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H3ABioNet Pan African Bioinformatics Network for H3Africa

H3ABioNet Pan African Bioinformatics Network for H3Africa. H3ABioNet Project Goal. T o build H3ABioNet -- a sustainable African Bioinformatics Network -- to provide bioinformatics infrastructure and support for the H3Africa consortium.

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H3ABioNet Pan African Bioinformatics Network for H3Africa

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  1. H3ABioNet Pan African Bioinformatics Network for H3Africa

  2. H3ABioNet Project Goal • To build H3ABioNet -- a sustainable African Bioinformatics Network -- to provide bioinformatics infrastructure and support for the H3Africa consortium. • H3Africa: NIH and Wellcome trust funded initiativeto encourage genomic research in Africa on relevant health issues. Funding: • Research projects (kidney disease, diabetes, cardio-metabolic disease, TB, Trypanosomiasis etc.) • Collaborative centres • Biorepositories

  3. H3Africa data expected 50% exome, 40% full genome, 10% metagenomics • Storage required for processed data for >12k samples: 2.5PB • Storage required for processed data for >30k samples: 52TB

  4. H3Africa’s needs • Large-scale data analysis for: • Genotyping by arrays • Next generation sequencing • GWAS • Support for analysis: • General questions • Access to computing resources • Technical computing support • Data access and visualization (public and new) • Data storage, backup and transfer • Data submission • Training

  5. Approach • Formalize existing networks and connections between bioinformatics institutions • Determine capacity at participating nodes, identify gaps • Determine bioinformatics needs of funded projects • Formulate plan to fill gaps and address needs through: • Training • Computing infrastructure development • Research into new tools • Effective communication • Interaction/collaboration with foreign institutions

  6. Network structure

  7. Partner institutions Administrative hub at UCT 34 partner institutions, 32 in 15 African countries, 2 in USA Nodes are full, associate or development nodes

  8. Project activities Research/tools User support Infrastructure Training

  9. Research and tools • Data management and storage • Patient databasing protocols • BioMart for genotyping data • Grid-based tool for data storage • Data analysis tools • Galaxy for NGS and Genotyping analysis • Genome assembly pipeline • Functional SNP calling pipeline • Admixture mapping and network tools • Data visualization tools • Recombination tools • Structural SNP analysis tool • Joint research projects

  10. User support • H3Africa research projects provide support on: • Small bioinformatics queries (scripts etc) • Data management • Large-scale analysis • Access to computing infrastructure (data & hardware) • Submission to EGA • Support provided through: • Helpdesk • Training

  11. Infrastructure development • Technical support –programming, pipeline development, sys admin • Access to HPC, Cloud, eBioKits • Access to public data • Standard operating procedures and guidelines for data analysis • Tools/support for data submission • Storage, movement & management of data

  12. H3ABioNet training • Researcher training • Train-the trainer • Graduate training MSc/PhD/Postdocs • Shared course curriculum • Co-supervision across nodes • Specialisedcourses • Technical staff • Computing/sys admin courses • HPC, Cloud, data management • Internships with external partners

  13. Course access & coordination • Technical course webcast using USTREAM • Bioinformatics course live Vidyo streaming to 2 sites Tunisia and Nigeria • All lectures are recorded • Coordinate with other training programs –Wellcome Trust, EMBO, etc. • Will work with GOBLET on training objectives, quality etc.

  14. Measuring our success • Assess and track node capability • 6 monthly reports to NIH • Assess and track other metrics: • Students graduated • Publications • Grants • Infrastructure • Node size

  15. Node assessment & accreditation • Assessing internet capacity at each node • Node assessment exercises • Set of workflows with simulated data covering: • Analysis of NGS data (exome and full genome) • Variant calling • Genotyping array data analysis • GWAS analysis • Nodes can undertake exercise at any time

  16. Internal database

  17. Internal database

  18. How to ensure success • Funding! • Good management structure • Effective and regular communication • Keeping everyone active and feeling a part of the activities • Providing access to new opportunities • Facilitating new projects and funding opportunities • Always keep an eye on milestones

  19. Management structure

  20. Communication • Meetings • WG meetings fortnightly, MC monthly • GA and SAB meet annually • Web portal: • Members info and expertise • Documents • Tools and resources, etc. • Mailing lists, monthly bulletin

  21. H3ABioNet website -public

  22. H3ABioNet website -private

  23. Monthly Bulletin

  24. Have we been successful? • Too early to tell, many challenges • Some success stories • >30 new staff or students • >100 people trained • Communication structures established • New projects and collaborations initiated • Funding proposals written • Egypt centre established

  25. Funding: NIH/NGHRI Acknowledgements

  26. Thanks: SumirPanji –Project Manager

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