Tag Archives: boyce thompson institute

Collaborative database development: Lessons from the NextGen experience

By Canaan Boyer

What does it take to create and maintain an open-access genomic database? This is the question that faced the Boyce Thompson Institute, which has been a part of the Next Generation Cassava Breeding project since its inception. Over the years, BTI has developed and supported Cassavabase, an open-access online repository for information from cassava breeding trials. More importantly, however, it has also worked to build capacity in database management and development for NextGen Cassava’s African partners.

Team members from BTI make trips to Africa for field work and visits at partner institutions, an important component of the database development. In addition to this, every year, database managers and data analysts from each breeding institute involved in NextGen Cassava come to BTI to exchange information on database management and collaborate on what needs to be developed for Cassavabase. In these month-long stays, the team is able to engage in in-depth, comprehensive collaboration, ensuring that feedback to make sure Cassavabase continues to meet breeders’ needs is incorporated into the code.

nextgencassava

Alex Ogbonna, Guillaume Bauchet, Rachel Mukisa, and Bryan Ellerbrock at a workshop during the 2017 annual meeting. Experience from fieldwork at partner institutions is critical to ensuring Cassavabase serves the needs of cassava breeders.

“Having all the database collaborators come together like this lets us discuss data curation and learn from each other,” said Guillaume Bauchet, who works at BTI managing Cassavabase. “The goal is to give autonomy to the teams to run their own databases at their institutions.”

Prasad Peteti of the International Institute of Tropical Agriculture (IITA), who has been coming to these trainings at BTI since the beginning of the project, reflected on how far the team has come. “Initially, we were coming to BTI just to learn about development and maintenance of databases. It was more of a one-way flow of information to gain the fundamentals. Now we are developing our own modules and more functionalities.”

Bauchet added, “At BTI, we actually learn a lot from the data and experiences that our partners bring back from their institutions. We’ve achieved a lot since Phase 1. A big part of that phase was all of the logistical things — getting a server, how to ship and install, and so on. That’s been sorted, so in the last couple of years, we’ve really been able to focus on developing tools responsive to the breeder’s needs instead.”

“Now we’re looking towards how we can make the database more useful and incorporate data from new tools, such as near-infrared spectroscopy (NIRS) into it. Phase 2 will focus more on creating a digital ecosystem with the partner institutes, an emphasis on quality, collecting data from farmers’ fields, and a full integration of genotyping data from field to lab.”

Those who have come to BTI for training include:

  • Afolabi Agbona and Prasad Peteti of the International Institute of Tropical Agriculture (IITA) in Nigeria
  • Racheal Mukisa of National Crops Resources Research Institute (NaCRRI) in Uganda
  • Uba Ezenwanyi of Tanzania Agricultural Research Institute (TARI)
  • Adeyemi Oloyede of the National Root Crops Research Institute (NRCRI) in Nigeria
  • Luciana Braatz de Andrade of the Brazilian Agricultural Research Corporation (Embrapa) in Brazil

In addition to the annual training/workshop, the database managers have weekly online meetings with Bauchet and frequently keep in touch with one another. Agbona and Peteti maintain the mirror of Cassavabase on servers hosted at IITA, and provide training to other institutions to help them begin to maintain their own databases.

Partner Spotlight: Boyce Thompson Institute

Feature Image: Guillaume Bauchet (2nd from left) guides workshop participants through a field exercise during the 2017 NextGen Cassava annual meeting. Photo by Bryan Ellerbrock.

More than 10 international institutions are affiliated with NextGen Cassava. In our partner spotlights, we feature profiles on individual institutions and the role each institution plays in the project.

The Boyce Thompson Institute (BTI) based in Ithaca, New York, is one of the founding partners of the NextGen Cassava project. Researchers at BTI code and maintain Cassavabase, an open-access database where cassava breeders can upload the genetic and phenotypic data from their field trials and access data from other breeders around the world.

Establishing a centralized database for  information tracking, genotypic and phenotypic data, and Genomic Selection (GS) prediction analyses was one of the main objectives of NextGen Cassava in Phase 1. Moving into Phase 2, Cassavabase will continue to develop in response to the feedback and needs of breeders. We interviewed Guillaume Bauchet and Lukas Mueller of BTI to learn more about the institute, their work, and how they fit into the NextGen Cassava project.

What is BTI’s role in NextGen Cassava? What are the main activities/objectives being accomplished here?

BTI’s main role in NextGen Cassava is developing  the Cassavabase site as a one-stop shop for NextGen’s breeding data. Our main activities include:

  • Managing data: we handle NextGen’s phenotypic and genotypic data management
  • Developing tools: we support breeders in their day to day activities through breeding database development
  • Capacity building: we train and assist NextGen collaborators in analyzing and bioinformatics.
Lukas Mueller at GCP21 Benin

Lukas Mueller of BTI delivered a presentation on Cassavabase at the 2018 Global Cassava Partnership for the 21st Century Conference in Couteau, Benin. Photo by Canaan Boyer

Are there any Masters/PhD students funded by NextGen at BTI? What is their work focused on?
Currently, there are no Masters/PhD students funded by NextGen at BTI, but we have a lot of institutional representatives involved as data managers/data analysts.

Has the partnership/involvement with NextGen benefited BTI? In what ways?NextGen has been an eye-opener on African agriculture and certainly a great asset to BTI. It has allowed us to see current and future plant research challenges and opportunities.

How does NextGen fit into BTI’s overall mission and goals?
BTI’s aim is to make valuable contributions to general scientific knowledge, biology, and medicine. William Boyce Thompson, BTI’s founder, was convinced that “agriculture, food supply, and social justice are linked.” This is also true of the future of the African continent. 

From its creation, BTI’s mission encompasses the “creation through genetic research of hardier, more nutritious, disease-resistant crop plants and more viable seeds; the study of insects that damage food crops; and the production of new pesticides.”

With NextGen, developing a breeding database for Africa’s major staple crop is fully in line with BTI’s vision and institutional missions.

05_cassavabase

As of the end of Phase 1, Cassavabase hosts a great amount of data related to cassava trials.

How do you see NextGen and BTI’s partnership moving forward?
Developing the “digital ecosystem” around breeding is a continuous, major goal within NextGen where BTI’s contribution is significant.

This will work in conjunction with new research activities developed in Phase 2, such as farmer’s knowledge, food preferences, and related methods/technologies (surveys, near-infrared spectroscopy) to tackle underlying research questions.