“Hackathon” Breeds Momentum for Plant Breeding Software

by | Aug 10, 2016

Hackathon Breakout Session.

Hackathon participants meet in a breakout session.

Sometimes the only way to get something done is to get everyone in a room and hack out a solution, especially when “everyone” is an international group of programmers from plant breeding centers working to create a single interface to unite databases from breeding programs worldwide.

More than two dozen programmers gathered at the Boyce Thompson Institute, July 25-29, for a “Hackathon”—an intense collaborative programming event. Their goal was to create a plant breeding application program interface, or BrAPI, a set of standard definitions and protocols to enable the creation of tools to help plant breeders to access and exchange information from different breeding databases. The Hackathon was funded by the Bill and Melinda Gates Foundation and spearheaded by BTI Associate Professor Lukas Mueller with Jan-Erik Backlund, a colleague from Dow AgroSciences. Participating programmers have worked on the project independently for two years, but the Hackathon gives them the opportunity to resolve issues and fix bugs. Afterward, they plan to release an initial version of BrAPI to the scientific community.

“The BrAPI is a key ingredient in the future of plant breeding software, as it will lead to better and more connected applications that will, in turn, make plant breeding more efficient,” said Mueller.

Researchers have the ability to generate huge quantities of genetic and genomic information from different crops, which can be used to breed new varieties that are more productive, disease resistant or better able to withstand drought or heat. But as the information piles up, scientists struggle to find ways to store and process the information. BrAPI will help researchers to share that information, which will make their crop improvement programs more effective.

“We all work on disparate but common software, so it makes a lot of sense to have an agreed mechanism for data exchange,” said Iain Milne, a research software engineer at the James Hutton Institute in Dundee, Scotland, who works primarily with barley genetic information.

With the BrAPI in place, anyone can develop software to access the James Hutton Institute’s barley data, Mueller’s Cassavabase—a database of genetic resources for cassava breeding, the International Rice Research Institute (IRRI) rice genome database, or other associated databases. These resources contain genetic information and physical traits from different varieties of individual crops. Some groups have also developed visualization software, statistical analysis programs and apps for handheld devices that can be used to collect data in the field. The BrAPI will enable all of these groups to exchange information using common software.

Companies like Facebook, Twitter and Amazon have their own APIs, which software developers can access and use to build applications that use that information, said Matthew Berrigan, Chief Technology Officer at Leafnode, the company providing the software for the group. “What we’re doing is creating [an API] for plant breeding systems so that anybody wanting to write an application for plant breeders can use the data from our systems,” said Berrigan.

Nikki Carumba, a software developer at IRRI, attended the workshop because they plan to use the API for their “fieldbook”—an app for handheld devices that can record and analyze breeding information in the field.

“We’re developing an API so our mobile application can retrieve or save measurements using the mobile devices. It uses the API to connect to our database,” said Carumba. “In the future, others from breeding institutes will also need the rice data from IRRI, and they can retrieve data for their analysis and studies.”

Attendees spent much of the week in small breakout groups, programming and hacking the software, to work on specific issues, such as standardizing formats, tracking sample information, dealing with missing data points and enabling data exchange for apps and handheld devices.

Once it is released later this year, BrAPI will enable peer-to-peer sharing for plant breeders.

“There’s no one source of information anymore,” said Berrigan. “No one can own all the information—it’s too big.”

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