3rd Annual Crops in silico Symposium & Hackathon
Software Carpentry Workshop: July 31
Symposium and Workshop: July 31 – August 2
Hackathon: August 2 – 3
Select Presentations for Download
About the Symposium, Workshop & Hackathon
Symposium and Workshop: Coordinating Cis research, training and education
The Symposium will explore advancements in plant modeling while highlighting what can be gained from tools and lessons learned from computer scientists. The goal of the Symposium is to establish steps toward coordinating research, training and educational activities
Hackathon: Lowering the barriers to model integration
The Hackathon will consist of short tutorials alternating with practical exercise that will guide participants through model integration using a prototype framework that enables communication, orchestration, and transformation. Computer programmers, software developers, interface designers and plant biologists will work side-by-side during this one day hands-on event. Only basic knowledge of coding and version control will be necessary. To get the most out of the Hackathon, we encourage you to attend the Software Carpentry workshop, which will cover basic research computing skills using Python and Git.
Software Carpentry Workshop: Example-driven tutorial on basic computing skills
Computing is an integral part of plant modelling, but most scientists are never taught how to build, use, validate, and share software well. As a result, many spend hours or days doing things badly that could be done well in just a few minutes. The goal of Software Carpentry is to change that so that scientists can spend less time wrestling with software and more time doing useful research. To ensure that researchers get the most out of the Hackathon, they are encouraged to attend the Software Carpentry Workshop.
Tuesday, July 31 8:00am-5:00pm
Software Carpentry workshop
Tuesday, July 31 5:00pm-7:00pm
Keynote Talk: Building a crystal ball for predicting crop production: marrying remote sensing, machine learning, and crop modeling – Kaiyu Guan, Department of Natural Resources and Environmental Sciences, University of Illinois
Wednesday, August 1 8:30am-5:00pm
Welcome and introduction
Session 1: Successful model integration
Multi-scale modeling and visualization platform for crop – Yu Wang, University of Illinois
A cross-scale modelling approach connecting photosynthesis with crop models to support crop improvement – Alex Wu, University of Queensland
Prospects of constraint-based modelling in whole-plant models – Sanu Shameer, University of Oxford
Lighting talks, round 1
Session 2: Advancements in plant modeling
Dynamic modeling of the iron deficiency modulated transcriptome response in Arabidopsis thaliana root – Alexandr Koryachko, North Carolina State University
Charting Plant Metabolism by Quantitative Analysis on Multiple Levels – Jorg Schwender, Brookhaven National Laboratory
Multi-disciplinary approaches to understanding growth in Arabidopsis – Siobhan Braybrook, UCLA
Workshop:Forming research collaborations
Thursday, August 2 8:30am-5:00pm
Session 3: Data for calibration and validation
Field-scale weed emergence simulations for training autonomous mechanical weeding robots – Girish Chowdhary, University of Illinois
Multi-scale mechanical modeling of leaf epidermal morphogenesis – Jing Li, Purdue University
Examining organ development using image analysis and multicellular modelling – John Fozard, John Innes Centre
Lighting talks, round 2
Increasing the yield of research through openness – Carly Strasser, Fred Hutchinson Cancer Research Center
Workshop: Developing a NSF Research Coordination Network to advance Crops in silico research
Session 4: Outreach and education: visualization and tools
Managed data and metadata for training, sharing and using models at scale – Nirav Merchant, University of Arizona and CyVerse
OpenAlea : an open source project for plant modelling at different scales. – Christophe Pradal, CIRAD/Inria
Connecting the dots between computational tools to analyse soil-root water relations – Guillaume Lobet, Forschungszentrum Juelich and the Université catholique de Louvain
Thursday, August 2 6:30pm-9:00pm
Friday, August 3 8:30am-5:00pm
Assistant Professor, Department of Natural Resources and Environmental Sciences, University of Illinois
Dr. Guan provides solutions for real-life problems, such as large-scale crop monitoring and forecasting, water management and sustainability, and global food security. He uses satellite data, computational models, field work, and machine learning approaches to address how climate and human practices affect crop productivity, water resource availability, and ecosystem functioning.
Assistant Professor of Molecular, Cell and Developmental Biology, UCLA
The Braybrook Group at UCLA studies the generation of form in walled organisms: plants and algae. Her research has two main goals: 1) to understand the mechanics of shape growth in plants and algae, and 2) to understand the cell wall as a dynamic composite material.
