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Plants in silico

Symposium & Workshop

May 18-20, 2016

National Center for Supercomputing Applications (NCSA)

University of Illinois at Urbana-Champaign

Videos of Presentations NOW AVAILABLE!

Watch your favorite presentations a second time! Videos of many of our speakers at the Plants in silico Symposium and Workshop are now available to view on iSEE’s Youtube channel.

Click on the left to view keynote speaker Daniel Beard’s talk about his Virtual Physiological Rat project, and click below to browse more videos.


Watch Presentation Videos

Accelerating crop improvements using plants in silico

Plants in silico (Psi) is a global research effort to provide comprehensive computer modeling of plants, growth, and productivity from different layers of organization spanning from genome to phenome to ecosystem, as well as spatial and temporal scales, in a modular framework. The integrated models can also be used as a heuristic tool for the analysis of processes that are difficult to measure empirically. Use of advanced computer graphics will enable the digital representation of actual 3-D details of real shoot and root structures. The ultimate goal of creating Plants in silico is to accelerate food and bioenergy production in a changing climate.

The purpose of the Psi Symposium & Workshop was to:

  1. Learn from similar modular multiscale modeling platforms that Psi can emulate;
  2. Exchange information on the latest developments in plant modeling from molecular to system levels; and
  3. Map a course to achieve plants in silico by creating a community framework model.

Experts in modeling plant processes, computation, and developing geometric and informational visualization will exchange information and collaborate to map a course to achieving plants in silico.

Read Project Manager Rachel Shekar’s post-event write-up on The Global Plant Council blog.

Our Sponsors

iSEE 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; the Genomic Ecology of Global Change Theme at IGB; iSEE; and NCSA.

Thanks to all of our sponsors!

Read more about the iSEE-funded Crops in silico Project.


The meeting will kick off on Wednesday night, May 18, with a keynote address, followed by a public reception. Thursday and Friday morning (May 19-20) will be a series of presentations on modeling of plants at different levels of organization, interspersed with presentations on how complete system models of microbes and mammalian systems have been achieved, and on computational tools that could accelerate achieving plant in silico. Thursday and Friday afternoons, participants will work toward developing a white paper — a sustainable plan of how the community can realize plants in silico.


The Schedule

Wednesday, May 18

5 p.m. — Welcome and Introduction

5:15 p.m. — Keynote Address

  • The Virtual Physiological Rat Project
    Daniel Beard, University of Michigan

6:15 p.m. — Reception and Poster Session

Thursday, May 19

8 a.m. — Registration

8:15 a.m. — Welcome and Introduction

8:20 a.m. — Opening Remarks

  • Evan DeLucia, University of Illinois

8:35 a.m.

  • Harnessing Arabidopsis and the Framework Model to Understand Growth
    Andrew Millar, Edinburgh University
  • Roots for the 10B
    Jonathan Lynch, Penn State University
  • Plants in silico for Crop Improvement: The Role of Crop Modeling
    Xinyou Yin, Wageningen University
  • Discussion

11:10 a.m.

  • Can Artificial Design Beat Natural and Artificial Selection, and How?
    Xinguang Zhu, Chinese Academy of Sciences
  • System Biology Modeling Approaches to Achieve Plants in silico
    Nathan Price, University of Washington
  • Computational Systems Analysis of Lignin Biosynthesis
    Eberhard Voit, Georgia Tech
  • Discussion

1 p.m. — Lunch

1:45 p.m. — Discussion

2 p.m.

  • Advanced Visualization for Insight and Education
    Donna Cox, University of Illinois

2:15 p.m.

  • Towards a National Data Service: Leveraging Tools, Frameworks, and Services Across Communities and Efforts
    Kenton McHenry, University of Illinois

2:30 p.m.

  • Using Isotopic Labeling and Flux Analysis to Analyze Metabolism in Plants
    Douglas Allen, Donald Danforth Plant Science Center
  • A Hybrid Model for Genome-scale Metabolism and Growth
    Jörg Stelling, ETH Zurich
  • Measuring Metabolic Flux and Growth
    Mark Stitt, Max Planck Institute of Molecular Plant Physiology
  • Discussion and Wrap-up

5 p.m. — End Day 1

Friday, May 20

8 a.m. — Registration

8:20 a.m. — Agenda and Goals

8:35 a.m.

