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
(apart from openGUTS), 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
platform. 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 data set). 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 specific 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 December 2019, the first
version of the openGUTS standalone software was released.
This is an easy-to-use and robust software that runs under
Windows. It can be freely downloaded from the dedicated
There is also a Matlab version of openGUTS, available from
the same website.
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 (presented in
SETAC posters in 2017 and 2018). This version is planned to
become available for free download, but is not available yet
(only on request). This version should be able to do the
reduced GUTS models (also SD and IT combined). Mentioned on
the Rifcon downloads
site under 'download software'.
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
I am not sure if and how they deal with the issue of
'improper posteriors' noted above for the web-based MOSAIC
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 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