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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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The iDynoMiCS software simulates the growth of microbial communities. iDynoMiCS is written in Java, and uses XML files for input and output. Input files allow the users to specify conditions, microbial species, and other parameters without the need to become a programmer. Also the positions and other variables of all individual microbes can be specified in another input file. This allows one to easily specify many different types of simulations. iDynoMiCS writes plain-text XML files as output, and these may be processed using any number of software tools (though we provide some general post-processing routines that run in Matlab and are working on R scripts). In addition to XML files, iDynoMiCS also writes scene description input files for POV-Ray, a virtual photography software which is used to render 3-D images of the simulated communities.
iDynoMiCS is under constant development by several different teams working in the realm of microbial ecology. If you are interested in contributing to the further development of this software, whether this be through the addition of new functionality, new routines for post-processing simulations, or additional PDE solvers or other numerical algorithms, please read the information in our Github repository wiki
iDynoMiCS has been a collaborative effort between an increasing number of people: Laurent Lardon, Brian Merkey, Joao Xavier, Andreas Dötsch, Barth F Smets, Cristian Picioreanu, Rob Clegg, Sonia Martins, Katrin Bohl, Kieran Alden, Jan-Ulrich Kreft and others.
The tool can be downloaded in two different ways. Should you wish to use the tool to perform experimentation, then download the Latest Stable release here . If however you wish to contribute to the future development of the tool (which we encourage), you can download the most up to date version of the source code from our Github repository. Full documentation that details how to contribute to iDynoMiCS development using this repository is available on the iDynoMiCS wiki, also located in the Github repository.
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. Click here for information on joining these lists
The best place to start with iDynoMiCS is to complete the tutorial. This can be found in our Github repository and a PDF can be found in the 'Tutorial' folder in the iDynoMiCS download.
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 idynomics@lists.bham.ac.uk. 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.
1.8.3.1
