|
Agrocampus
Ouest, Centre d'Angers Dépt.
STPH UMR1345
Institut de Recherche en Horticulture et Semences (IRHS), Equipe
Arboriculture Fruitičre |
|
University of Göttingen Chair
for Computer Graphics and Ecological Informatics Büsgenweg
4, 37077 Göttingen, Germany http://www.uni-goettingen.de/en/67072.html |
Final Programme:
Tutorial and Workshop
"Functional-Structural
Plant Modelling with GroIMP and XL"
combined with
the 7th GroIMP user and developer meeting
co-funded by
Date: 5 – 7 May 2015
(Start
and Introduction: 5 May, 15:00; Workshop: 5 May, 15:00-18:30, and
6
May, 08:30-09:00, Tutorial: from 6 May, 09:00, until 7 May, 12:00)
Location: Agrocampus Ouest, Centre d'Angers
2,
rue André le Nôtre, Angers, France
Announcement:
This event is
open for all who want to learn how to work with the software tool GroIMP – Growth-grammar
based Interactive Modelling Platform – and to write models in the rule-based
programming language XL (see www.grogra.de). Particularly, it is open for M.Sc. and
Ph.D. students in Applied Computer Science, Botany, Agriculture, Horticulture
or Forest Science with focus on information processing and modelling, and also
for interested guests from other disciplines.
The
accompanying workshop will provide a forum to present some results for those who
have already made some experiences in XL.
The
GroIMP user and developer meeting, which will be integrated in the workshop,
will provide an opportunity for exchange concerning the future development of
the language XL and the software GroIMP.
The
language will be English. No congress fee is required.
Please send your request for registration to gerhard.buck-sorlin (at) agrocampus-ouest.fr. Do not
forget to indicate if you want to participate in the workshop, in the tutorial,
or in the whole event.
Programme:
5
May (Lecture theatre C "Rosalind Elsie Franklin") - Workshop
-
15:00 Introduction to the
Workshop (Gerhard Buck-Sorlin and Winfried Kurth) [pdf]
15:25 Brief introductory round of every workshop participant
15:35 Junqi
Zhu: Process-based grape model for simulation of berry development and
composition in response to climate change
16:05 Emna
Bairam: Modeling carbon transport within the carrier branch of apple
16:35 Franca J.
Bongers: Game theoretical analysis of phenotypic plasticity: a case study
of shade avoidance responses in Arabidopsis thaliana
17:05 Coffee break
17:35 Jorad de
Vries: Modelling plant plasticity; disentangling complex and dynamic interactions
one step at a time
18:05 Ningyi
Zhang: Optimizing ornamental crop production using functional-structural plant
modelling: the case for lily
18:20 Martin
Sikma: Functional-structural plant models for climate change studies:
quantifying feedbacks between rice architecture, physiology, and microclimate
18:35 END of the
workshop programme of the day
19:30 – 22:00: Workshop dinner (Restaurant Palais de
Kashmir, 11 pl. Mendes France)
6
May (room B201)
Workshop
(contd.)
