Plants in silico project
The Plants in silico project fits into the iSEE research theme of Climate Solutions.
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 plants 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 Plants in silico 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 Psi 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, 2016, 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.
iSEE, NCSA, and the Plants in silico team are grateful for a generous gift from the Olga G. Nalbandov Lecture Fund, which helped to make this 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.
Faculty PIs 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. His Realizing Increased Photosynthetic Efficiency (RIPE) page.
- Amy Marshall-Colon, 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, Graduate Student in Computer Science (not pictured). His webpage.
- Kavya Kannan, Graduate Student in Plant Biology (not pictured).
- 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, Graduate Student in Plant Biology (right). Read more about Stuti and her work
- Venkat Srinivasan, Postdoctoral Researcher in Realizing Increased Photosynthetic Efficiency (RIPE) (in group photo above). His lab page.
- Yu Wang, Postdoctoral Researcher in RIPE (in group photo above). Her lab page.
- Yiwen Xu, Graduate Student 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, Senior Research Scientist at the National Center for Supercomputing Applications (NCSA) and NCSA Director of the High-Performance Biological Computing group (right). His Carl R. Woese Institute for Genomic Biology page. His NCSA page. His group 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).
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