H3ABioNet Data Management Workshop June 3 - 6, 2014, Cape Town

    About

    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.

    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.


    The recorded presentations and materials from the H3ABioNet Data Management workshop are available below.

    To access the recorded presentations, click on the link for the description of the topic.

    To access the presentation slides, click on the link for the Speaker's name.

     

     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

     

    Attachments:
    Download this file (Bika_LIMs_Lemoene_Smit_3rd_June_2014.pdf)Bika_LIMs_Lemoene_Smit_3rd_June_2014.pdf [ ] 2640 Kb
    Download this file (Computational_resources_GWAS_Scott_Hazelhurst_6th_June_2014.pdf)Computational_resources_GWAS_Scott_Hazelhurst_6th_June_2014.pdf [ ] 1073 Kb
    Download this file (Consent_for_Data_Sharing_in_Genomics_Jantina_de_Vries_3rd_June_2014.pdf)Consent_for_Data_Sharing_in_Genomics_Jantina_de_Vries_3rd_June_2014.pdf [ ] 687 Kb
    Download this file (Data_management_Radhika_Ketani_6th_June_2014.pdf)Data_management_Radhika_Ketani_6th_June_2014.pdf [ ] 1980 Kb
    Download this file (EGA_EBI_resources_Ilka_Lappalainen_4th_June_2014.pdf)EGA_EBI_resources_Ilka_Lappalainen_4th_June_2014.pdf [ ] 6470 Kb
    Download this file (Freezerworks_Slee_Mbhele_3rd_june_2014.pdf)Freezerworks_Slee_Mbhele_3rd_june_2014.pdf [ ] 2612 Kb
    Download this file (GWAS_testing_handout_Scott_Hazelhurst_5th_June_2014.pdf)GWAS_testing_handout_Scott_Hazelhurst_5th_June_2014.pdf [ ] 1073 Kb
    Download this file (GWAS_testing_Scott_Hazelhurst_June5th_2014.pdf)GWAS_testing_Scott_Hazelhurst_June5th_2014.pdf [ ] 1073 Kb
    Download this file (H3Africa_Data_Archive_and_submission_4th_June_2014_Suresh_Maslamoney.pdf)H3Africa_Data_Archive_and_submission_4th_June_2014_Suresh_Maslamoney.pdf [ ] 487 Kb
    Download this file (H3Africa_Data_sharing_Policy_Nicola_Mulder_3rd_June_2014.pdf)H3Africa_Data_sharing_Policy_Nicola_Mulder_3rd_June_2014.pdf [ ] 600 Kb
    Download this file (Introduction_GWAS_Shaun_Aron_June_5th_2014.pdf)Introduction_GWAS_Shaun_Aron_June_5th_2014.pdf [ ] 2839 Kb
    Download this file (NGS_analysis_for_varient_calling_Radhika_Ketani_June_5th_2014.pdf)NGS_analysis_for_varient_calling_Radhika_Ketani_June_5th_2014.pdf [ ] 9497 Kb
    Download this file (NGS_for_Microbiome_analysis_Radhika_Ketani_June_5th_2014.pdf)NGS_for_Microbiome_analysis_Radhika_Ketani_June_5th_2014.pdf [ ] 9449 Kb
    Download this file (Ontologies_Controlled_Vocabularies_Nicola_Mulder.pdf)Ontologies_Controlled_Vocabularies_Nicola_Mulder.pdf [ ] 1073 Kb
    Download this file (OpenLIMS_Alan_Christoffels_3rd_June_2014.pdf)OpenLIMS_Alan_Christoffels_3rd_June_2014.pdf [ ] 715 Kb
    Download this file (OpenMRS_Pascal_Brandt_H3ABioNet_workshop_June_2014.pdf)OpenMRS_Pascal_Brandt_H3ABioNet_workshop_June_2014.pdf [ ] 4106 Kb
    Download this file (Post_GWAS_analysis_Shaun_Aron_6th_June_2014.pdf)Post_GWAS_analysis_Shaun_Aron_6th_June_2014.pdf [ ] 2393 Kb
    Download this file (Public_data_resources_available_Ayton_Mentjies_6th_June_2014.pdf)Public_data_resources_available_Ayton_Mentjies_6th_June_2014.pdf [ ] 3762 Kb
    Download this file (QC_GWAS_Shaun_Aron_5th_June_2014.pdf)QC_GWAS_Shaun_Aron_5th_June_2014.pdf [ ] 5039 Kb
    Download this file (REDCap_Irma_Mare_June_3rd_June_2014.pdf)REDCap_Irma_Mare_June_3rd_June_2014.pdf [ ] 632 Kb

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