Add-my-pet curator workshop III

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13-20 August 2018, in Voorschoten (the Netherlands)


  • Starrlight Augustine
  • Sebastiaan A.L.M. Kooijman
  • Konstadia Lika
  • Nina Marn
  • Mike Kearney
  • Elke Zimmer

Objectives and conclusions

The AmP collection is an important source of energetical and ecological (referenced) data, and implied properties for over 1200 species. We aim to maximize its visibility, usability, and compatibility with other approaches. On this workshop we have discussed the collection, possible extensions and applications, and the supporting code (DEBtool_M and AmPtool). We have briefly discussed the oncoming and potential workshops and symposia, as well as funding possibilities.

The main conclusions are:

  • Technical aspects of the collection:

- We are working on assigning a doi to (zipfiles of) each entry, have improved how an entry is cited, and added the free licence (CC-BY) information in the disclaimer.

  • Creating and curating and entry; using the code :

- The AmP Wiki estimation manual has received a makeover

- New results_output options: -1 : no figures produced, useful for continuations. 3: an html with implied properties and search options (for a name, symbol and similar) is produced

- We revisited and refined the process of entry curation, streamlining the workflow and making the curator functions modular and easier to use. This should minimize the time lapsed between the entry submission and upload to the web. Curation guidelines are published in AmPtool.

- New templates for std, abj and stx typified models are in zip folders in <DEBtool_M\lib\pet>. Notation of the code is improved and now ome is used instead of w, and tau instead of t

- Code for calculating confidence intervals of parameters in DEBtool_M is under development.

  • AmP in context

- We have worked on linking DEBtool_M routines with R and NichMapR. Code for reconstructing experimental temperature from environmental temperatures (in R) is described here. Mike has also shown us how to import AmP parameters into R, see here.

- Aplications menu has been created in the AmP website: Population dynamics, Physical Biology, Ecotoxicity.

- Mike and his student Raph presented their work on the DEB plant model.

We thank Truus and Bas for their hospitality!

Navigate past events:

Event Location Dates
Summer school "Dynamic modelling of toxic effects" Denmark 10-19 Aug 2020 NOTE: due to the COVID-19 situation, the 2020 course has been cancelled. // More information on the course page. Download flyer.
Ecotox (GUTS)focused training courses at SETAC Europe Dublin, Ireland 03-07 May 2020 A course on the openGUTS software by Tjalling Jager and Roman Ashauer - an afternoon's hands-on course for using the software, with very limited attention to the backgrounds of the GUTS model itself. This course is now available for everyone via Leanpub:

TC01 - GUTS Modelling: From the Theory to the Practice (3rd May). A full-day training course organized by Sandrine Charles. Details on the course can be found here. (Practical: R software and MOSAIC web platform)

