Transcript The dynamics of isotopes in the standard DEB model

8th AQUAdeb meeting
Bas Kooijman
Dept theoretical biology
Vrije Universiteit Amsterdam
[email protected]
http://www.bio.vu.nl/thb/
Camaret-sur-Mer, 2010/11/30-12/03
Updates DEBlab
http://www.bio.vu.nl/thb/deb/deblab/
DEB3:
comments
concept-summary
notation
errata
micro-lectures
exercises
quizzes
question & answers
Basic Methods in Theoretical Biology
Life cycles in phylogenetic perspective
DEBtool: see “what is new?” in the manual
add_my_pet: manual + LikaFrei2011
pars_my_pet
mydata_my_pet
predict_my_pet
weight, g
Add_my_pet: Phyton_regius
time since birth, d
Growth efficiency
Energy investment ratio
scaled length
scaled length
(
)
scaled age
)
scaled time since birth
abundant food
no growth since birth
no maturation since birth
Graduations 2011 + 2012
2011/??/??
Freitas, Vania
“Predator growth in relation to prey abundance”
2011/??/??
Marques, Gonçalo
“Life Engine”
2011/??/??
Augustine, Starrlight
“Effects of Uranium on zebrafish”
2012/??/??
Saraiva, Sofia
“Mussel eco-energetics”
2012/??/??
Emmery, Antoine
“Isotope dynamics in oyster larvae”
2012/??/??
Carlos Teixeira
“Conservation biology for birds”
Proposals
- Jan Baas: Long Range Research Initiative (LRI)
CEFIC - The European Chemical Industry Council
- Tjalling Jager: NSF-Vidi at VUA
- Bas Kooijman: ERC-AdG (with Lisbon & Marseille)
+ Mike Kearney & Craig White 2011: testing metabolic theories (3 M$, 5 yr)
+ Fred Jean 2011: Pecten Maximus
? Tiago Domingos 2011/01-ITN-call for DEB-training
? future funding for AQUAdeb
PTRS 2010 vol 365 (1557)
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
Tânia Sousa & Tiago Domingos & Jean-Christophe Poggiale & Bas Kooijman Formalised DEB theory
restores coherence in core biology
Susana Vinga & Rute Neves & Helena Santos & Bernd Brandt & Bas Kooijman Subcellular metabolic
organisation in the context of DEB and biochemical systems theories
Ingeborg van Leeuwen & Julio Vera González & Olaf Wolkenhauer Dynamic Energy Budget approaches
for modelling organismal ageing
Laure Pecquerie & Roger Nisbet & Ronan Fablet & Anne Lorrain & Bas Kooijman The impact of
metabolism on stable isotope dynamics: a theoretical framework
Michael Kearney & Steve Simpson & David Raubenheimer & Brian Helmuth Modelling the ecological
niche from functional traits
Virginie Ducrot & Alexandre Péry & Laurent Lagadic Modelling effects of diquat under realistic exposure
patterns in genetically differentiated populations of the gastropod Lymnaea stagnalis
Jean-Christophe Poggiale & Melika Baklouti & Bernard Queguiner & Bas Kooijman How far details are
important in ecosystem modelling: the case of multi-limiting nutrients in phytoplankton - zooplankton
interactions
Antonio Lorena & Gonçalo Marques & Bas Kooijman & Tânia Sousa Stylized facts in microalgal growth interpretation in a DEB context
Odo Diekmann & Hans Metz How to lift a model for individual behaviour to the population level?
Tjalling Jager & Chris Klok Extrapolating toxic effects on individuals to the population level; the role of
Dynamic Energy Budgets
Roger Nisbet & Ed McCauley Dynamic Energy Budget theory and population ecology: lessons from Daphnia
Vânia Freitas & Joana Cardosa & Konstadia Lika & Joana Campos & Myron Peck & Bas Kooijman &
Henk van der Veer Temperature tolerance and energetics, a Dynamic Energy Budget-based comparison of
North Atlantic marine species.
