2021 Annual Meeting

    5th Annual Crops in silico Symposium & Hackathon

    Keynote: Time TBA June 8

    Symposium: 8 a.m.-noon June 8-9

    Hackathon: 1-5 p.m. June 10

    A virtual event!


    The Symposium

    The Crops in silico organizing committee will bring together international experts from computer sciences, mathematics, and plant sciences developing and using plant computational models to exchange information on the rapidly expanding advances, opportunities for collaboration, and challenges for achieving in silico crops. We will focus on recent improvements and applications of plant simulation models and associated software and computational tools that facilitate comparisons between models and opportunities for sharing and integration.

    Crops in silico (Cis) envisions a digital representation of layered dynamic sub-models, reaching from gene networks and metabolic pathways through to cellular organization, tissue and organ development, and resource capture in dynamic competitive environments, and allowing a mechanistic simulation of the plant or community of plants in silico.

    The Hackathon

    During this event, we will further lower the barriers to collaborate on model integration within the Crops in silico community. It will consist of short tutorials alternating with practical exercise that will guide participants through model integration using the Crops in silico framework, which enables communication, orchestration, and transformation. Additionally, Cis team member and event organizer Meagan Lang will provide updates about the latest version of yggdrasil, a Python package for integrating computational models across languages and scales.

    Computer programmers, software developers, interface designers, and plant biologists will work side-by-side during this hands-on event. Only basic knowledge of coding and version control will be necessary. We will be offering an optional pre-conference Software Carpentry Workshop on June 3-4 that will help prepare participants for the Hackathon.


    Register today to join us for the Crops in silico Symposium and Hackathon at https://forms.illinois.edu/sec/1232669162. The Cis events are free, but registration is required to receive a link to the virtual meeting.
    Interested in presenting a talk or poster? Please register by April 28 using the link above!.

    Pre-conference Software Carpentry Workshop registration: https://docs.google.com/forms/d/e/1FAIpQLSfSvQOyKnddmEW4hPTQ89XyDEoMGFbyYXGBDYm5pHHIUo_DZQ/viewform


    The Symposium will occur the mornings of June 8-9, and the Hackathon will be the afternoon of June 10. Check back for a full pdf agenda!


    Michael Pound

    Nottingham Research Fellow in Computer Vision, University of Nottingham, UK
    “Data-Hungry Models: Deep Learning of Phenotypes in Crop Plants”

    Abstract: Coming soon!
    Bio: Pound is a computer scientist whose research focuses on the development of novel computer vision techniques. Within the Beacon, he is working with bioscientists to apply these computer vision techniques to plant phenotyping, providing accurate measurement of 2D and 3D shape information of plants. The bioscientists can use this information to explain the underlying mechanisms for how plants grow. Pound has developed tools that allow biologists to measure plant root systems. These have been adopted by researchers all over the world.


    Cyrille Midingoyi

    Montpellier University / French National Institute for Agriculture, Food, and Environment (INRAE)
    “Crop2ML: An Open-Source, Multi-Language Modeling Framework for the Exchange and Reuse of Crop Model Components”

    Abstract: Coming soon!
    Bio: Midingoyi recently defended his doctoral thesis in December 2020. His research interests include CyML programming languages and simulation platforms.

    Andrea Schnepf

    Jülich Institute of Bio- and Goesciences
    “Functional-Structural Plant Modeling with CPlantBox – Local Processes and Emerging Patterns”

    Abstract: Coming soon!
    Bio: Schnepfe researches mathematical modeling, rhizosphere (soil-root interactions), root architecture, arbuscular mycorrhiza, resource acquisition efficiency, and the fate of plant protection products in the soil-root system.

    More speakers and details coming soon!


    Meagan Lang

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

    Steve Long

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

    Amy Marshall-Colón

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

    Traci Quigg Thomas

    Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign

    Matt Turk

    School of Information Sciences and Department of Astronomy, University of Illinois at Urbana-Champaign

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