Crops in silico project
As the Earth’s population climbs toward 9 billion by 2050 — and the world climate continues to change, affecting temperatures, weather patterns, water supply, and even the seasons — future food security has become a grand world challenge. Accurate prediction of how food crops react to climate change will play a critical role in ensuring food security.
An ability to computationally mimic the growth, development and response of crops to the environment will allow researchers to conduct many more experiments than can realistically be achieved in the field. Designing more sustainable crops to increase productivity depends on complex interactions between genetics, environment, and ecosystem. Therefore, creation of an in silico — computer simulation — platform that can link models across different biological scales, from cell to ecosystem level, has the potential to provide more accurate simulations of plant response to the environment than any single model could alone.
As a leader in plant biology, crop sciences and computer science, Illinois is uniquely positioned to head this initiative. Developments in high-performance computing, open-source version-controlled software, advanced visualization tools, and functional knowledge of plants make achieving the concept realistic. The interdisciplinary Crops in silico (Cis) team will take advantage of resources in the National Center for Supercomputing Applications (NCSA) and the Institute for Sustainability, Energy, and Environment (iSEE) — and its academic and research expertise in plant biology, crop sciences, and bioengineering — to build a user-friendly platform for plant scientists around the globe who are working on the food security challenge.
The 2017 Crops in silico Symposium & Workshop is set for June 26-28 at the University of Oxford, UK. This second annual gathering is for experts in experimentation, agronomy, physiology, plant development, phenotyping, as well as experts in computational modeling, software development, and data visualization. The event aims to harness the great strides in understanding of plant function from genes to whole plants, to accelerate forward approaches to crop breeding and bioengineering. Read more on the Cis website >>>
Registration is now open. Visit the Oxford website to register >>>
The 2016 Plants in silico Symposium & Workshop — which brought together local, national, and international experts to exchange information and collaborate on a course for achieving plants in silico — was May 18-20 at the National Center for Supercomputer Applications (NCSA) on the Urbana-Champaign campus of the University of Illinois. It featured presentations by leading experts in modeling plant processes, top scientists in achieving in silico representation of other organisms, and computational scientists. Read more about the 2016 event >>>
iSEE, NCSA, and the Crops in silico team are grateful for a generous gift from the Olga G. Nalbandov Lecture Fund, which helped to make the event possible. Other contributors: the Carl R. Woese Institute for Genomic Biology (IGB); the College of Agricultural, Consumer and Environmental Sciences (ACES); the Department of Crop Sciences; the School of Molecular and Cellular Biology (MCB); the Department of Plant Biology; and the Genomic Ecology of Global Change Theme at IGB.
Cis co-PI Amy Marshall-Colón and team member AJ Christensen, a National Center for Supercomputing Applications (NCSA) Visualization Programmer, attended the Global Open Data For Agriculture and Nutrition (GODAN) Summit in September 2016 in New York. Marshall-Colón and Christensen created a writeup on the summit and a mini-documentary on the power of visualization and digital labs in helping to solve the impending world food crisis.
In the past year, some technical developments …
- Cis has developed multiple models:
- a molecular model of At1, a key nitrate transporter;
- a gene-level model of the effects of changing nitrate uptake rate and cellular concentrations on transcript and metabolite levels;
- a gene-level model of the effects of changing atmospheric carbon dioxide concentrations on transcript and metabolite levels;
- a metabolic model that simulates the processes of photosynthesis under elevated atmospheric CO2 concentrations;
- a system-level model that simulates carbon partitioning between the leaf and roots, and sugar-starch portioning under elevated atmospheric CO2 concentrations;
- a solar light absorption model using bi-directional path tracing.
- Cis has rendered plant- and canopy- level data derived from the system model and measured field data of soybean over the course of a growing season. This data includes phenotypic differences between soybean growing under ambient and elevated atmospheric CO2.
- Cis constructed a run-time communications system for integration. The system provides global control, logging, and debugging support and permits new models to be integrated without requiring change to existing models. The metabolic and bio-system models are on line, with others being added as they become ready for testing.
Principal Investigators and co-PIs
- Stephen Long, Professor of Crop Sciences and Plant Biology (in group photo at right). His Crop Sciences page. His Plant Biology page. His lab page.
- Amy Marshall-Colón, Assistant Professor of Plant Biology (in group photo at right). Her departmental page. Her lab page.
- H. Edward Seidel, Director of the National Center for Supercomputing Applications (right). His NCSA page.
- John Hart, Professor of Computer Science (in group photo at right). His departmental page. His parallel computing page.
- Diwakar Shukla, Assistant Professor of Chemical and Biomolecular Engineering (in group photo at right). His departmental page. His lab page.
- James O’Dwyer, Assistant Professor of Plant Biology (in group photo at right). His departmental page. His lab page.
- Xinguang Zhu, Group Leader at the Institute of Computational Biology in the Chinese Academy of Science (right). His institute page.
- Kalina Borkiewicz, Visualization Programmer, Advanced Visualization Lab, NCSA (not pictured). Her departmental page.
- AJ Christensen, Visualization Programmer, Advanced Visualization Lab, NCSA (right). The AVL team page.
- Apollo Ellis, Ph.D. Candidate in Computer Science (not pictured). His webpage.
- Kavya Kannan, Ph.D. Candidate in Plant Biology (not pictured). Read more about Kavya and her work >>>
- Balaji Panneerselvam, Postdoctoral Researcher in Chemical and Biomolecular Engineering (in group photo above).
- David Raila, Senior Research Programmer for NCSA National Data Service (in group photo above). His NCSA page.
- Stuti Shrivastava, Ph.D. Candidate in Plant Biology (right). Her NCSA page. Read more about Stuti and her work >>>
- Venkat Srinivasan, Postdoctoral Researcher at Carl R. Woese Institute for Genomic Biology (in group photo above). His lab page.
- Yu Wang, Postdoctoral Researcher at Carl R. Woese Institute for Genomic Biology (in group photo above). Her lab page.
- Yiwen Xu, M.S. Candidate in Computer Science (in group photo above).
- Gabrielle Allen, Associate Professor of Astronomy and NCSA Director of Computing and Data Sciences (right). Her departmental page. Her NCSA page.
- Donna Cox, Professor of Art + Design and NCSA Director of Advanced Scientific Visualization Laboratory (in group photo above). Her NCSA page. Her lab page.
- Victor Jongeneel, Director of Bioinformatics at the Carl R. Woese Institute for Genomic Biology (IGB) (right). His IGB page.
- Bertram Ludäscher, Professor of Library and Information Science and Director of the Center for Informatics Research in Science and Scholarship (right). His departmental page. His center page.
- Donald Ort, Professor of Plant Biology (right). His departmental page. His lab page.
- Cameron Pittelkow, Assistant Professor of Crop Sciences (right). His departmental page. His lab page.
- Rachel Shekar, Grant Program Manager (in group photo above).
Partners, Departments & Units
Publications & Presentations
(iSEE project members’ names in bold)
- Presentation and video: “How Supercomputers and Visualization Can Help the Global Food Crisis,” Global Open Data for Agriculture and Nutrition (GODAN) Summit, New York, NY, September 2016.
- Presentation: “In-silico Model Integration of Nitrogen Transporter, NRT1.1 with Nitrogen Responsive Transcription Factor Network,” Shrivastava, S. Poster session at the Plant Biology 2016 Meeting in Austin, TX, July 2016.
- Presentation: “In-silico Predictions of Conformational States of Plant and Bacterial Transporters,” Selvam, B., Mittal, S., Shukla, D. Poster session at the Plant Biology 2016 Meeting in Austin, TX, July 2016.
Read More about Cis …