Genomics – the analysis of the function and structure of genomes – is one of the fastest growing application areas for high performance computing. Established only in the last ten years, the field has generated vast quantities of data in a very short period of time.
As Denis Murphy, Professor of Biotechnology at the University of South Wales, explains:
“The first human genome was sequenced only ten years ago and cost over a billion dollars. Now you can have a genome sequenced for about $5000, so that is a really big change. This has resulted in there being a lot more information that we don’t know how to analyse. Much of it is what we call uncurated, just sitting in databases, and the algorithms that have been used to try to make sense of such data are now quite old and not capable of dealing with such a large amount of data. So one of our problems is to develop new algorithms, new techniques, to mine the data and make it into something useful.
“We’re trying to develop tools to analyse this data using high performance computing. We’ve got a few already. One is called cisExpress. That was developed as part of a collaboration between the University of South Wales, HPC Wales and Fujitsu Laboratories of Europe and the University of Southern California, with much of the work being carried out by a student of mine called Martin Triska. Speed and capacity are vital to this work. We find that some jobs that might take as much as six months to run normally can be run in just a few days or less on HPC Wales. It’s really that radical!
Solving this data analysis problem could lead to significant economic benefits, both for Wales and the rest of the world. Professor Murphy has recently helped to found Myregulome Ltd, a small startup enterprise located in Pontypridd that he hopes will be able to commercialize some of his research outputs. He told us of his plans for the company:
“We’re just incubating Myregulome Ltd at the moment, but what we want to do is to use it as a vehicle both to generate good commercial R&D and also to attract additional investment. For example to help us bring funding from Government sources or elsewhere to further extend our research and the application of that research. We have a number of possible projects. One is about finding our ancestors. People are really interested in this. So, you send off a swab from your cheek and we can look at some parts of your DNA to tell us about your ancestry. For example, you may have a European background, but the DNA may show something unexpected – maybe it indicates that somewhere in the recent past one of your ancestors was Asian. There are some similar products out there at the moment but we think we can do much better.”
Professor Murphy has previous experience of delivering commercially valuable genomic research. For the past fifteen years he has been an advisor to the palm oil industry in Malaysia and Indonesia. Over this time the growing population in Southeast Asia has led to a growth in demand for palm oil – which is used as a food, as fuel and in industry. Large areas of tropical rainforest have been converted to palm plantations, destroying the habitat of many animals (e.g. the orangutan). Professor Murphy’s work helps the industry to modernize in order to extract more and better quality palm oil from the existing plantations, thus reducing the need for further encroachment on the rainforests. According to Professor Murphy, the input of HPC Wales is also vital in this work:
“We are developing a new research and development agreement from HPC Wales offering support for our work with the palm oil industry. As part of the agreement researchers from Malaysia will come here for training – which HPC Wales will help us to deliver – so this work provides inward investment into Wales, but also helps to transfer skills to a developing country.
“We hope that as a result of our input the Malaysian palm oil industry will be able to use the latest technologies to increase the yield of their crops. This means using the best genomics software – which we plan to develop. We’ve already advised the industry to sequence the palm genome. They’ve done that, and the paper describing the work was published in Nature in August 2013. Now we’re working with our Malaysian colleagues to use our tools to unlock the information in the genome. It’s like a code and what we want to do is find out what it says, and then we can work out how to change the plant. There’s a lot of money in palm oil – billions of dollars – so Malaysia is very keen to invest in this new technology if it will increase yield. As well as quantity, we are also trying to increase the quality of the oil. One thing it’s used for is food, so we would like to make it more nutritious. It also has industrial uses as a biodegradable and renewable replacement for oil from fossil fuels. Developing that as a product might have environmental benefits.”
This is an exciting time for Professor Murphy. The variety of his work is what he enjoys most – and he has never been able to work on so many different projects. In addition to work with the palm oil industry he also has students working on identifying genes which could suppress cancer, on understanding the toxicity of E.coli (a bacterium that occurs naturally in our digestive system, but can also cause food poisoning) and on developing new workflows that can improve the way in which genomics databases are used. Professor Murphy says that:
“HPC Wales has enabled me to do more things, with the same amount of time in the day. Since getting access I’ve been able to branch out into different research areas and help start up Myregulome Ltd. Previously, I couldn’t have worked in multiple areas simultaneously like I am now. It’s like we have ten balls in the air at the same time, and HPC Wales is helping us to keep them there. Several years ago high performance computing looked really hard to a non-specialist. Just very difficult to get your head around and the chances of me being successful then were low. But with the support of HPC Wales and their staff we’ve learned how to do things much faster. It’s opened up a whole new research area for me that wasn’t really an option before.
Access to HPC Wales has been a key factor in enabling Professor Murphy to perform far more sophisticated analysis of genomes than he was previously capable of. This increased capability has led to an expansion in his research portfolio, to inward investment in Wales from his collaborators in the Malaysian palm oil industry and even enabled him to set up Myregulome Ltd to exploit his research and provide new jobs in Pontypridd.