System.out.println("Welcome to the MalariaGEN Informatics team blog!");
We are a small team of software engineers, bioinformaticians and systems admins/engineers (well, there’s only one of those). We’re a distributed team, with some of us at the Wellcome Trust Centre for Human Genetics in Oxford, some at the Sanger Centre near Cambridge, and an outlier at the Mahidol Tropical Medicine Research Unit in Thailand. We work on systems to support the Malaria Genomic Epidemiology Network.
What is genomic epidemiology?
Lots of people get malaria and live. Some people don’t. It seems that some people are naturally more resistant to the most severe forms of malaria. So what is different in those people? And one bug is not like the next. Some malaria parasites are resistant to certain drugs, some aren’t. And one mosquito is not like the next. Some are resistant to certain insecticides. Some carry more parasites than others.
Genomic epidemiology is about investigating those differences, by looking at genetic variation. Unfortunately, you need to have a lot of samples of human DNA, or parasite DNA, or mosquito DNA, before you can start to reliably spot important differences. More than any single research group has access to. And you also need the best DNA sequencing machines you can get your hands on. So MalariaGEN was set up to enable researchers around the world share samples and data, and to provide those researchers with access to some advanced DNA sequencing technology based at the Sanger Centre near Cambridge.
Segway to code
Most of what MalariaGEN does depends on software and data, and that’s where we come in. We develop and run data processing pipelines to turn terabytes of raw sequence data into knowledge about genetic variation and evolution in populations of parasites and mosquitos. We develop and maintain LIMS systems to help manage thousands of samples and track their progress through our lab in Oxford and the sequencing operations at Sanger. We develop web applications for exploring, analysing and visualizing the data. And we develop web-based systems that allow researchers around the world to securely access and share data and collaborate with each other.
Hopefully this blog will help us connect with others out there on the interweb who are into similar things or facing similar challenges, both in terms of the technology and the science. Things do get a bit hectic around here from time to time, however, so apologies if it’s a bit sporadic…