08:30 – 9:00: Lifeng Xu: Simulating genotype-phenotype
interactions using FSPMs with GroIMP (via Skype)
Tutorials
(6 & 7 May)
6 May, 9 – 12:30, 14:00 – 17:00 (parallel)
|
Beginners (room B201) |
Advanced (room B202) |
|
9:00 – 10:00:
Winfried Kurth: Introduction
to rule-based programming, L-systems and the programming language XL [pdf] 10:00 – 10:30: (Team
session 1) Simple branched structures modelled with XL |
9:00 – 10:00:
Gerhard Buck-Sorlin: Modelling physiological processes with GroIMP 10:00 – 10:30: Special modelling questions (on user
demand) |
10:30
– 11:00: Coffee break
|
11:00 – 12:00:
Winfried Kurth: Programming
in XL [pdf] 12:00 – 12:30: (Team
session 2) Using interpretive and instantiation rules |
11:00 – 12:30: Jorad
de Vries: About
the use of queries in GroIMP |
12:30
– 14:00: Lunch break
|
14:00 – 14:45: Gerhard
Buck-Sorlin: How to model a daisy in 45 minutes 14:45 – 15:00: (Team
session 3) Improving the daisy model 15:00 – 16:00:
Winfried Kurth: Programming
in XL (continued) [pdf] |
14:00 – 15:00:
Michael Henke: Advanced
light modelling with GroIMP 15:00 – 15:30:
Michael Henke: GroIMP 1.5 – A
closer look at the new features 15:30 – 16:00: Case
studies of advanced users I (Q & A session) |
16:00
– 16:30: Coffee break
|
16:30 – 17:00:
Winfried Kurth: Programming in XL (continued; link see above) |
16:30 – 17:00: Case
studies of advanced users II (Q & A session) |
GroIMP
User and Developer meeting (room B201)
17:00 – 17:30: Users'
questions and suggestions for improvement
7
May, 9 – 12:00 (room B201):
9:00 – 10:30: Winfried
Kurth: How to develop
a simple FSPM with GroIMP [pdf]
10:30
– 10:45: Coffee break
10:45 – 11:15: Solving ordinary
differential equations in XL [pdf]
11:15 – 11:45: Modelling multiscale
structures in XL [pdf]
11:45 – 12:00: Questions and answers, final
discussion.
Further
links:
Dissertation Reinhard
Hemmerling
Publications of the
Plant Modelling group, Göttingen
Venue
The
workshop and tutorial will take place at Agrocampus Ouest, the national institute
of Horticulture, located in Angers, a city of art and history renowned for its
quality of life, historic capital of Anjou, gateway to the Loire Valley, and
listed as a UNESCO World Heritage Site since 2000.
Agrocampus
Ouest Angers is situated at Belle-Beille, a northwestern quarter of Angers. You
can reach it by taking the bus no. 1 to “Belle Beille Université” or
“Beaucouzé”, and get off at the terminal stop “Angers - Maison de Technopole
Belle Beille”. More information on public transport can be found here: http://bustram.irigo.fr/pages/index.php?page=calcul
You
can find further practical information here:
Angers
city council:
www.angers.fr
Angers
tourist information centre: www.angers-tourisme.com
Angers Urban Community: www.angersloiremetropole.fr
Location: Agrocampus
Ouest
Location of the restaurant "Palais de
Kashmir" for Tuesday evening:
Abstracts of Workshop Contributions
Junqi Zhu1
Joint Research
Unit 1287 EGFV (Ecophysiology and Functional Genomics of Vine), National
Institute of Research in Agronomy (INRA), Bordeaux, France
Climate change will affect various aspects of the wine
industry and consequently challenge the sustainability of grape production.
However, little work has been done on quantifying the response of berry
composition to climate change. Process-based models may fill this gap by
integrating berry development and quality formation with whole plant status and
environmental factors. This ongoing research project provides a novel approach
for incorporating whole plant development and berry development via xylem water
potential and phloem carbon concentration.
Franca J. Bongers1,2, Ronald Pierik2, Jochem B.
Evers1 and Niels P.R. Anten1
1Centre
for Crop Systems Analysis, Plant Sciences Group, Wageningen University, The
Netherlands
2Plant
Ecophysiology, Department of Biology, Utrecht University, The Netherlands
The shade avoidance syndrome (SAS) is one of the best-studied forms of
plant phenotypic plasticity, and several studies have showed that SAS increases
performance when competing for light with plants that do not show SAS. However,
it is unknown how natural selection could have acted on these plastic traits.
With a virtual plant model of Arabidopsis
thaliana we study the effect of specifically the petiole shade avoidance
responses on the performance of plants competing for light. The plant is
composed of small organ parts (e.g. petiole and the tip or base of the lamina),
resulting in all parts being able to perceive signals and respond independently
of each other. By also separating the responses in separate factors we can
study the responses in detail, and thus get a better understanding of how
phenotypic plasticity as traits could have evolved in time.
