iDynoMiCS example of the month


This example is about metabolic switching between aerobic and anaerobic respiration (denitrification) depending on oxygen availability. Some species can switch denitrification on faster but incur a higher cost of switching. Colours for fastest switcher (1 hour lag) are black=on, white=off; intermediate (3 hour lag) red=on, green=off; slowest switcher (3 hour lag) yellow=on, blue=off; EPS particles in pink.

[For more information and the paper ...]

Executive summary

iDynoMiCS has been developed by an international team of researchers in order to provide a common platform for further development of all individual-based models of microbial biofilms and such like. All features of various predecessor models have been merged and some new features added.

We hope that non programmers will be able to use the software for a range of projects without having to be able to program Java since the properties of microbial species can be specified in an input file, and many options are also accessible by editing the input file. The current code and any future additions are made available upon publication of the work describing the respective code or additional features.

While we make the code available under a GNU GPL type open source licence called CeCILL, we kindly request that you join the iDynoMiCS mailing lists when you download the code. This will help us find out how many scientists are using iDynoMiCS, which we will use to support future grant applications to further develop the code, which in turn is in your interest. We will also use the email lists to send updates concerning the ongoing development of iDynoMiCS. For more information, see the Mailing list page [link to page]

Should you have any issues with using iDynoMiCS, you can seek support in two ways. The first of these is to ask your question via the Issue tracking system on our GitHub repository. There is more information on how to use the Issue tracking system in our wiki part of the GitHub repository. Secondly, you may send questions to the developers via the mailing list The developers will aim to respond via email as swiftly as time allows. Your query will also be logged as an Issue in our GitHub repository with the appropriate reply, in order that this remains available for other users who may have the same question.