Meet the people building software to enable high-throughput genomics at the Sanger Institute.
By Alison Cranage, Science Writer at the Wellcome Sanger Institute
Many credit Ada Lovelace for writing what would have been the first piece of computer software, back in 1843. She worked with polymath Charles Babbage, after he proposed the first mechanical general-purpose computer; the analytical engine. Though it was never completed, she saw its potential to do more than calculate sums.
Nearly 200 years later, the software that runs modern computers is an integral part of all our lives. It enables everything from communications to traffic lights, to financial systems and manufacturing. The people who code and create such software are vital.
Software developers also underpin and enable science, especially large-scale genomic studies. We spoke to two software developers about their roles here at the Wellcome Sanger Institute.
From choreography to coding
Harriet Craven is a software developer in the Laboratory Information Management Systems (LIMS) group at the Sanger Institute. It’s not the career she had in mind when she first left school; she studied A-levels at a dance college.
“I studied English and Maths. But by the time I finished college, I knew I wanted to pursue computing, rather than dance. I was always drawn to the creative, but logical side of things.”
Harriet undertook an intensive 12-week course in computer coding and software development. She applied for a job at the Sanger Institute after that, and is now half way through her Open University degree in Computing and IT.
“Software development is incredibly creative. You get to design solutions to problems.”
The LIMS, as described by team leader Rich Livett, is ‘the indispensable companion of genomics pipeline analysis’. It underpins all of our high-throughput DNA sequencing work at the Sanger Institute.
LIMS allows a single person’s DNA to be tracked on its journey through the Institute. From arriving (usually with hundreds or thousands of other people’s genomes), through processing in the laboratory, loading onto a sequencing machine, conversion to digital data and analysis – the software keeps track of a sample and the processes it’s been through.
There is no room for mix-ups. The samples contain the most personal of information; an individual’s unique DNA sequence. The LIMS manages 5,000 human genome samples like this every month, plus thousands of others going through different processes, as they flow through the Institute’s sequencing facility.
The software needs to be user friendly for laboratory teams, as well as provide comprehensive data for reports and downstream analysis. It is updated regularly, based on what its users suggest to change.
“Scientific developments are increasing at such a rate there aren’t enough developers to keep up. It is a really exciting, innovative sector to build software for,” Harriet says.
Explaining computing concepts and technologies is something Harriet not only does at the Sanger, but also in schools. She is passionate about inspiring the next generation of software developers, and runs a lunchtime ‘Code Club’ at a nearby primary school.
Rich agrees and sees outreach work, like the time Harriet spends in schools, as an investment for the future. “I think it’s important that children become digital makers, not just consumers.”
Advancing genome science
The LIMS team is one of the biggest software teams at the Sanger, but software developers work within most areas of the Institute.
Peter Keen is a senior software developer in the Stem Cell Informatics team, supporting the Institute’s High-Throughput Gene Editing and Bespoke Gene Editing teams. Any researcher at the Sanger Institute can order cells from the High-Throughput Gene Editing team, with any particular gene taken out. Many experiments will use thousands of these ‘knock-outs’, for example to systematically test the effects of a drug. The team use the latest CRISPR-Cas9 technology to precisely ‘cut out’ a particular gene and create the genetically-modified cells, which are then sequenced to check the gene has been disrupted as expected.
Peter has recently created software to analyse that genome sequence data. It involves pulling in information from LIMS and other data sources here, as well as external databases. He created a graphical representation of the outcomes, so the scientists can easily visualise their results.
Peter didn’t study biology, but has picked up knowledge along the way, with help from the scientific teams he works closely with. “I will always go and speak to a scientist to find out exactly what they’re trying to achieve, before I start to build any new software.”
Peter told us why he enjoys his job. “I enjoy the variety of work at the Sanger Institute. I can get involved in a range of projects. I’m really interested in machine learning and I’m able to explore that here.
“It’s exciting to be involved in advancing genome science and our understanding of human health and disease.”
Find out more
You can read more about how Peter got into software development on the Technician Commitment website. The Sanger Institute is a signatory of the Technician Commitment and we are committed to valuing, developing and rewarding our highly skilled technical employees, including software developers.