H3ABioNet

Pan African Bioinformatics Network for H3Africa

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

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