Supercomputers accelerate the search for HIV/Aids cure
Engineering News 23 January 2006

Supercomputers accelerate the search for HIV/Aids cure
South Africa is becoming involved in fighting the HIV/Aids pandemic in a multitude of ways.

Thanks to technology, the country is able to harness a wide arsenal of weapons in this fight, and South African researchers are now able to use supercomputers to make use of the knowledge that has been gleaned from the biological building blocks of life, such as genes and proteins, and determine how interactions between these can help to fight the disease, points out Meraka Institute technology research manager Johan Eksteen.

A $1-million supercomputer donated in November by the US-based Intel organisation will now be put to work with the aim of fast-tracking the process of finding a cure for some of South Africa`s most devastating illnesses.

“Building on a growing, innovative base of bioinformatics, the donation positions the South African initiatives close to a number of leading initiatives globally in terms of computational and innovation capability.

“In some respects, it is a modest start compared to massive computational capacity in the developed world, but provides a strong platform to accelerate the use of high-performance computing in South Africa to add our own challenges and opportunities.

“At the same time, it positions South African institutions well to participate concretely with our international colleagues in programmes such as the European Union`s Framework Programme (FP6/FP7).” South African National Bio-informatics Institute (Sanbi) director Win Hide explained at the time of the donation that the machine was earmarked for innovation, and professionals such as medics, bio-informatics experts, health researchers or molecular researchers would be able to use it - as long as they had a good idea.

The scourge that is Aids
In searching for a vaccine for the global pandemic, there can be no doubt that time is of the essence.

The recently-released 2005 South African National HIV Prevalence, HIV Incidence, Behaviour and Communication survey indicated that the prevalence of HIV in people over two years old is around 10,8%.

Females show a higher prevalence than males, at 13,3%, compared to 8,2%.

However, HIV prevalence in-creases with age from 3,3% of children aged two to 14% to 16,2% in adults between the ages of 15 and 49. HIV prevalence peaks at 33,3% among young females between 25 and 29 years of age. In males, this peak is at 23,3% in the 30 to 34 years and 35 to 39 years age groups. However, from 40 years of age, males have a higher HIV prevalence than women.

The HIV/Aids pandemic is responsible for 13-million orphans worldwide, according to www.aids-research.org.

The Website goes on to say that over 40-million people are currently living with HIV.

Some five-million new HIV infections occurred in the world last year, and more than three-million lives were lost last year worldwide to Aids.

The site goes on to lament that conventional cocktail therapy is too expensive for use in regions hit hardest by HIV, such as the de-veloping world, which has 95% of all new infections.

“Continued focused research for a cure is needed now more than ever.”

South Africa is not the first country to investigate a vaccine, as an American has already been injected with an experimental HIV vaccine.

The volunteer received his initial injection of either the vaccine or the placebo in West Hollywood in April last year.

“After receiving his first injection, Al Walz, from North Hollywood, will receive two additional shots over the next six months and will be followed for approximately four years by ARA clinical staff,” according to Aids Research Alliance.

Hope from IT
However, there is hope from the IT sector, as high-performance computing enables researchers to investigate all the proteins and genes in the virus and in the human genome, as well as looking at every single piece of DNA.

Now, a world-class computing resource for the South African life-sciences and bioinformatics research community is to be created by Intel and its partners.

Initially, research will focus on HIV-vaccine definitions, image analysis of health-related data and protein-structure protection analysis, while the computing resource is aimed at advancing research into areas such as genome and statistical analysis, moving into the full spectrum of biomedical informatics applications, including, for instance, population statistics.

Goals of the project include accelerating the process of finding a cure for communicable diseases, such as HIV/Aids, malaria and tuberculosis, through advances in bioinformatics research.

This is to be done by meeting the rising demand for computing power and developing next-generation solutions, tools and expertise.

In addition, the project aims to provide high-performance solutions to tackle complex problems in the biomedical informatics domain that could not be dealt with previously, owing to a lack of technological capacity.

Another goal is to provide a scaleability solution that will be able to handle complex data-intensive processing for experiments measuring tens of thousands of data points in hundreds of thousands of samples.

The machine is to be hosted and managed by the Meraka Institute, which is also known as the African Advanced Institute of Information and Communication Technology and is fully supported by the South African Medical Research Council.

But researchers are not expected to handle all this computing power alone.

Intel employees from the Software and Solutions Group will assist the South African life-sciences and bioinformatics research community working on the cluster.