Assistant Professo, Forschungszentrum Jülich (IBG3, Agrosphere) and the Université catholique de Louvain (Earth and Life Institute)
The aim of Guillaume’s research is (i) to understand how various signals that carry information are interacting and being conveyed and integrated at the plant level and (ii) to amplify discrete physiological knowledge into functional plant processes. All of that using Functional Structural Plant Models.
Director, UA Data Science Institute (Data7) Co-PI, CyVerse Image Informatics (Interim), University of Arizona
Nirav’s research focuses on developing scalable platforms for supporting open science and open innovation, with emphasis on improving research productivity for geographically distributed interdisciplinary teams. His interests include large-scale data management platforms, data delivery technologies, managed sensor and mobile platforms for health interventions, workforce development, and project based learning.
Researcher in Plant Modelling and Computer Science, UMR AGAP, Univiversité de Montpellier, CIRAD, INRA, Inria
Christophe has developed software for plant modelling including OpenALEA, a scalable, modular and open software platform for plant modeling and simulation and V-Plants, the software components of Virtual Plants. He also specializes in geometrical and topological modeling for plant representation and scientific workflow and software engineering.
Principal Investigator, Biology, Brookhaven National Laboratory
The Schwender group is interested in increasing the basic understanding of control and regulation of plant central metabolism, with focus on heterotrophic sink tissues like seeds. They use isotope labeling experiments, mathematical models and computer simulation to describe and analyze metabolism quantitatively.
Post-doctoral Research Assistant, Department of Plant Sciences, University of Oxford
Sanu’s research aims to develop a better understanding of the behavior of the metabolic systems of plants in order to devise metabolic engineering strategies that will improve the productivity and quality of crop plants. He uses both computational and experimental approaches to achieve this.
Director of Academic Alliances and Data Strategy, Fred Hutchinson Cancer Research Center
Carly Strasser specializes in creating new opportunities for and promoting collaborative research.
Postdoctoral Research Associate, University of Illinois
Yu Wang is a postdoctoral researcher at the University of Illinois. Her research focuses on the metabolic modeling of the photosynthetic process in plants.
Research Officer, Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation
Alex conducts research on the physiology and genetics of complex adaptive traits in field crops. He developed the Diurnal Canopy Photosynthesis Simulator (DCaPS) online application, which calculates diurnal canopy CO2 assimilation and daily biomass increment for a crop under well-watered conditions.
Registration for the Symposium and Workshop is free and includes lunch thanks to generous support from the Institute for Sustainability, Energy, and Environment at the Universe of Illinois. You must register by May 31 to be considered for a presentation.
Registration for the Software Carpentry workshop is separate. The $25 fee for this workshop includes lunch.
receive funding to attend
The Crops in silico organizers are committed to increasing diversity at the Symposium and Workshop and have therefore set aside funds to support the participation of eligible underrepresented minority students, faculty and scientists.
Click here for more information and to fill out the application. Applicants are encouraged to apply for funding early. Support is limited and available at the organizer’s discretion. The funding application period is now over.
about the software CARPENTRY workshop
This supplementary workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Trained Software Carpentry instructors will present short tutorials alternated with hands-on practical exercise. Participants are encouraged both to help one another, and to try applying what they have learned to their own research problems during and between sessions. Everyone is welcome, and this will be especially useful to interns, graduate students, postdocs, and researchers who have not begun to leverage the power of scripting and version control for reproducible research.
This event is hosted by Computational Science and Engineering at the University of Illinois and has a $25 registration fee that includes lunch. Click this link for additional information and register. This workshop is open to the public – participants do not need to attend the Crops in silico Symposium to join this workshop.
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.
Early career participants (Grad Students and Postdocs) are encouraged to present their research during the program in either the full presentation (15 min + question time) or a lightning talk (5 min total). Note that in case of more interest than time available we will make a selection based on variety of topic and fit with the overall program. You must register by May 31 to be considered for a presentation.
Attendees must arrange their own lodging. There is a block of rooms at the Hampton Inn under “Crops in Silico.” There are many other places to stay in the Champaign-Urbana area. However, you will need to secure your own transportation to and from the meeting.
Departments of Plant Biology and Crop Sciences, University of Illinois
Department of Plant Biology, University of Illinois
School of Information Sciences and Department of Astronomy, University of Illinois