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

: Data Management; 12 December 2017; Hits: 15873

Communications

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.

past , data management