.
    • Participants will be able to engage with H3ABioNet on their needs and issues.

    Workshop limitations: This workshop will provide a foundation for continued learning in the handling of H3Africa project data. It will not make one an expert in specific data  analysis pipelines.

    Workshop Program

     

    Time Topic
    8:30 am Registration
    9:00 am Welcome and Participant introductions (Nicky)
    9:10 am Discussion in groups on workshop expectations and report back (All)
    9:30 am Clinical data storage (Freedom) & CRF harmonization (Alia)
    10:00 am Overview o fNGS data analysis pipeline for human genomes & microbiomes (Fourie)
    10:30 am Tea break
    11:00 am Overview of GWAS data analysis pipelines (Scott)
    11:30 am Down stream analysis varian tannotation and analysis (Nicky)
    11:50 am Data processing options - Cloud & Galaxy (Scott & Fourie)
    12:20 pm Data transfer, storage and security considerations (Ayton)
    12:40 pm H3Africa Archive and EGA submission (Ayton)
    1:00pm Lunch break
    2:00pm Developing a Data Management plan (Sumir,Faisal)
    2:20pm Group sessions on data management plans (Break-out sessions)
    3:00pm Tea Break
    3:30pm Report back on data management sessions (group leads)
    4:00pm Group sessionson data analysis requirements(Break-outsessions)
    4:40pm Report back on data analysis break-out sessions (group leads)
    5:00pm Workshop End

     

    Attachments:
    Download this file (DMWS2016 - 01 - security.pdf)DMWS2016 - 01 - security.pdf [ ] 1776 Kb
    Download this file (DMWS2016 - 02 - archive.pdf)DMWS2016 - 02 - archive.pdf [ ] 1315 Kb

    In focus: Data Resolution Workflows

    When the Data Resolution Workflow option is enabled, users will be allowed to open a workflow for documenting the process of resolving issues with data in the project (i.e. opening, responding to, and closing data queries).

    This data resolution workflow, often called 'data queries' in clinical trials and studies, can be utilized either on a data entry form (clicking the balloon icon next to the field) or on the Data Quality page when finding data discrepancies. The Data Quality module will then display a new 'Resolve Issues' tab, which will allow users to view all resolved and unresolved data queries and thus resolve any queries that are still open. Different user privileges may be given to users that control whether or not users can view, open/close, or respond to data queries. For a brief overview, view the Data Resolution Workflow video.  VIDEO: Data Resolution Workflow

    Course overview: The goal of the H3ABioNet Data Management workshop is to prepare H3Africa researchers for management of their data, including knowing what data to collect, what file formats, etc. to use. The course will present options for setting up and storing patient data, discuss the EGA requirements to ensure the researchers collect all the necessary data, and determine the computational needs for storing, processing and mining of the data.

    Keywords: Data handling, Genomics, Genetics, Biological data resources, Protein analysis, Sequence analysis, Systems Biology, Structure Analysis

    Language: English

    Skill level: Advanced

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

    Credential awarded: none

    Proposed workshop outcomes: The outcome will be that researchers have a better idea of what to expect when their data is generated and how to manage this data effectively.

    Proposed workshop relevance: Most of the H3Africa projects are in the stage of data generation and it is important that they know as soon as possible what is involved in data collection and management.

    Target audience of the proposed workshop: Data managers from the H3Africa research projects.

    Applications are now closed.


     

    Programme: 

     Presentation 

        Topic      

    Description (Recorded Lecture)

    Speaker (Slides)

    1

    H3Africa data access policy

    Detail the H3Africa data sharing and access policy, and H3ABioNet's role

    Nicola Mulder1

    2

    Data consent

    Ethics/privacy/consent issues for the data

    Jantina de Vries1

    3

    LIMS systems

    Freezerworks

    Slindile Mbhele1

    4

    LIMS systems

    BIKA LIMS systems

    Lemoene Smit2

    5

    LIMS systems

    Open source LIMS systems

    Alan Christoffels3

    6

    LIMS systems

    Live demonstration of The ARK system

    Freedom Mukomana5

    7

    Patient databases

    OpenMRS

    Pascal Brandt4

    8

    Patient databases

    REDCap

    Irma Maré5

    9

    EBI Variation Resources

    Overview of EBI Variation Archives

    Ilkka Lappalainen6

    10

    EGA and SRA

    EGA overview,process of submission (NGS and GWAS), data required, metadata, formats etc.

    Ilkka Lappalainen6

    11

    EVA

    European Variation Archive

    Ilkka Lappalainen6

     12

    DGVA

    Database of Genomic Variants Archive

    Ilkka Lappalainen6

    13

    H3Africa phenotypes

    Ontologies available and phenotype requirements, metadata

    Nicola Mulder1

    14

    H3ABioNet archive solution

    H3ABioNet data archive and storage plan and processes

    Suresh Maslamoney1

    15

    GWAS

    Introduction to GWAS and analysis steps

    Shaun Aron5

    16

    GWAS

    Quality control

    Shaun Aron5

    17

    GWAS

    Genome Wide Association testing

    Scott Hazelhurst5

     18

    GWAS

    Computing requirements for GWAS

    Scott Hazelhurst5

    19

    NGS data

    Introduction to using NGS for variant detection, Sequencing technologies, File formats, QC and Variant calling

    Radhika Khetani7

    20

    NGS data

    Computing requirements and file sizes for NGS

    Radhika Khetani7

    21

    NGS data

    NGS for Microbiomes

    Radhika Khetani7

    22

    GWAS Downstream analysis

    Additional analysis options, considerations

    Shaun Aron5

    23

    Public datasets

    Where to find them, Ensembl, USCS, extracting data using Galaxy, BioMarts

    Ayton Meintjes1

    24

    Data management

    Data security, safe storage and data transfer

    Radhika Khetani7

    1: University of Cape Town, 2: BIKA laboratories, 3: South African National Bioinformatics Institute, 4: Jembi Health Systems, 5: University of the Witwatersrand, 6: European Genome-phenome Archive, 7: University of Illinois.

    Group picture of participants and speakers for the H3ABioNet Data Management 2014 workshop.

    H3ABioNet Data management workshop participants 2014

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19130024. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.


    Subcategories

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