Software section
Use the sub-menu to navigate
through the various categories. Here, you can find (links
to) software to analyse your data, or for simulations. Can't
find what you're looking for? Check out the website on Ecotoxicology and
Models. The BYOM platform and its packages for Matlab
are maintained by Tjalling
Jager (DEBtox Research). The DEBtoxM software is no
longer offered or maintained; the web page is kept to make
sure that old links still resolve. If you find the BYOM
platform useful, please consider paying for my e-books. That way, I can continue
to allocate time to updating the packages (and the e-books).
The 'other software' includes a short explanation and links
to the GUTS R-packages, the NETlogo DEB-IBM package,
DEBtool, and more if things pop up.
What if I have questions about the software?
Use e-mail to contact me with your questions. I
will personally make sure that your questions regarding the
BYOM implementation will be addressed (as I developed the
Matlab code). However, I do not run a help desk! I will try
to answer simple questions ASAP, but for assistance in doing
model analyses, I would need to be funded from somewhere (which is also an
option). For the other software, I cannot provide any
support, but I can forward your question to the developer if
you like. Most of this software is not developed by
professional software engineers, so be prepared to do some
work yourself (but it's totally free, so don't complain).
What happened to the DEBtox Windows software?
That software is no longer offered
or maintained. The underlying equations for sub-lethal
endpoints contained a few errors (see Jager
& Zimmer, 2012 for a corrected set of equations),
and it was programmed in such a way that it is almost
impossible to update. The Matlab implementations as part of
BYOM that you can find on this site are much more flexible,
but of course, much less user-friendly.
Can't you do the analysis for me?
Being self-employed, I have to
operate commercially, so I have little possibility to work
for free. If it's a very limited (or very interesting)
analysis, and if time permits, I might help you for free. If
it's more work (or boring), I have to be funded from
somewhere (see DEBtox
Research).
Why don't you have some nice user-friendly software for
me?
Because we are not software
engineers. The people that made these Matlab, Octave, R and
NetLogo packages are scientists, who do not get paid to
develop nice software for everybody to use (and probably
also do not have the expertise for that). But, if you are a
programming enthousiast, and you are willing to build
something (that can be distributed for free, or used as a
web-application) ... do not hesitate to contact me! However, for GUTS, several user-friendly
platforms are available or will become available soon. I
will link to these and other relevant softwares on my other-software page.
Under what conditions can I use your Matlab files?
The Matlab BYOM implementation and
packages that I offer on debtox.info are freely available
for all uses, including commercial applications. They are
distributed under an MIT-style licence that can be downloaded here.
Additional comments:
- As I state on my web pages for DEBtoxM
and BYOM: "The files are
prepared with care, but not extensively tested (and I
adapt them all the time), so I cannot give any
guarantees as to their correctness (in fact, I am pretty
sure that they will contain errors). I do not accept
liability or responsibility for any damage or costs
incurred as a result of using these files."
- Do not represent these Matlab files, or parts thereof,
as your own work. Please clarify in your application
(paper, report, software, etc.) that you used these
files, with a reference to my web pages and the version
number.
- Feel free to modify the files to suit your needs.
However, if you do, please clarify in your
application/report that you modified the files. If you
spot errors or come up with improvements, I would
appreciate some feedback.
- I accept no liability whatsoever regarding these
implementations, but also do not provide a help desk. I
may help you with some straightforward, explanatory,
questions, but for more substantial help I would need to
be funded (which
is also an option).
- The DEBtoxM implementations have been removed for
download as it has been quite a while since I last used
them, and development has ceased. The BYOM files, I use
on a very regular basis, which means they are more
up-to-date and better tested.
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