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Concepts and tools for collaborative weed demographic modeling. Niels Holst Århus University Denmark. (c) 2009 Niels.Holst@agrsci.dk. Acknowledgments. European Network for the Durable Exploitation 0f Crop Protection Strategies (ENDURE)

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concepts and tools for collaborative weed demographic modeling

Concepts and toolsfor collaborative weed demographic modeling

Niels Holst

Århus University

Denmark

(c) 2009 Niels.Holst@agrsci.dk

acknowledgments
Acknowledgments
  • European Network for the Durable Exploitation 0f Crop Protection Strategies (ENDURE)
  • International Centre for Research in Organic Food Systems (ICROFS)

(c) 2009 Niels.Holst@agrsci.dk

weed modeling why
Weed modeling: Why?
  • Proximate
    • fun
    • profitable
  • Ultimate
    • science (research, education)
    • technology (tactics, strategy, policy)

(c) 2009 Niels.Holst@agrsci.dk

models are thinking tools
Models are thinking tools

Models help us formulate notions about the dynamics of the different species that an ecosystem comprises.

AP Gutierrez 1996

(c) 2009 Niels.Holst@agrsci.dk

modeling for weed science
Modeling for weed science
  • Research
    • integration
    • analysis
    • idea generation
  • Education
    • theory
    • practice

(c) 2009 Niels.Holst@agrsci.dk

models make you think
Models make you think

The purpose of models is not to fit data but to sharpen the questions.

S Karlin

(c) 2009 Niels.Holst@agrsci.dk

a diversity of models
A diversity of models
  • 134 scientific papers
  • 60 weed species
  • 40 crops

Holst et al. (2007). Weed Research 47: 1-14.

(c) 2009 Niels.Holst@agrsci.dk

modeling life cycle
Modeling life cycle
  • Formulate
  • Implement
  • Test
  • Publish

(c) 2009 Niels.Holst@agrsci.dk

weedml components
WeedML components

annualweed

(c) 2009 Niels.Holst@agrsci.dk

weedml components1
WeedML components

GALAP

SETVI

STEME

(c) 2009 Niels.Holst@agrsci.dk

weedml components2
WeedML components

GALAP

SETVI

STEME

crop

(c) 2009 Niels.Holst@agrsci.dk

weedml components3
WeedML components

GALAP

SETVI

STEME

maize

winter wheat

(c) 2009 Niels.Holst@agrsci.dk

weedml components4
WeedML components

GALAP

SETVI

STEME

maize

maize

winter wheat

(c) 2009 Niels.Holst@agrsci.dk

weedml components5
WeedML components

GALAP

SETVI

STEME

maize

maize

winter wheat

competition

(c) 2009 Niels.Holst@agrsci.dk

weedml components6
WeedML components

GALAP

SETVI

STEME

maize

maize

winter wheat

hyperbolic

INTERCOM

(c) 2009 Niels.Holst@agrsci.dk

weedml ancestry
WeedML ancestry

WeedML

WeedMarkup Language

SBML

Systems Biology Markup Language

XML

eXtensible Markup Language

(c) 2009 Niels.Holst@agrsci.dk

slide17
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide18
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide19
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide20
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

/

(c) 2009 Niels.Holst@agrsci.dk

slide21
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide22
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide23
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide24
<weedml version=“1.0”>

+ . . .

<model class=“weather::log_file”>

<parameter name=“file” value=“paris01.txt“ />

<parameter name=“date” col=“1“ />

<parameter name=“temperature” col=“2” />

<parameter name=“irradiation” col=“4” />

</model>

+ ...

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide25
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide26
<weedml version=“1.0”>

+ . . .

<model class=“crop” name=“winter_wheat”

from=“doc(www.weedml.org/models/simple-winter-wheat.xml)” />

+ . . .

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide27
<weedml version=“1.0”>

+ <model class=“annual_weed” name=“galap”>

+ <model class=“crop” name=“winter_wheat”>

+ <model class=“competition::hyperbolic”>

+ <model class=“weather::log_file”>

+ <output class=“xy_plot”>

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

slide28
<weedml version=“1.0”>

<model class=“annual_weed” name=“galap”>

+ <model class=“stage” name=“seed”>

+ <model class=“stage” name=“juvenile”>

<model class=“stage” name=“flowering”>

+ <model class=“reproduction”>

+ . . .

</model

</model>

+ . . .

</weedml>

(c) 2009 Niels.Holst@agrsci.dk

weedml architecture
WeedML architecture

Base library

Engine library

Plug-ins

Applications

WeedML

Output

(c) 2009 Niels.Holst@agrsci.dk

weedml architecture1
WeedML architecture

Base library

Engine library

Plug-ins

Applications

WeedML

Output

(c) 2009 Niels.Holst@agrsci.dk

weedml architecture2
WeedML architecture

Base library

Engine library

Plug-ins

Applications

WeedML

Output

(c) 2009 Niels.Holst@agrsci.dk

weedml architecture3
WeedML architecture

Base library

Engine library

Plug-ins

Applications

WeedML

Output

(c) 2009 Niels.Holst@agrsci.dk

weedml organisation
WeedML organisation
  • www.weedml.org
    • applications
    • plug-ins
    • models
    • annual meetings
  • weedml.sourceforge.net
    • source code

(c) 2009 Niels.Holst@agrsci.dk