Computing Infrastructure

Building & Empowering African Bioinformatics

Tools & Services

Computing Infrastructure

H3ABioNet has several initiatives to further the aim of increasing bioinformatics research capacity on the African continent by providing access to computing infrastructure for data transfer, storage and processing.

Data transfers

Transferring the large datasets typical in current genomics research poses its own challenges in the African context. Network speeds, reliability, costs and even latency are challenging.

Globus Online

For transfers between larger institutions we use Globus online, and have set up almost 20 Globus Endpoints across H3ABioNet.

Netmap

Often the network speeds to the final destination is not as performant as to the institution's edge. To test network speed between the infrastructure of our nodes, and monitor improvement we have a project called Netmap, that captures TCP throughput between nodes.

Physical transfers

Sometimes transfers of data is still most efficient via Sneakernet (using portable hard drives). Our biggest single transfer so far was of 140TB. If you need assistance with a data transfer open a ticket on the helpdesk.

Node hardware

High Performance Computing in Africa

Where larger HPC capacity is required, we encourage using local resources where it makes sense. Researchers at our member nodes routinely run analyses on regional African HPC resources, including:

Name	Institution	Number of cores	Ave RAM GB/core	Max RAM GB	Storage (TB)	DTN	Scheduler	Access type	Location (City, Country)	Website / docs	Used in any H3Africa Projects
ZA-Wits-Core	University of the Witwatersrand	1348	6.7	1024	1300	Several GO endpoints	Slurm	Limited access for H3A Projects and researchers.	Johannesburg, South Africa	http://grid.core.wits.ac.za/	AWI-GEN and H3AChip
Biocluster	University of Illinois Urbana-Champaign	1044	5.3-27	2048	1300	GO endpoint	Slurm	Limited access for H3A Projects and researchers.	Illinois, USA	http://biocluster.igb.illinois.edu/	No
CHPC	South African National HPC platform	32832	5.3; 2.6; 18.5	1024	4000	GO endpoint	PBS	Requires registration and approval of PI and project to allocate resources	Cape Town, South Africa	https://www.chpc.ac.za/	Used for the H3A Chip project
CBIO Cluster	Computational Biology (UCT / H3ABioNet	336	8	1024	300	Several GO endpoints	PBS/Torque	Limited access	Cape Town, South Africa	None	Used for the H3A Chip project
Ilifu	UCT/UWC/Stellenbosh/Sol Plaatjie/Cape Peninsula University of Technology/SARAO	1856	7.5	512	1200	GO endpoint	Slurm	Limited access for H3A Projects and researchers.	Cape Town, South Africa	http://www.ilifu.ac.za/ https://docs.ilifu.ac.za/#/	Training - GWAS and 16S IM BT Refimpute
UCT HPC	University of Cape Town	960	9.375	375	345	scp	Slurm	Can get third party account if collaborator is from UCT	Cape Town, South Africa	http://hpc.uct.ac.za/ http://hpc.uct.ac.za/index.php/account/
Discovery	Kwame Nkrumah University of Science and Technology	288	2.0; 3.2	32; 64	50	none	SGE	Requires approval	Kumasi, Ghana	None	No
Virtual Lab - KENET	Kenya Education Network Trust (KENET)	176	3	384	75	scp	NA	Users are from KENET Member Institutions (Universities, Research institutions & affiliates)	JKML University of Nairobi and USIU	https://vlab.ac.ke	No
Hpc01	Icipe	64	7.8	512	252	None	Slurm	Formal Project application	Kasarani,Nairobi,kenya	github.com/mbbu	h3bionet 16s rRNA microbiome intermediate bionformatics training 2019
UVRI Bioinformatics Cluster	Uganda Virus Research Institute	32	4	128	5	GO endpoint	Slurm	Requires Requisition and Approval of PI to allocate resource	Entebbe, Uganda	None	No
PUBReC	Pwani University	16	2	16	14	No	Slurm	Collaboration with Institution	Kilifi, Kenya	None	No
Research Unit in Bioinformatics (RUBi)	Rhodes University	256	6.5	512	23	GO endpoint	PBS/Torque	H3A projects, researchers and collaborators	Grahamstown, South Africa	https://rubi.ru.ac.za	Database, web services and compute for the HUMA project. Cluster also used for training and bioinformatics
Pathogens Biology	Malawi-Liverpool-WellcomeTrust	56	4;12	360	55	scp	None	Collaborators only	Blantyre, Malawi	None	No
IPT	Insitute Pasteur of Tunis	72	72;512	1024	22	scp	None	Project members and collaborators	Tunis, Tunisia	tesla.pasteur.tn	Yes
CUBRe	Covenant University	64	8	512	96	GO endpoint	None	Formal Project application and collaboration with Institution	Ota, Nigeria	http://cubre.covenantuniversity.edu.ng/	Yes
NABDA-CGRI	NABDA	8	24	192	4.4	GO endpoint	None	H3A projects, researchers and collaborators	Abuja, Nigeria	None	Yes
ECBAG- EGYPT	Zagazig university	24	2.5	60	12	scp	None	Collaborators only	zagazig, Egypt	None	H3ABioNet accredaitions and H3ABioNet training

If you would like to get in contact with any of the centers above please create a ticket on the H3ABioNet helpdesk and we will assist you from there.

Commercial cloud providers that have DC's on the African continent include:

Microsoft Azure
Amazon Web Services (announced)