DIgital Agriculture Group

DIgital Agriculture Group

Data Science Institute

University of Arizona

Group Vision

Our software will be used and collaboratively developed by researchers at major land grant universities, global ag research centers (e.g. CG), and industry. We will enable scientists to spend less time engineering bespoke pipelines and collecting redundant data so that they can spend more time developing algorithms, augmenting existing data with strategic data collection, and analyzing data.

People

Group Leader

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David LeBauer

Director of Data Science, Agricultural Experiment Station

Current Members

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Ryan Bartelme

Postdoctoral Associate

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Julian Pistorius

Engineer, Research Computing

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Kristina Riemer

Scientific Programmer

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Christophe Schnaufer

Scientific Programmer, Data Scientist

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Jessica Guo

Scientific Programmer

Affiliates

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Jeanette Clark

Projects Data Coordinator

Alumni

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Emily Cain

Scientific Programmer

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Kimberly Huynh

Applications Programmer

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Jorge Barrios

Scientific Programmer

Projects

TERRA-REF

The overall purpose of this project is to improve breeding of plant crops by using modern remote sensing and high throughput phenotyping methods to gather important information about plant traits. We collect high resolution phenomic data and make these publicly available, which can be combined with weather and genomic data to produce insights about plant structure and function. We also aim to provide the tools and training needed to effectively leverage TERRA REF data. Visit terraref.org for more information.

PEcAn

The Predictive Ecosystem Analyzer (PEcAn) is a framework for running ecosystem models. Our mission is to Develop and promote accessible tools for reproducible ecosystem modeling and forecasting. It provides a workflow and standard inputs and outputs to support modeling, as well as a Bayesian approach to integrate information contained in biophysical models and data across multiple sources and scales.

Drone Pipeline

The drone pipeline effort is derived from the larger TERRA REF project, and we are working to adapt these tools to facilitate the use of drones and other platforms for agricultural research. Additional code and information can be found on our project page.

Sentinel

The purpose of the Sentinel project is to design plants to sense and detect biological compounds. We are using a grass species that will have varying traits, including height and fluorescence, in response to exposure to certain compounds.

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Services

Data Access and Curation

We help scientists manage and curate their data. Our services include: Advising on all stages of the data lifecycle, from collection to publication and reuse. Writing and Implementing data management plans. Sharing data through CyVerse, the UA Library, DataOne and other repositories.

Custom Pipelines

We can help users automate computational pipelines to improve the efficiency and consistency of their data intensive research.

Crop & Ecosystem Simulation Models

We use crop, ecosystem, and land surface models, and are interested in more closely integrating models and data.

Training

We teach best practices in computational and data intensive science and reproducible research.

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Recent Posts

Successful Completion of Open Life Science Program!

Our group has successfully completed the Open Life Science (OLS) program, which we previously wrote about getting accepted to. The purpose of OLS, an offshoot of Mozilla Open Leaders, is to improve open science practices within life sciences communities.
May 22, 2020 4 min read

Hackathon For Building the Agricultural Research Data Network

The first week of May, David and I participated in a hackathon on agricultural data formats. This event was part of a project called the Agricultural Research Data Network (ARDN), which was funded by a NIFA FACT grant (2019-67021-29921).
May 8, 2020 4 min read

FOSS 2020

This year I was lucky enough to attend the second CyVerse Foundational Open Science Skills ( FOSS) camp, which took place here at the University of Arizona during the week of February 17, 2020.
Mar 13, 2020 3 min read

rstudio::conf + workshop 2020

I represented our group at rstudio::conf 2020 during the last week of January. This conference is hosted by the organization responsible for the RStudio development environment and for many other improvements in the useability of the R programming language over the past decade, including packages and training.
Feb 18, 2020 3 min read

Our work presented at the 2020 Plant and Animal Genome Conference

The Plant and Animal Genome XXVIII conference (PAG) is the largest agricultural genomics conference in the world, and there is a lot of interest in statistics, sensing, data sharing, and software.
Jan 20, 2020 3 min read
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Recent Publications

An open, scalable, and flexible framework for automated aerial measurement of field experiments

Unoccupied aerial vehicles (UAVs or drones) are increasingly used in field research. Drones capable of routinely and consistently …
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Beyond modeling: A roadmap to community cyberinfrastructure for ecological data-model integration

In an era of rapid global change, our ability to understand and predict Earth’s natural systems is lagging behind our ability to …
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Exosphere -- Bringing The Cloud Closer

Description of Exosphere, a simple user interface for research cloud computing. Presented by Julian as part of the SuperCompCloud workshop at SC20, The International Conference for High Performance Computing, Networking, Storage, and Analysis. Learn more about Exosphere
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TERRA-REF, An Open Reference Data Set From High Resolution Genomics, Phenomics, and Imaging Sensors. Dryad Digital Repository.

PDF DOI

BrAPI - An application programming interface for plant breeding applications

Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in …
Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar E. Benites-Alfaro, Clay Birkett, Viana C. Calaminos, Pierre Carceller, Guillaume Cornut, Bruno Vasques Costa, Jeremy D. Edwards, Richard Finkers, Star Yanxin Gao, Mehmood Ghaffar, Philip Glaser, Valentin Guignon, Puthick Hok, Andrzej Kilian, Patrick König, Jack Elendil B. Lagare, Matthias Lange, Marie Angélique Laporte, Pierre Larmande, David S. Lebauer, David A. Lyon, David S. Marshall, Dave Matthews, Iain Milne, Naymesh Mistry, Nicolas Morales, Lukas A. Mueller, Pascal Neveu, Evangelia Papoutsoglou, Brian Pearce, Ivan Perez-Masias, Cyril Pommier, Ricardo H. Ramírez-González, Abhishek Rathore, Angel Manica Raquel, Sebastian Raubach, Trevor Rife, Kelly Robbins, Mathieu Rouard, Chaitanya Sarma, Uwe Scholz, Guilhem Sempéré, Paul D. Shaw, Reinhard Simon, Nahuel Soldevilla, Gordon Stephen, Qi Sun, Clarysabel Tovar, Grzegorz Uszynski, Maikel Verouden, Jonathan Wren
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Contact

  • 520-621-4381
  • 1230 N Cherry Ave, Tucson, AZ 85721
  • Enter Biosciences Research Laboratory (BSRL) and wait in the lobby - someone will need to let you in
  • Book an appointment