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NIAID-led Partnership Seeks to Establish Bioinformatics Centers in Africa

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NEW YORK (GenomeWeb) – The National Institutes of Health's National Institute of Allergy and Infectious Diseases (NIAID) plans to establish African Centers of Excellence in Bioinformatics (ACEs) that will provide high-performance computing infrastructure, bioinformatics tools, mentorship, and training to researchers across the continent.

The goal of the initiative, which has funding and logistical support from the Foundation for NIH, is to create a network of specialized centers that will provide African researchers with the resources they need to enable independent and collaborative biomedical research around infectious diseases such as malaria, tuberculosis, and HIV, and to develop more effective drugs and vaccines.

Working in partnership with bioinformatics consultancy firm BioTeam, Intel Corporation, and EMC, NIAID officially opened the first of these centers today at the University of Sciences, Techniques, and Technologies (USTTB) in Bamako, Mali. This first center serves as a proof of concept, offering NIAID the opportunity to test the efficacy of its plan, identify areas for improvement, and inform its plans moving forward.  If this initial effort is successful, NIAID plans to seek additional resources to establish four more such centers at other institutions across the continent.

Commenting at the opening ceremony of the center, Susan Solange Zelle, Charge d’Affaires to the US Embassy in Mali, noted that the recent Ebola epidemic "reminded us that we need to build strong health systems to prevent and fight diseases, to augment capacity to understand pathogens using the latest technology, and to share the information with a global network. We hope that this program, a first in West Africa, will be replicated in other countries and contribute to the sustainable development of bioinformatics capacity at African centers."

For this first center, BioTeam, Intel, and EMC have provided in-kind donations of software and hardware valued at about $750,000 in total. Specifically, BioTeam is providing a customized version of its SlipStream appliance loaded onto a system from Intel's HP ProLiant DL Server product line. EMC, for its part, is providing secure storage resources.

On the hardware side, Intel is providing one of its HP ProLiant DL580 Gen8 Servers, one of the highest-end implementations of the company's DL Server range of products. Ketan Paranjape, Intel's general manager of life sciences and analytics, told GenomeWeb that his company chose this system for the Mali Center because of its ability to handle multiple users and scale as needed. It also provides high performance and is easy to install, run, and connect to existing infrastructure such as sequencing instruments, he said.

The particular configuration of the system that Intel has provided is an HP four-socket x86 server that comes with four Intel E7-4800 v2 processors, 96 memory slots, and nine PCIe Gen3.0 slots for greater bandwidth. It comes pre-loaded with four terabytes of storage and offers increased storage performance — 12 gigabits per second — compared to other HP systems. It retails for just over $50,000. The system is also optimized to work with commonly used open source bioinformatics packages such as the genome analysis toolkit, BWA, and Blast, Paranjape said.

The Bamako center has also been equipped with a customized version of BioTeam's SlipStream server appliance, which comes preloaded with an implementation of the Galaxy bioinformatics analysis software. Anushka Brownley, BioTeam's senior scientific consultant, told GenomeWeb that the company did some reengineering of the standard version of the appliance so that it could run on Intel infrastructure — it has historically been run on a Dell platform — and take advantage of the larger storage, memory, and compute capacity that the Intel infrastructure provides.

A base configuration for the current SlipStream appliance includes two Intel Xeon E5-2690 processors — 16 cores total — and 384 gigabytes of random access memory. The Intel system offers 60 cores and a terabyte of memory so "we've had to basically reengineer the way Galaxy was going to leverage [the infrastructure]," she said. Depending on the center's analysis requirements, the system should be able to support many tens of users, according to Brownley. 

Meanwhile, researchers from NIAID's Office of Cyber Infrastructure and Computational Biology (OCICB) will be responsible for training the Bamako researchers to use their new infrastructure. Members from the Bioinformatics and Computational Bioscience Branch provided some in-person training at USTTB this week and, moving forward, will provide additional training remotely. They'll use a tele-learning facility — equipped with video conference capabilities — that has been set up at the Bamako ACE.  Moreover, some NIAID researchers will serve as adjunct professors for a newly minted masters in bioinformatics program at the USTTB which will launch next week.

 

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