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Crops in silico project awarded $5 million

The Crops in silico project (Cis), led by the University of Illinois, has been awarded a $5 million grant extended across four years from the Foundation for Food and Agriculture Research (FFAR). This grant will help to extend the original Cis project, creating a computer platform that links models across different biological scales — from genetic to ecosystem level — with potential to provide more accurate simulations of plant growth, development, and response to the environment.

The National Center for Supercomputing Applications (NCSA) has provided $212,000 in seed funding in addition to designing the Cis infrastructure and interface, and developing many of the tools used to visualize crops and simulate conditions. Cis has worked in collaboration with NCSA’s Advanced Visualization Lab, led by Donna Cox, to produce high-resolution visualizations using data to explore how genotypes and phenotypes are linked. NCSA is also building a ray tracer to visualize the crops as they develop and to provide input to simulations of the photosynthetic processes by simulating sunlight through full canopies of crops. Cis is the first attempt to centralize and combine this knowledge into whole plant models that will provide the complete framework for improving crops in a fully informed, quantitative manner.

This will include developing a general purpose framework named Yggdrasil, designed by Research Scientist at NCSA, and Cis co-PI Meagan Lang, to tie together computational models from widely different length scales, time scales, computer programming languages, and across disparate computational resources.

Computer (in silico) modeling allows researchers to conduct more experiments than can be realistically achieved in a field while they seek to help feed an increasing world population in the face of environmental challenges like more extreme seasons and weather.

Illinois Assistant Professor of Plant Biology Amy Marshall-Colón is the Principal Investigator for the new four-year grant, which will build a computational framework to link models at several levels (gene, cell, plant, field, ecosystem).

“We are thrilled with the support we have received from FFAR,” Marshall-Colón said. “New strategies are needed to address current and future food insecurity, and this funding allows us to make whole-plant models of corn, soybean, sorghum, and wheat.”

“Those four crops account directly or indirectly for more than 60 percent of human calories. Yet they are susceptible to declining yields due to impending stress from climate change, including water shortages, elevated carbon dioxide levels, and soil degradation. Cis2.0 will identify bioengineering and breeding strategies that will improve photosynthetic efficiency and the use of resources such as water and nitrogen in these crops,” said Marshall-Colón.

Co-Investigators on the FFAR grant include Matthew Turk, Assistant Professor of Information Sciences and Faculty Affiliate at NCSA; Stephen P. Long, Professor of Plant Biology and Crop Sciences, Kaiyu Guan, Assistant Professor of Natural Resources and Environmental Sciences, Meagan Lang, NCSA Research Scientist; Jonathan Lynch, Professor of Plant Science at Pennsylvania State University; Bedrich Benes, Professor of Computer Graphics Technology at Purdue University; Lee Sweetlove, Professor of Plant Sciences at Oxford University; and James Schnable, Assistant Professor of Agronomy and Horticulture at the University of Nebraska.

The Institute for Sustainability, Energy, and Environment (ISEE) gave $350,000 in seed funding to establish the original Crops in silico project in 2015 in collaboration with NCSA. Marshall-Colón and Turk received a $274,000 grant from FFAR in 2017 to extend the work.

View the FFAR news release here


The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign provides supercomputing and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students, and collaborators from around the globe use advanced digital resources to address research grand challenges for the benefit of science and society. NCSA has been advancing one third of the Fortune 50® for more than 30 years by bringing industry, researchers, and students together to solve grand challenges at rapid speed and scale.


The Institute for Sustainability, Energy, and Environment (iSEE) has a three-fold mission: funding and shepherding interdisciplinary research projects that have an immediate and lasting impact in solving global grand challenges related to sustainability, energy, and the environment; leading efforts to make the U of I campus a leading model of sustainability, energy efficiency, and environmental friendliness; and educating and preparing students to be leaders in these fields when they leave campus.


The Foundation for Food and Agriculture Research, a 501(c)(3) nonprofit organization established by bipartisan congressional support in the 2014 Farm Bill, builds unique partnerships to support innovative and actionable science addressing today’s food and agriculture challenges. FFAR leverages public and private resources to increase the scientific and technological research, innovation, and partnerships critical to enhancing sustainable production of nutritious food for a growing global population. The FFAR Board of Directors is chaired by Mississippi State University President Mark Keenum and includes ex officio representation from the U.S. Department of Agriculture and the National Science Foundation. Learn more at

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