The Meraka Institue, which is based in Tshwane, is a centre for conducting advanced research in information and communications technologies.

Very much a `behind the scenes` institute, the Meraka Institute (which is located at the Council for Scientific and Industrial Research) derives its mandate as a national strategic initiative from President Thabo Mbeki`s 2002 State of the Nation Address, where the concept of an ICT university was first announced.

The institute is essentially a large-scale intervention in the ICT space that aims to deal with challenges in both the first economy and the second economy.

The Meraka Institute cooperates with international research institutes and companies to undertake this advanced research.

According to business-development manager Envir Fraser, it has a broad research mandate, so the institute concentrates its efforts in trying to create an enabling environment in key areas of research and development critical to its specific context.

Fraser explains that this means trying to establish the infrastructure and supporting research mechanisms which enable South African researchers to perform world-class research in the field of biomedical informatics.

The initiative, which has not yet been named, requires high-tech computing to split out proteins and work through the billions of possible interactions in order to find a potential cure.

Previously, access to such equipment was limited to `shared time` with international colleagues or to a Cray machine.

US-based Cray donated the first research-orientated supercomputer on the continent to Sanbi in 2002.

The machine, donated with research into why some African people are immune to HIV in mind, is, however, a bit cumbersome, according to Hide.

At the time, the machine was also earmarked for improving the understanding of both tuberculosis and malaria, both of which exacerbate HIV/Aids.

Information technology advances
Advances in ICT, together with a growing understanding and knowledge of health issues, ranging from population-linked statistics right through to knowledge of the human genome, are responsible for opening up new avenues and opportunities for the study of complex diseases.

However, there is a need to translate this growing knowledge base into concrete benefits for all citizens, which is becoming more pressing.

This has led to a shift in focus to providing solutions in the area of neglected diseases, such as malaria and even HIV/Aids, which is spelled out in strategies such as the New Partnership for Africa`s Development Science and Technology Strategy.

Machines such as the one donated in November by the Intel Corporation - perhaps better known for its Pentium range of computer chips used in desktop PCs - are aiding and speeding up the necessary research.

The machine, donated by chairperson Craig Barrett, is what Fraser refers to as a computational cluster, where a number of computers are tied together in parallel to tackle computationally-intensive problems.

He says that this donation “provides opportunities for South African researchers to take part in a concrete fashion in the area of biomedical informatics research with a specific focus on dealing with the critical area of HIV/Aids”.

Biomedical informatics deals with integrating health-related data on all levels, such as molecule, cell, tissue, organ, people and the entire population.

Often, this is based on computationally-demanding activities, such as data-mining, modelling, simulation and visualisation.

In addition, biomedical informatics is a demanding area of research, as it covers areas such as disease prevention, all the way through to individually-suitable medicines.

“The field of biomedical informatics provides a rich source of appropriate research, development and implementation opportunities ranging from more effective disease-prevention mechanisms through to individualised medicines and treatments,” says Fraser.

At the same time, he adds, in-silico modelling and simulation can accelerate the process of drug design and development, as well as improve one`s understanding of the under-lying biological processes.

ICT-enabled research efforts into developing an HIV vaccine will concentrate on issues ranging from population models - in order to plan better preventive programmes in an evidence-based fashion - through to research in functional genomics and proteomics to accelerate the search for vaccines and medicines to counteract the spread of the disease.

Fraser adds that the computational technology used for this initiative comprises a cluster of PC-based server nodes based on 64-bit Intel technology, connected through a high-speed interconnection network.

A high-volume, high-speed storage system that deals with the huge volumes of data typically associated with applications in the biomedical informatics field supports the supercomputer.

But there are challenges, such as trying to provide a `sensible` level of access to the computational infrastructure as researchers are scattered across the country.

As such, specific attention is given to broadband Internet-based connectivity from the research groups from all parts of South Africa.

In addition, adds Fraser, the need for “appropriately-skilled and experienced human resources in both the biomedical informatics field and the computer engineering and computational science domains within the country is clear”.

Part of the activities of the centre will be focused on this issue through supporting not only the research, but also the human-capital development component.

The Meraka Institute is also involved in the establishment of the national Centre for High Performance Computing (CHPC), in Cape Town.

The aim of the centre is similar to this initiative, but is broader in scope, dealing with research ranging from climate modelling through to material science.

The CHPC strategy, driven by the Department of Science and Technology through the Meraka Institute, provides synergistic opportunities to enhance the impact of this initiative.

Nicola Mawson, Engineering News