debX 2020 online 17 Feb-23 Mar 2020 A 5-week course (MOOC) providing a framework for modelling metabolism at the organism level, covering the full life-cycle, using the Dynamic Energy Budget (DEB) Theory. A free online course about DEB theory that has been running for 4 years. This year it will have new French subtitles thanks to the LEMAR group in Brest.
Preditox 2020 - Ecotoxicology and Predictive Modelling Lyon, France 2020/Jan/06-10 (Ecotox) Winter school covering the following topics: Introduction to R software, Dose-response and TKTD modeling, Distribution fitting, Bayesian inference
DEB session/symposium at the ISEM conference Salzburg, Austria 2019/Oct/01-05 Dynamic energy budgets are one of the main topics on the International Society for Ecological Modelling conference. Abstract submission deadline 26th April.
Ecological applications of DEB at the Biomathematics ESMTB Summer School 2019 - Modelling in Marine Ecology Sicily, Italy 2019/Sep/8-21 The school aims to cover several themes on modelling in marine ecology and provide several courses within each theme. Five diverse themes were negotiated, with some of them having as many as five courses. Among modelling strategies, frameworks, and concepts, DEB theory and DEB-based models are presented and applied.
DEB2019: Practical course, Workshop & Symposium Brest, France 2019/Apr: 1-6 & 8-9 & 10-12 DEB School practical course (a continuation of the tele-course, including practical exercises). The course is followed by 2-day DEB workshops, and the 6th international symposium! Application for the school and abstract submission are open (deadline October 20th).
DEB2019: Tele-course Online 2019/Jan 24-Feb 28 10th edition of the DEB tele-course: general theoretical part. Focus is on chapters 1-4 of the DEB-book, which deal with the principles of the theory and (the simplest) univariate DEB models.
Add-my-pet curator workshop III Voorschoten, the Netherlands 2018/ Aug/13-20 Developments in AmP
debX 2018 Online 2018/Feb/19 - Mar/26 A 5-week course (MOOC) providing a framework for modelling metabolism at the organism level, covering the full life-cycle, using the Dynamic Energy Budget (DEB) Theory.
DEB2017: Practical course & 5th International DEB Symposium Tromsø, Norway 2017/ May/21-30; May/31-Jun/02 Continuation of the DEB Tele-course. The focus of the practical course is mastering the skills involved in the interface between the empirical world and mathematics. The course is followed by the symposium covering advances in research and developments of DEB theory in the context of ecosystem based approaches to managing resources. (Akvaplan-niva AS)
debX micro Online 2017/ May/12-25 A framework for modelling metabolism for microorganisms using the Dynamic Energy Budget (DEB) Theory is provided in this course.
9th DEB Tele-course 2017 Online 2017/Mar/02 - Apr/06 The tele-course focuses on chapters 1-4 of the DEB-book, which deals with the principles of the theory and with univariate DEB models. (Akvaplan-niva AS)
Add-my-pet curator workshop II Voorschoten, the Netherlands 2017/ Jan/23-27 Developments in AmP/ DEB course and symposium 2017
MEMS Summer School Brest, France 2016/ Aug/29- Sep/02 "Combining Modeling and Experimental Approaches for Marine organisms under Stress".
TKTD summerschool 'DynModTox' 2016 Holbæk, Denmark 2016/ Aug/09-17 Learning the basics of toxicokinetic and toxicodynamic modelling, how they can be linked and how to analyse and interpret body residue and toxicity data on a mechanistic basis. The course follows the same format as in 2014, but with more freedom in the group projects Impressions
Add-my-pet curator workshop I Voorschoten, the Netherlands 2016/ Jun/25- Jul/02 Developments in add-my-pet/ DEB course 2017
Effective Strategic Renewal workshop Copenhagen Business School, Copenhagen Denmark 2016/Jun/22 Study of applicability of DEB theory in Economics
Eco(toxi)cology tool for produced water workshop Statoil, Trondheim, Norway 2016/ Mar/03-04 Improving risk assessment for produced water in the Bering Sea using DEB theory
Multispecies parameter estimation workshop LEMAR, Brest, France 2015/ Sep/07-08 Introduction to multispecies DEB parameter estimation
DEB2015 course and Symposium Online and Marseille, France 2015/ Feb/19-Mar/26, Apr/20-30 8th DEB Tele-course (19 Feb - 26 Mar): general theoretical part (5 weeks part-time) in tele-mode (at your working place) Participants.; practical training part (20 Apr - 27 Apr): 7 days in class-room mode in the CIRM (Centre for International Meetings in Mathematics) in campus Luminy, Marseille (France); 4th Symposium on DEB theory (28 Apr - 30 Apr): at campus Luminy, Marseille (France) DEB 2015 is organised conjointly by the CIRM, the Mediterranean Institute of Oceanography (MIO) and the Institute Pytheas (OSU). These are components of Aix-Marseille University (AMU).
TKTD summerschool 'DynModTox' 2014 Roskilde, Denmark 2016/ Aug/05-13 Focus on (basic) toxicokinetics and toxicodynamic modelling (sub-lethal effects) using DEB theory in the form of the simplified DEBkiss model. Use of OpenModel next to Matlab. Impressions.
DEB2013 course and Symposium Online and Texel, Netherlands 2013/ Feb-Mar, Apr/15-26 7th DEB Tele-course (Feb - Mar): general theoretical part in tele-mode Participants; practical training part (15 Apr - 23 Apr): in class-room mode in the Royal Netherlands Institute for Sea Research (NIOZ), Texel (Netherlands). Program. Most participants.; 3rd Symposium on DEB theory (24 Apr - 26 Apr): at NIOZ on Texel, Netherlands.
TKTD summerschool 'DynModTox' 2012 Holbæk, Denmark 2012/ Aug/11-18 Learning the basics of toxicokinetic and toxicodynamic modelling, how they can be linked and how to analyse and interpret body residue and toxicity data on a mechanistic basis. TKTD modelling in general, and GUTS and DEBtox in particular. Impressions
DEB2011 course and Symposium Online and Lisbon, Portugal 2011/ Feb-Mar, Apr/04-15 6th DEB Tele-course (Feb - Mar): general theoretical part in tele-mode. Participants.; practical training part (04 Apr - 12 Apr): in class-room mode at the Instituto Superior Técnico (Técnico Lisboa), Lisbon (Portugal).Most participants.; 2nd Symposium on DEB theory (13 - 15 Apr) at Técnico Lisboa in Lisbon.
DEB2009 course and 1st Symposium Online and Brest, France 2009/ Feb-Mar & Sep-Oct, Apr 5th DEB Tele-course in tele-mode: 12 Feb-19 Mar (5 weeks), plenary introductory program about chap 1-5 of the DEB book, and 17 Sep - 22 Oct (again 5 weeks), advanced parallel program with selected topics related to the various symposium sessions. Practical training part (19 and 23 Apr): course and discussion day in Brest, France; 1st Symposium on DEB theory (19 - 22 Apr) DEB Theory: 30 years of research for metabolic organization.
Previous DEB courses Online 2001-2007 On-line courses on DEB theory were held bi-annualy. You can view some information about the participants of the previous DEB courses here.