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Software / Links to other software

Miscellaneous software


On this page, I will collect links to freely-available software packages provided by other parties to perform calculations on GUTS and DEB(tox). I have not been involved in the production of these packages, so I cannot provide any assistance or support for them. I am responsible for the Matlab implementations of GUTS, DEBtox and DEBkiss as part of the BYOM and DEBtoxM series. Several more implementations for GUTS are known to exist, of which a number is planned to be offered for free download by their developers in the near future. When more information is available I will update the list below.

R-packages for GUTS


Two R-packages are available to make the GUTS calculations in a Bayesian framework. The first package was developed by Carlo Albert & Sören Vogel, is currently maintained by RIFCON, and can be found at https://cran.r-project.org/package=GUTS. A user interface for this package is currently being developed by RIFCON under the name EasyGUTS (see this SETAC poster). This version is planned to be available for free download by the end of 2017. This version can do the reduced GUTS models (also SD and IT combined).

The second is the MORSE R-package, as developed and maintained by the University of Lyon. It contains the reduced SD and IT models. This package can be found at https://cran.r-project.org/package=morse. A web-based user interface is under development and will be available in the near future at http://pbil.univ-lyon1.fr/software/mosaic/survival/.

Python-package for GUTS


A Python toolbox is available for GUTS calculations. The toolbox is developed and maintained by Raymond Nepstad (SINTEF, Trondheim), and can be downloaded from GitHub: https://github.com/nepstad/epytox 

DEB-IBM in NETlogo


The individual-based modelling implementation of DEB in NetLogo of Martin et al. (2012) can be found CREAM website or on Ben Martin's personal pages. This is a flexible model for population dynamics using DEB individuals, and quite user friendly. The associated publication is:

Martin B, Zimmer EI, Grimm V and Jager T (2012). Dynamic Energy Budget theory meets individual-based modelling: a generic and accessible implementation. Methods in Ecology and Evolution 3:445-449. http://dx.doi.org/10.1111/j.2041-210X.2011.00168.x

DEBtool in Matlab and Octave


Bas Kooijman has developed an extensive library of code in Matlab and freeware Octave (not updated anymore!) to perform all sorts of DEB calculations. DEBtool can be found at the VU DEB laboratory or via the DEB portal. The correct use of this software requires a sturdy background knowledge of DEB theory, and user-friendliness is limited. The DEBtool software is used in the DEB course, so the course is the best place to get started with it.






The DEBtox information site, www.debtox.info, since July 2011