Fighting Cancer; how supercomputing is helping to make the impossible, possible
Dr Tatiana Tatarinova, Head of Glamorgan Computational Biology Research Group has been using High Performance Computing (HPC) Wales’ services with her team at the University of Glamorgan to study the genes, proteins, evolution and processes inside a cell using mathematical modelling and computational simulation. Here, Dr Tatarinova discusses the exciting progress she is making.
How ground breaking could your research be?
"In the very near future, when every person is genotyped, the notion of personalised medicine becomes a reality. Health care decisions and practices will be tailored to the individual patient by integrated use of genotypic and phenotypic information as well as medical and family history. Due to the computational complexity of the task, computational biology is essential to the development of tools for personalised medicine.
“We have developed a novel method for identifying a person's ancestry based on DNA analysis. Given global population migration patterns, many people are not aware of their origins. Aside from the sentimental benefits, understanding an individual’s origins is essential to choosing the correct medical treatments and the best diet.”
Why is high performance computing (HPC) important to your research?
“HPC is an essential part of computational biology research. Our research would be slow, hard, even impossible, without access to HPC technology and support.”
What inspired you to get involved in this area of research?
“One of the saddest moments of my life was when my mother was diagnosed with cancer. She had surgery and then developed secondary cancer and subsequently died five years later. One of the problems with cancer treatment is that drugs are not made specifically for individual patients; medicine should take into account a person’s genotype, not just age and gender, and should be tailored to their needs.
“Computational biology has the potential to do this and I will try to dedicate my life to try to prevent tragedies like this happening to other families. Although I couldn't save my mother, maybe I can save other people.”
What is Computational Biology?
“Computational biology is a tool used to rigorously and mathematically describe and investigate biological processes. It has the potential to become a majorly important science of the century, impacting our understanding of genetics and healthcare.”
How do computing technologies and biology integrate?
“There’s a revolution in the lab-based sciences and computing technologies. We can process enormous volumes of diverse data quite cheaply, and at the same time new experimental techniques are continuously being developed. Through integrating both, we can produce unprecedented information about biological processes: with the use of high performance computing this has the potential to impact all aspects of life and all scientific disciplines.”
What have you already achieved through the use of HPC Wales’ services?
“So far, we have completely changed our concept of programming. Among others, we have developed new methods of regulatory elements prediction, genome annotation, analysis of bacterial clusters and discovered rules of bacterial evolution.”
In what ways has HPC Wales supported and enabled your work?
“HPC Wales has given us training, support and access to their technology and services. They have motivated me to aim higher, to make my projects more ambitious. They installed software, trouble-shot our codes and scripts, and liaised with software manufacturers to fix bugs.
“As an example, we were operating under a strict deadline to deliver results to our collaborators in the USA. The program that we were using was able to handle small chromosomes, but failed with the large ones. The software developers did not have access to a cluster compatible to HPC and hence never attempted to analyse large chromosomes. HPC Wales discussed the bug with the software developers, a fix was implemented and we finished our project on time.”
What are your hopes for the future? What does success look like to you?
“Very little is known about genomics and there are discoveries to be made on a daily basis. I hope to continue making discoveries every day. I also hope to make Glamorgan Computational Biology group a large and globally influential research group working on a wide array of biological problems.”
How will your research benefit Wales’ economy/society?
“Our research will facilitate other areas of science, assisting web-lab researchers, plant scientists, agronomists, pharmaceutical scientists and medical doctors in finding cures for cancer and other diseases.”
What advice would you give to other researchers/businesses interested in finding out more about high performance computing?
“It may feel scary and overwhelming in the beginning, but every researcher that needs to analyse a large volume of data needs to at least give it a try. You will be hooked before you know it!”
Keen to learn more? See Dr Tatiana Tatarinova discuss her project in a video case study