H3ABioNet

Pan African Bioinformatics Network for H3Africa

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 initiative to 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

SNP Arrays NGS Data (Exome, RNA Seq, Full Genome)

Other (Biorepository)0%

10%20%30%40%50%60%70%80%90%

Types of Data To Be Generated H3Africa Projects

Types of Data Generated

Perc

enta

ge o

f H3A

frca

Pro

ject

s (N

=9)

Illumina

454

Other

0% 10% 20% 30% 40% 50% 60%

Sequencing Platform Used

Percentage of H3Africa Projects Using a Sequencing Platform (N=9)

Type

of S

eque

ncin

g Pl

atfor

m U

sed

50% exome, 40% full genome, 10% metagenomics

Storage required for processed data for >30k samples: 52TB

Storage required for processed data for >12k samples: 2.5PB

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• 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

Network structure

Partner institutions

Administrative hub at UCT

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

USANodes are full, associate or development nodes

Project activities

Patient databaseData storage

& management

Pipelines and tools

Data submission

scripts

SOPs, ontologiesStorage & transfer facilities

Running of pipelines, analysis

Data submission

process

Database servers Databases Access to

hardwareStorage area of EGA files

Training in patient DB

Training in data

management

Training in data analysis

How to submit

Sample collection Data generation Data analysis Data submission

Research/tools

User support

Infrastructure

Training

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• 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

• 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• Researcher training• Train-the trainer• Graduate training MSc/PhD/Postdocs

• Shared course curriculum• Co-supervision across nodes• Specialised courses

• Technical staff• Computing/sys admin courses• HPC, Cloud, data management

• Internships with external partners

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• 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

• 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

Internal database

Internal database

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

Management structure

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

H3ABioNet website -public

H3ABioNet website -private

Monthly Bulletin

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

Acknowledgements Funding: NIH/NGHRIName Institution CountrySimani Gaseitsiwe Botswana Harvard AIDS Institute Partnership BotswanaAhmed Mansour Alzohairy Zagazig University EgyptJames Brandful NMIMR Ghana Ellis Owusu-Dabo KNUST Ghana Daniel Masiga ICIPE KenyaDean Everett Malawi-Liverpool Wellcome Trust Clinical research Programme MalawiSeydou Doumbia University of Bamako MaliYasmina Jaufeerally Fakim SANBio MauritiusHassan Ghazal University Mohammed First MoroccoAzedine Ibrahimi Faculte de Medecine et de Pharmacie de Rabat MoroccoAhmed Moussa Abdelamlek Essaadi University, Tangier MoroccoFouzia Radouani Pasteur Institute Casablanca MoroccoFouad Seghrouchni Institut National d'Hygiène, Rabat MoroccoFatima Gaboun National Institute of Agronomic Research, Rabat MoroccoKhalid Sadki Mohammed V University, Rabat MoroccoAlami Raouf Centre National de Transfusion Sanguine, Rabat MoroccoOdile Ouwe Missi CERMES NigerEzekiel Adebiyi Covenant University Bioinformatics Research NigeriaOyekanmi Nash NADBA NigeriaNicky Mulder University of Cape Town South AfricaJudit Kumuthini CPGR South AfricaNicki Tiffin SANBI, University of the Western Cape South AfricaOzlem Tastan Bishop Rhodes University South AfricaScott Hazelhurst Wits University South AfricaFourie Joubert University of Pretoria South AfricaHugh Patterton University of the Free State South AfricaFaisal Fadlelmola Future University SudanSylvester Lyantagaye University of Dar es Salaam (UDSM) TanzaniaNzovu Ulenga MDH TanzaniaJulie Makani MUHAS TanzaniaAlia Benkahla Institute Pasteur of Tunis TunisiaJonathan Kayondo UVRI UgandaVictor Jongeneel NCSA USAWin Hide Harvard School of Public Health USA

Thanks: Sumir Panji –Project Manager