Software development is in play even before a species sample arrives at the Sanger Institute, be that a tiny piece of frozen leaf, tissue, or blood. Sample collectors input data about the species, including where it was found and who identified it, into a system called COPO. Samples arrive at the Sanger in barcoded tubes which are scanned in and managed using the aptly named ‘Sample Tracking System’ or ‘STS’. Because STS links to COPO, the team can use the system to match up what has arrived, to what was expected. This link also allows legal and compliance teams to complete and record their checks, before a sample is even shipped.
Andrew Varley leads a team of software developers, who develop and maintain bespoke programmes, including STS. STS stores all these metadata – with the aim of making things as easy, and as quick as possible for the scientists scanning in the samples. STS interfaces with a range of systems, including commercial laboratory software, and bespoke genome analysis programmes.
The team works using the Scrum methodology, in sprints. These are two-week cycles of development, where an updated version of the software is released at the end of each sprint. Working like this enables the team to stay ‘agile’ and close to the needs of the scientists, partners and users of the software. They work together to define and prioritise what is needed for each sprint. Andrew’s team then work to decide how something can be delivered. The result is an IT system that is being constantly improved, and has already enabled laboratory staff to record and process thousands of samples.
“For STS we were building systems from the ground up, so there was the opportunity to do it any way we wanted. We could choose the technologies to use, we weren’t tied to a 20-year-old legacy system,” says Andrew.