Optimizing ornamental crop production using
functional-structural plant modelling: the case for lily
Ningyi Zhang1,2,3,
Jochem B. Evers2, Leo M.F. Marcelis1, Niels P.R. Anten2,
Weihong Luo3
1Horticulture and Product Physiology, Plant Sciences
Group, Wageningen University, The Netherlands
2Centre for Crop System Analysis, Plant Sciences Group,
Wageningen University, The Netherlands
3College of Agriculture, Nanjing Agricultural
University, China
Unlike food
crops and vegetables in which biomass production is the main interest, in
ornamental crops morphological traits are also very relevant for economic
benefit. Although descriptive models have been developed for ornamental crops
to predict morphological traits such as plant height, number of leaves and
flower size, there is a demand in predicting morphological traits that are
relevant for ornamental quality, through more mechanistic methods for better
understanding the physiological control of plant morphology and optimizing
ornamental crop production. Functional-structural plant models (FSPM) simulate
plant structural development as governed by physiological processes and include
visual 3D output of plant phenotype. Lily was chosen for this case study due to
its importance in ornamental crop market. A lily FSPM will be developed and
used to optimize production in terms of morphological traits in relation to
light management and plant density.
Martin Sikma1,2,
Bert. G. Heusinkveld2, Albert A.M.Holtslag2, Toshihiro
Hasegawa3, Mayumi Yoshimoto3, Michaël Chelle4,
Xinyou Yin1, Niels P.R. Anten1, Jochem B. Evers1
1Centre for Crop Systems Analysis, Wageningen
University, Wageningen, the Netherlands
2Meteorology and Air Quality Group, Wageningen
University, Wageningen, the Netherlands
3National Institute for Agro-Environmental Sciences,
Tsukuba, 305-8604 Japan
4INRA, UMR1402 Ecosys, F-78850, Thiverval-Grignon,
France
Climate change
will modify the interactions between microclimate and plant architecture and
physiology by changes in local temperature, CO2 concentration and
light. As these interactions strongly influence crop yield, understanding these
modifications and deciphering the involved key mechanisms are an important
issue in the context of food security. To reach this goal, we aim to develop a
hybrid FSP-SVAT model that could be used to investigate crop responses to such
changes. Data for model calibration will be collected in a FACE experiment near
Tsukuba, Japan.
Modelling plant plasticity; disentangling complex and
dynamic interactions one step at a time
Jorad
de Vries1,2, Jacob C. Douma1, Liesje
Mommer3, Marcel Dicke2, Niels P.R. Anten1
,Erik H. Poelman2, Jochem B. Evers1
1Centre for Crop Systems Analysis, Wageningen
University, Wageningen, the Netherlands
2Laboratory of Entomology, Wageningen University,
Wageningen, the Netherlands
3Nature Conservation and Plant Ecology, Wageningen
University, Wageningen, the Netherlands
Plants grow up
competing over resources in ever changing environments, being able to react to
both competing neighbours and other environmental changes is vital to their
survival. The growth-defence trade-off is one example of a dynamic system in
which plant responses to light competition and insect herbivory interact on a
four dimensional scale. Another example is plasticity in root architecture in
response to neighbours or nutrient levels and distributions, the mechanisms
driving root plasticity are still a mystery. Both these systems offer a range
of opportunities for three dimensional plant modelling.
Modeling carbon
transport within the carrier branch of apple
Bairam E., Delaire M., le-Morvan C, and
Buck-Sorlin G.H.
UMR 1345 Institut
de Recherche en Horticulture et Semences (IRHS), Agrocampus Ouest, Angers,
France
In the apple
branch, assimilates are carried from the sugar synthetizing organs (sources) to
other developing or storage organs (sinks). A sugar transport model for the
carrier branch of apple was conceived and built as a Functional-Structural
Plant Model using the GroIMP modeling platform. This model was based on water
and sugar fluxes in the phloem and the xylem. In this presentation we will
discuss how the model could be further parameterized to adjust it using data of
observed growth kinetics of apple tree organs.