Tineke Troost & Jeroen Wijsman & Sofia Saraiva & Vânia Freitas Modeling shellfish growth with Dynamic
Energy budget models: an application for cockles and mussels in the Oosterschelde (SW Netherlands)
Bob Kooi & Jaap van der Meer Bifurcation theory, adaptive dynamics and DEB-structured populations of
iteroparous species.
http://www.bio.vu.nl/thb/deb/course/PTRS.html
J. Sea Res. 2011
• Alunno-Bruscia, M., Veer, H. van der and Kooijman, S. A. L. M.
The AquaDEB project (phase II): what we’ve learned from applying the DEB theory on aquatic organisms
• Jusup, M., Matsuda, H. and Kooijman, S. A. L. M.
Applicability of Dynamic Energy Budget approach to cultivation of bluefin tuna (Thunnus thynnus)
• Kooijman, S. A. L. M and Kooi, B.W.
DEB-based body mass spectra for planktontic consumers
• Mateus, M., Domingos, T. and Kooijman, S. A. L. M
Can we reach consensus between marine ecological models and metabolic theories in ecology?
A look at primary producers.
• Lika, K. and Kooijman, S. A. L. M.
The topology of energy allocation
• Lika, K., Freitas, V., Veer, H. van der and Kooijman, S. A. L. M.
Marine species diversity as reflected by DEB parameters.
• Kooijman, S. A. L. M., Pecquerie, L., Augustine, S., Jusup, M. and
Understanding growth patterns of fish larvae in the context of the DEB theory.
• Pecquerie, L., Kooijman, S. A. L. M. and Nisbet, R. M.
The variability of salmon life histories in a DEB context.
• Saraiva, S., Sousa, T., Alunno-Bruscia, M., Pouvreau, S., Meer, J. van der and Kooijman, S. A. L. M.
From individuals to ecology in mussel energetics.
Lisbon 2011/04/13-15 auditorium IST
2011/03/30-04/12 (wed-tue) DEB course, 2011/04/16 (sat) discussions
We can recruit speakers from the PTRS/JRS-pool
23 "expressions of interest" at 2010/04/24, never has been that high
= Steering committee:
selection of keynote speakers + scientific and organising committees:
Tiago Domingos, Tania Sousa, Bas Kooijman
= Scientific committee (chaired by Tiago):
selection of speakers on the basis of submitted abstracts:
Tiago Domingos, Tania Sousa, Goncalo Marques, Bas Kooijman,
Marianne Alunno-Bruscia, Jaap vd Meer, Henk vd Veer, Tjalling Jager,
Jean-Christophe Poggiale, Roger Nisbet, Stephane Pouvreau
= Organising committee (chaired by Tania):
logistics
Tiago Domingos, Tania Sousa, Goncalo Marques, Nuno Sarmento, Sonia Barbosa
= Keynote speakers:
Michel Loreau (opening)
Mike Kearney, Jaap vd Meer, Marianne Alunno-Bruscia, Tom Anderson
= Welcome: Tiago Domingos & Tania Sousa; Closure: Bas Kooijman
Texel 2013/04/13-27 NIOZ
Computational Science workshop at the Lorentz Center on DEB
Leiden 2010/04/01-13
1-2 week meetings, 30-60 junior and senior researchers.
Dr. Henriette Jensenius ([email protected], 071-5275580)
http://lorentzcenter.nl/infoorg.php
41 potential candidates (in computational sector):
Morten Alver N
Tom Anderson GB
Pierre Auger F
Starrlight Augustine F
Cedric Bacher F
Melika Baklouti F
Hugo vd Berg GB
Martin Boer NL
Sandrine Charles F
Odo Diekmann NL
Tiago Domingos P
Yoan Eynaud F
Ulrike Feudel D
Ido Filin Fin
Matz Gyllenberg Fin
Tjalling Jager NL
Marco Jusup Jap
Tin Klancjek Kro
Bob Kooi NL
Bas Kooijman NL
Ingeborg van Leeuwen S
Dina Lika G
Goncalo Marques P
Irene Martins P
Jaap vd Meer NL
Hans Metz NL
Erik Muller USA
Roger Nisbet USA
Erik Noonberg USA
Laure Pecquerie USA
Jean-Christophe Poggiale F
Eric Rannou F
Joao Rodrigues P
Andre de Roos NL
Pedro Santos P
Sofia Saraiva P/NL
Tania Sousa P
Tineke Troost NL
Susana Vinga P
Jeroen Wijsman NL
Elke Zimmer NL