Transatlantic Collaboration Builds a Better Database

A team of French bioinformaticians made the trip to snowy Ithaca this week to visit the lab of Associate Professor Lukas Mueller with the goal of creating better tools for genome databases.

Alexis Dereeper of the Institute of Research for Development in Montpellier, France, Gaëtan Droc of CIRAD, a French research center for international agriculture, also in Montpellier, and Manuel Ruiz of CIRAD and CIAT, the International Center for Tropical Agriculture in Cali, Colombia, spent a week at BTI discussing ways to build compatible components that will work across multiple databases.

The group collaborates on a bioinformatics platform called South Green. The platform provides tools for genomic databases for rice, coffee, cocoa and other plants. Multiple French institutes involved in agricultural development collaborate on the project, which allows them to exchange new advances in bioinformatics, to share servers and to provide training to biologists.

“The idea of this visit is to extend this network to BTI,” said Ruiz.

“This collaboration is really exciting,” said Mueller. “We can combine tools that will enable research by breeders to be more effective.”

As the cost of DNA sequencing has dropped off over the past five years, scientists have had access to increasing amounts of genomic information. To make sense of this flood of data, biologists need accessible databases and visualization tools.

“Biology is becoming a data science,” said Ruiz. “Biologists need to learn to use bioinformatics tools.”

The team aims to design a platform that will allow biologists to use the same tools to analyze different species. Ultimately, the program will be used to identify and compare genes on the genomes from banana, coffee, rice, palm, cassava and other crops, and to compile genetic information useful for breeding better plant varieties.

To fund this transatlantic collaboration, Mueller and his colleague Mathieu Rouard, a bioinformatics scientist at Bioversity International in Montpellier, received a grant from CGIAR, an international collaboration involved in agricultural research and development. The visit is part of a CGIAR project called Roots, Tubers and Bananas, which aims to improve agricultural methods for these crops.

The partnership began when Mueller met Manuel at a conference with CIAT in November. Dereeper, Gaëton and Ruiz have worked together for 10 years, but they sought Mueller’s input on the project because of his work on Cassavabase, a database of cassava genetic information. Mueller also runs the SOL genomics network, a similar compilation of data on Solanaceae plants such as tomato, potato and pepper, and has experience with standardizing data and “good practices” for developing databases.

“It’s a domain that is evolving a lot, so you always need to challenge yourself with new technologies, new methods and new things to learn,” said Ruiz. “I like that, because you are at the interface between two domains, biology and informatics.”