Bas KooijmanDept theoretical biology

Vrije Universiteit AmsterdamBas@bio.vu.nl

http://www.bio.vu.nl/thb/

8th AQUAdeb meeting

Camaret-sur-Mer, 2010/11/30-12/03

Updates DEBlab

DEB3: comments concept-summary notation errata micro-lectures exercises quizzes question & answers

Basic Methods in Theoretical Biology

Life cycles in phylogenetic perspective

http://www.bio.vu.nl/thb/deb/deblab/

DEBtool: see “what is new?” in the manual

add_my_pet: manual + LikaFrei2011 pars_my_pet mydata_my_pet predict_my_pet

Add_my_pet: Phyton_regiusw

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time since birth, d

Growth efficiency

Energy investment ratio

scaled agescaled time since birth

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abundant foodno growth since birthno maturation since birth

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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. Tânia Sousa & Tiago Domingos & Jean-Christophe Poggiale & Bas Kooijman Formalised DEB theory

restores coherence in core biology 2. Susana Vinga & Rute Neves & Helena Santos & Bernd Brandt & Bas Kooijman Subcellular metabolic

organisation in the context of DEB and biochemical systems theories3. Ingeborg van Leeuwen & Julio Vera González & Olaf Wolkenhauer Dynamic Energy Budget approaches

for modelling organismal ageing4. Laure Pecquerie & Roger Nisbet & Ronan Fablet & Anne Lorrain & Bas Kooijman The impact of

metabolism on stable isotope dynamics: a theoretical framework5. Michael Kearney & Steve Simpson & David Raubenheimer & Brian Helmuth Modelling the ecological

niche from functional traits 6. Virginie Ducrot & Alexandre Péry & Laurent Lagadic Modelling effects of diquat under realistic exposure

patterns in genetically differentiated populations of the gastropod Lymnaea stagnalis 7. 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

8. Antonio Lorena & Gonçalo Marques & Bas Kooijman & Tânia Sousa Stylized facts in microalgal growth - interpretation in a DEB context

9. Odo Diekmann & Hans Metz How to lift a model for individual behaviour to the population level?10. Tjalling Jager & Chris Klok Extrapolating toxic effects on individuals to the population level; the role of

Dynamic Energy Budgets11. Roger Nisbet & Ed McCauley Dynamic Energy Budget theory and population ecology: lessons from Daphnia12. 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.

13. 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)

14. 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 IST2011/03/30-04/12 (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 NIOZComputational 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 (jensenius@lorentzcenter.nl, 071-5275580) http://lorentzcenter.nl/infoorg.php 41 potential candidates (in computational sector): Ingeborg van Leeuwen S

Dina Lika GGoncalo Marques PIrene Martins PJaap vd Meer NLHans Metz NLErik Muller USARoger Nisbet USAErik Noonberg USALaure Pecquerie USAJean-Christophe Poggiale FEric Rannou FJoao Rodrigues PAndre de Roos NLPedro Santos PSofia Saraiva P/NLTania Sousa PTineke Troost NLSusana Vinga PJeroen Wijsman NLElke Zimmer NL

Morten Alver NTom Anderson GBPierre Auger FStarrlight Augustine FCedric Bacher FMelika Baklouti FHugo vd Berg GBMartin Boer NLSandrine Charles FOdo Diekmann NLTiago Domingos PYoan Eynaud FUlrike Feudel DIdo Filin FinMatz Gyllenberg FinTjalling Jager NLMarco Jusup JapTin Klancjek KroBob Kooi NLBas Kooijman NL