  • Modeling Inflorescences: From Molecular Processes to Macroscopic Forms
    Przemyslaw Prusinkiewicz, University of Calgary
  • Molecular Models of Nitrate Transport In Plants
    Diwakar Shukla, University of Illinois
  • Discussion

10:10 a.m. — Plants in silico: A Multi-scale Modeling Platform

  • Amy Marshall-Colon, University of Illinois

10:45 a.m. — Workshop

Noon — Lunch

12:45 p.m. — Workshop

5 p.m. — End Day 2

Speakers and Hosts

Douglas Allen

USDA Research Scientist, Donald Danforth Plant Science Center

(Allen’s website)

Daniel Beard

Department of Molecular and Integrative Physiology, University of Michigan

(Beard’s website)

Donna Cox

Director of the Advanced Visualization Laboratory (AVL) at NCSA, Director of the Illinois Emerging Digital Research and Education in Arts Media Institute (eDream), and Professor in the School of Art + Design, University of Illinois

(Cox’s website)

Evan H. DeLucia

Department of Plant Biology, University of Illinois at Urbana-Champaign. Director of the Institute for Sustainability, Energy, and Environment at Illinois

(DeLucia’s website)

John Hart

Department of Computer Science, University of Illinois at Urbana-Champaign

(Hart’s website)

Stephen P. Long

Departments of Crop Science and Plant Biology, University of Illinois at Urbana-Champaign

(Long’s website)

Jonathan Lynch

Department of Plant Science, Penn State University

(Lynch’s website)

Amy Marshall-Colón

Department of Plant Biology, University of Illinois at Urbana-Champaign 

(Marshall-Colon’s website)

Kenton McHenry

National Data Service Consortium, Deputy Director for Scientific Software & Applications, National Center for Supercomputing Applications (NCSA), University of Illinois at Urbana-Champaign

(McHenry’s website)

Andrew Millar

Chair of Systems Biology, University of Edinburgh, UK; Associate Director of SynthSys Centre for Synthetic and Systems Biology; Fellow of the Royal Society 

(Millar’s website)

Nathan Price

Departments of Bioengineering, Computer Science & Engineering, and Molecular & Cellular Biology, University of Washington; Associate Director, Institute for Systems Biology

(Price’s website)

Przemyslaw Prusinkiewicz

Department of Computer Science, University of Calgary 

(Prusinkiewicz’s website)

Diwakar Shukla

Department of Chemical and Biomolecular Engineering, University of Illinois

(Shukla’s website)

Jörg Stelling

Department of Biosystems Science and Engineering, ETH Zurich

(Stelling’s website)

Mark Stitt

Metabolic Networks Department, Max Planck Institute of Molecular Plant Physiology, UK

(Stitt’s website)

Eberhard Voit

Laboratory for Biological Systems Analysis, Georgia Tech

(Voit’s website)


Xinyou Yin

Centre for Crop Systems Analysis, Wageningen University, Netherlands

(Yin’s website)

Xinguang Zhu

Plant Systems Biology Group, Chinese Academy of Sciences and German Max Planck Society

(Zhu’s website)



National Center for Supercomputing Applications

1205 W. Clark St., Urbana, IL 61801

View on Google Maps or the Illinois Campus Map.

Getting Here

You can also arrive by train or bus at the Illinois Terminal, which is 2 miles away from campus, or you can fly into Willard Airport, which is 5 miles from campus.

Metered parking is available in the garage just north of NCSA, on Clark Street, and on surrounding streets. Rates are $1 per hour, and all meters accept quarters, dimes, nickels and dollar coins. While you can park all day in the garage, street parking is generally limited to two hours.

Bicycle racks are available, and active transportation is encouraged.


Hampton Inn Champaign/Urbana is conveniently located in Urbana, directly across the street from NCSA.

The Hampton Inn features a free hot breakfast and WiFi access, as well as a 24-hour business center and on-site gym/fitness center. The Hampton also provides shuttle service to and from the airport.