Blog

An Overview of G2F data management tools

March 16, 2016

The Genomes to Fields initiative has an active GxE subroup. That group is collecting data from cooperators including students, postdocs, and technicians across 20+ trial locations. As you might imagine, coordination data collection is not without its challenges! The GxE data management team has leaned heavily on Cyverse (formerly known as the iPlant Collaborative) and has leveraged the Google Sheets to coordinate data collection:

The Discovery Environment (DE) is a web interface to a cloud based data store with secure access to raw and curated data files. The DE provides the capacity to store data files from the smallest of notes to to multi-megabyte image files.

Atmosphere is a cloud service that allows the team to deploy virtual work environments to store and retrieve granular trial data. The Breeding Management System (BMS) is built on a virtual Atmosphere server and is a core system to store and retrieve breeding and associated metadata. BMS is a central component of the Integrated Breeding Platform, whose overall goal is to accelerate the development of new crop varieties worldwide by harnessing both traditional and new approaches to plant breeding. The BMS allows plant breeders to plan, execute, and analyze their nurseries and trials all within a single, centralized system. The BMS is under active development by the Leafnode software team engaged by the IBP and the GxE data management team is working with them to both test, and extend the capabilities of the BMS. As a first step towards full integration of the BMS into the GxE trials, GxE trial data from 2014 and 2015 are currently being loaded into the BMS software suite with an eye towards total deployment of the BMS in the 2016 field season.

Confluence wiki “space” hosted by the CyVerse infrastructure facilitates training and knowledge transfer through illustrative documentation that links out to services core to the Genomes to Fields project. The wiki is secure with access restricted to cooperators and their technicians.

Google Sheets are easy to access and work like the spreadsheet tools many are already using. They are a public resource that meets the needs of the cooperators to report and retrieve data from all web based applications from almost any device. Google Sheets provide a familiar Excel-like interface that allows for data validation and formatting that facilitates aggregation at the end of the growing season.

This current list of resources will likely change over time as technology changes. The data management team strives to leverage solutions that are readily available and accessible.


Industry Update Call

March 14, 2016

A teleconference was held on February 26, 2016 to provide an update to our industry, state commodity groups and other industry associations and stakeholders regarding progress of the G2F initiative. About 25 people attended the call.