Research
Research Consortium
H3Africa Cross-Consortium “Genome Analysis of Repeat Expansions in WGS data” project
This project aims to characterize, on a genome-wide scale, novel tandem repeat expansions among Africa populations and how such expansions and other variants contribute to African phenotypes. This is a multi-site collaboration between personnel from Covenant University, Nigeria; University of Cape Town (UCT), South Africa; Makerere University, Kampala; University of California, San Diego, USA; Baylor College of Medicine, USA; Wellcome Genome Campus, UK and University of Witwatersrand, South Africa. Details on the people involved in the project can be found in Figure 1 below.
The research kicked off with the transfer of over 25TB of whole genome sequencing (WGS) data (H3A-Baylor and TrypanoGEN) from UCT to the high performance computing (HPC) facility at the African Center of Excellence (ACE) in Bioinformatics and Data Intensive Sciences at Makerere University, where the team is performing the analyses, in addition to using the HPC facility at UCT. To start, the biggest challenge was how to transfer the 25TB of data to Makerere University HPC. Therefore, to get the data transferred successfully, we employed three different methods, listed in the order that we were able to sort them for use, namely 1) rsync Linux utility, 2) shipping the data in external hard drive and 3) Globus transfer.
The Globus tool was our first option, as Globus is considered to be a fast and reliable data transfer tool. However, the enormous challenge in using Globus is its technical requirements and setting up procedure. To overcome this challenge, system administrators from Covenant University Bioinformatics Research (CUBRe) and the African Center of Excellence (ACE) in Bioinformatics and Data intensive Sciences, Makerere University, met couple of times to debugged issues arising, after the system administrators team from Makerere University did the first installation. The following are key resultants that helped to finalize the Globus installation for our use: 1) It is advisable to install Globus in a separate computer node because it uses specific setting, including firewall setting, network setting and system setting (the first installation was done on a computer node with other applications. Hence, the installation was not functional). 2) Upon Globus installation, endpoint ID and endpoint domain need to be created (and checked to be opened, preferably from another site different from the one with the Globus installation of interest) on the machine where Globus has been installed using this command: globus-connect-server endpoint setup. 3) To complete the setting up, another computing node should be added to host the targeted data. Adding a data transfer node to the Globus endpoint can be done using the following command: globus-connect-server node setup. However, the latter step needs extra firewall and network setting by applying particular network ports (these ports, preferably need to be checked, to be opened (for data transfer) from another site). 4) The data should be secured by creating a user group for those having access right to the data sets.
While debugging the Globus installation problems, we tried to use rsync Linux utility in parallel for the data transfer. Nevertheless, we stopped the rsync transfer once we resolved the issues with Globus. We found that Globus transfer is about 6 times faster compared to the original rsync transfer. At the initial stage of starting the Global transfer, we discovered that the transfer was terribly affected by the available internet speed. Therefore, we estimated that the transfer will be completed in 3 months. At this stage, we decided to explore the option of couriering external hard drive (the time to copy the data into the drive was about 3 weeks) from UCT to Makerere University. While working out this option, we upgraded the speed to 4.5MBps. Although such speed is still slow, we succeeded in using Globus to move the data across the two servers, bumping up of the bandwidth speeds from the Ugandan NREN made the complete transfer possible after close to a month.
Based on the above experience, Globus tool is the still, the tool of choice, for transferring huge data sets across different computing sites, even in Africa.
CODE MALARIA
The overall goal of this project (CODE MALARIA: Eradication Developments for the Decade) is to produce effective four high-tech products for the control and final eradication of malaria, starting with Nigeria. The malaria parasite needs man and the mosquito to continue surviving. Therefore, our first targeted product (from project I), a cuisine of anti-malaria drugs (design and production cost are expected to be cheap to enhance large-scale usage possibility), is to allow rapid cure of malaria in humans. This is to reduce to zero the chance of an uninfected mosquito being infected after a bite. The second targeted product (from Project II), an advanced but human-friendly pesticide (a cocktail of agents), is to help delete rapidly all malaria-infected mosquitoes.
The third (from Project III) aimed at producing mathematical modelling for the prediction of mosquitoes’ metapopulation dynamics towards understanding and validating the seasonal dynamics of this vector. Integration of novel genetic control methods such as SIT (Sterile Insect Technique), lethal densovirus, and genetically manipulated endopathogenic fungi into this mathematical modelling, will allow us to push down the population of the mosquitoes in some areas as may be necessary during the deployment phase of the first two products. And to sustain the gains of the expected malaria eradication after the deployment of the CODE MALARIA technologies, we have another project (project IV), geared at creating a technology (a hand-held machine) that will allow us to detect malaria infection at the liver stage. From the understanding of our environment, in particular West Africa, it is perhaps the place where malaria originated, and from the weather set-up, it will continue to be reservoir of mosquitoes. The malaria parasite goes through the liver before arriving at the blood stage, where it manifests.
It is therefore imperative to note that many lives (in particular the people with sickle cell anaemia) will be saved if these parasites can be detected and treated at the asymptomatic liver stage instead of waiting till the disease manifestation at the blood stage. The expected result of the successful execution and application of our work will make Nigeria and eventually Africa free of malaria-infected humans and mosquitoes like the Western world. Currently, Covenant is investing directly twenty-four million naira to Project I and another fourteen Million naira to project IV, in addition to various millions of dollars from external funding bodies.
The last newspaper interview from Vanguard Nigeria can be found at:
http://www.vanguardngr.com/2012/10/we-aim-to-eradicate-malaria-in-africa-ezekiel-adebiyi/
The account in this editorial account also presents key landmarks so far on the project till October 2012.
Human Heredity and Health in Africa (H3Africa)
The Human Heredity and Health in Africa (H3Africa) Initiative aims to facilitate a contemporary research approach to the study of genomics and environmental determinants of common diseases to improve the health of African populations. To accomplish this, the H3Africa Initiative aims to contribute to the development of the necessary expertise among African scientists and to establish networks of African investigators.
H3AbioNet
Covenant University Wins NIH Research Grant Award. H3ABioNet is an NIH-funded Pan African Bioinformatics network comprising 32 Bioinformatics research groups distributed amongst 15 African countries and 2 partner institutions based in the USA. For a complete list of partners, see Consortium Members. The main goal of H3ABioNet is to create a sustainable Pan African Bioinformatics Network to support H3Africa researchers and their projects through bioinformatics capacity development on the African continent.