Crops in silico



    June 26-28th 2017
    University of Oxford, UK

    Select Presentations for Download

    Meeting Recap

    The second annual Crops in silico Symposium and Workshop was hosted at St. Catherine’s College, University of Oxford, on June 26-28, 2017. The goals of this Symposium and Workshop were:

    • Briefly introduce the Crops in silico concept as an integrative and multi-scale modeling platform.
    • Learn from plant and computer scientists who have progressed plant modeling or tools to enhance modeling in different domains.
    • Discuss where sustainable and practical collaborations may be valuable and achievable in bridging layers of organization.
    • Map the next steps for the community

    57 registrants from 23 institutions and companies and six countries convened for the Symposium.

    The event kicked off June 26 with Keynote Speaker Eberhard Voit, Professor and GRA Eminent Scholar and Flanagan Chair in Biological Systems at the Georgia Institute of Technology.  His talk addressed the difficulties of modelling complex biological systems and how those difficulties can be overcome by dividing a complex modeling task into a coarse, framework model and more detailed, finer-grained models of subsystems.

    The meeting included five presentations on recent developments in plant modelling at different levels of biological organization, three presentations on recent developments in model integration, four presentations on users and usability of models, and one presentation outlining the steps to the successful deployment of a community driven software platform to advance and support research in astrophysics.

    The overall goal of the workshop was to identify ways to build the Cis community. The first part of the workshop focused on identifying ways to establish successful research collaborations. Next, attendees brainstormed ideas of how to build a Crops in silico research community. The second portion of the workshop was focused on fostering new research collaborations.

    Who should attend?

    Join experts in experimentation, agronomy, physiology, plant development, phenotyping, as well as experts in computational modeling, software development, and data visualization.


    Download the program.

    5 – 7 pm

    Keynote talk – Templates, Anchors and Matryoshkas: A vision for crop systems biology / Everhard Voit, Georgia Tech University

    This talk is free and open to the public.

    Crops have been the subject of unending attempts for improvement since the dawn of humanity, first through trial and error and later through selective breeding. Indeed, comparing modern crops with their early predecessors, one can only be astounded by the success of these methods. Unfortunately, both trial and error and selective breeding require much time, thus raising the question of whether the process can be sped up through rational crop modifications. The challenge of such an approach is the enormous complexity of plants. The Norway Spruce has close to 60,000 genes, and metabolites within the plant kingdom are estimated to range collectively between 200,000 and 1 million. Confounding these numbers are other features of complexity, including simultaneous operation at multiple scales, counterintuitive nonlinearities, synergistic and antagonistic effects, and unpredictable threshold effects. The convolution of these features cannot be grasped reliably by the unaided human mind and suggests the employment of methods of computational systems biology. In this presentation, I will sketch the contextual landscape in which computational systems biology might help advance the goals of crop science and propose a modular strategy for realizing the development of effective models.

    7 pm

    Conference dinner

    8 – 9 am


    9:00 – 9:30 am


    9:30 am – 1:00 pm

    Session 1: Recent developments in plant modelling
    Cassava source-sink – Expression of genes involved in central carbon metabolism / Frank Ludewig, Universität Erlangen-Nürnberg
    Constraints-based modelling of leaf metabolic networks / Lee Sweetlove, University of Oxford
    Signal integration in the control of shoot branching / Ottoline Leyser, Cambridge University
    Organ scale models: lessons from the hidden half / Malcolm Bennett, University of Nottingham
    Crop modelling to underpin food security / Matt Reynolds, CGIAR

    1:00 – 2:00 pm


    2:00 – 5:00 pm

    Session 2: Recent developments in model integration
    Models for model interoperability / Daniel S. Katz, University of Illinois
    Integrative Dynamic Modeling Using Diverse Biological Datasets / Cranos M. Williams, North Carolina State University
    A Computational Framework for Connecting Models Across Languages and Scales / Meagan Lang, National Center for Supercomputing Applications
    Workshop: Identifying gaps, challenges, and potential solutions

    7 pm

    Conference dinner

    8 – 9 am


    9 – 1 pm

    Session 3: Users and usability
    Four Levels of Visualization / Min Chen, University of Oxford
    Semantic Annotation of Biosimulation Models for Model Reuse and Composition / Brian Carlson, SemGen
    Education Using Crops in silico / Gabrielle Allen, University of Illinois
    Scaling from mechanistic models to crop stands and beyond / Steve Long, University of Illinois
    Workshop: Identifying users and opportunities to enhance usability

    1 – 2 pm


     2 – 5:30 pm

    Session 4: Next steps for Crops in silico
    Workshop: Identifying crop improvement goals
    Workshop: Developing future collaborations


    Eberhard Voit, Keynote Speaker

    Professor and GRA Eminent Scholar, Flanagan Chair in Biological Systems, Georgia Institute of Technology

    Gabrielle D. Allen

    Professor of Astronomy and Associate Dean for Research and Research Education, University of Illinois

    Malcolm Bennett

    Professor of Plant Sciences, The University of Nottingham

    Brian Carlson

    Research Assistant Professor, Molecular & Integrative Physiology, University of Michigan

    Min Chen

    Professor of Scientific Visualisation, Oxford University

    Daniel S. Katz

    Assistant Director for Scientific Software and Applications, National Center for Supercomputing Applications & Research Associate Professor, Electrical and Computer Engineering & Computer Science, University of Illinois

    Meagan Lang

    Postdoctoral Research Associate in the National Center for Supercomputing Applications at the University of Illinois

    Ottoline Leyser

    Director of the the Sainsbury Laboratory, Cambridge University

    Steve Long

    Gutgsell Endowed Professor, Department of Crop Sciences and Plant Biology, University of Illinois
    Newton Abraham Visiting Professor,Department of Plant Science, Oxford University

    Frank Ludewig

    Scientific coordinator of the Cassava Source-Sink project, Universität Erlangen-Nürnberg

    Matt Reynolds

    Wheat Physiologist, CGIAR and International Maize and Wheat Improvement Center

    Lee Sweetlove

    Professor of Plant Sciences, University of Oxford

    Cranos M. Williams

    Director of the EnBiSys Research Laboratory and Assistant Professor of Electrical and Computer Engineering at North Carolina State University


    The poster session will provide the opportunity for individuals to present their research and offers an excellent venue for extended informal discussion with meeting attendees.

    Learn More


    The £390.00 registration fee includes lodging the nights of the 26th and 27th of June at Porters’ Lodge at St. Catherine’s College. Registration without accommodation is £290.00


    How to get to Oxford
    Arriving by coach? The closest stop is Queens Lane, which is a 10 min walk to St. Catherine’s College.

     Symposium Location

    The Symposium will be held at The Bernard Sunley Building auditorium at St Catherine’s College.

    Meeting Organizers

    Steve Kelly

    University of Oxford

    Steve Long

    University of Illinois

    Amy Marshall-Colon

    University of Illinois


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