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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 project goal
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
h3africa data expected
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
h3africa s needs
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
approach
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
partner institutions
Partner institutions

Administrative hub at UCT

34 partner institutions, 32 in 15 African countries, 2 in USA

Nodes are full, associate or development nodes

project activities
Project activities

Research/tools

User support

Infrastructure

Training

research and tools
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
user support
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
infrastructure development
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
h3abionet training
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
course access coordination
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.
measuring our success
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
node assessment accreditation
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
how to ensure success
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
communication
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
have we been successful
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