DEBtox information
Making sense of ecotoxicity test results



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DEBtox information

Software

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 DEBtoxM and BYOM packages for Matlab are maintained by Tjalling Jager (DEBtox Research). If you find these packages useful, please consider paying for my e-books. That way, I can continue to allocate time to updating the packages. 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 DEBtoxM and BYOM implementations 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. None of this software is developed by professional software engineers, so be prepared to do some work (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 DEBtoxM and 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 implementations that I offer on debtox.info are freely available for all uses, including commercial applications. With a few 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 these errors."
  • 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, I do not recommend. 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.



 






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