APL’s Basestack simplifies genomics work

Genomics work has historically been the province of small, highly specialized laboratories with access to top-of-the-line hardware, infrastructure support and technical expertise. Now, a software platform developed largely by the Johns Hopkins Applied Physics Laboratory (APL) in Laurel is making advanced genomics tools accessible and user-friendly for scientists and public health workers around the world.

The platform, called Basestack, is a modular, open-source software suite for complex informatics work that also serves as a pipeline for sharing the innovative tools developed at APL with the global community. Applications that previously were difficult to set up and unwieldy to use and required powerful hardware and high-speed internet can now be run locally, on off-the-shelf laptops, by way of a clean and intuitive interface.

Now used in more than 20 countries for genomic infectious disease surveillance, Basestack grew from a series of international workshops, developed and hosted by APL researchers in collaboration with the National Institutes of Health (NIH) Fogarty International Center, that focused on teaching public health workers a particular method for sequencing DNA.

These workshops highlighted that genomics data analysis has typically been done using the command line – typing long strings of obscure instructions into an intimidating black window for the computer to execute. This approach is commonly used by software developers but is poorly suited to public health employees looking to quickly analyze data.

“Within the first few sessions with front-line public health groups, it was clear that a lot of participants were not familiar with the command line,” said Brian Merritt, a bioinformatician and software developer in APL’s Research and Exploratory Development Department and the primary developer of Basestack. “We spent a lot of time just debugging and setting up software environments, and then once it was set up, people were uncomfortable running commands within the terminal window. We needed a better solution.”