DEBtox information
Making sense of ecotoxicity test results



Main menu


Submenu

DEBtox information

DEBtox information

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 (the BYOM version is much more up to date!). 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.

Web-based GUTS calculations


A web-based and user-friendly way to perform GUTS calculations (reduced SD and IT models only) is available at http://pbil.univ-lyon1.fr/software/mosaic/guts/. See also the paper of Baudrot et al. Under the hood, it applies Bayesian inference with the MORSE R-package. This is a very elegant implementation, but the user needs to realise that the software applies weakly informative prior distributions (i.e., the output is more than just the information from the model fit). The priors are based on test design, which I believe is awkward (see my comment in ES&T and the author's response to that). In general, these priors will not affect the results. However, in more extreme cases (when a parameter runs away to zero or infinity, e.g., 'slow kinetics'), they will influence the results (to some extent). In the current version, these cases are flagged with a warning, so the user is aware that the priors are affecting the results.

This touches upon a general issue for Bayesian inference (and MCMC) when the posterior is insufficiently constrained by the data (and becomes 'improper'). For more information I suggest the excellent and readable paper from Raue et al. (2013). At this moment, it is unclear to me how other Bayesian GUTS applications address this issue.

Standalone GUTS software


In June 2018, the Fraunhofer Institute has launched the first version of their standalone GUTS-3S. More information. A test version of this software was included in the ring test (which is part of the GUTS e-book). I have not looked at this version yet, so I cannot provide you with my opinion just yet.

A user interface for the GUTS-R (see below) package is currently being developed by RIFCON, turning it into a standalone software under the name EasyGUTS (see this SETAC poster, and this SETAC poster). This version is planned to become available for free download, but is not available yet. This version can do the reduced GUTS models (also SD and IT combined).

We will be preparing a GUTS standalone software, which is planned to become available by the end of 2019. More information.

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. I am not sure if and how they deal with the issue of 'improper posteriors' noted above for the web-based MOSAIC software.

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. There is a web-based interface around it as well (see previous item above).

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