University of Birmingham
We are proud to develop the next generation individual-based modelling platform iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), dedicated to individual-based modelling of microbial communities such as biofilms. While the initiative to develop this common platform for individual-based modelling came from our desire to facilitate collaboration and maximize synergies, the software not only implements capabilities, previously scattered over separate programs, in the same software package, but also adds a number of improvements, particularly in (i) representation of EPS, (ii) inclusion of a stochastic chemostat mode, (iii) biomass spreading or shrinking on a coarser scale according to a biomass pressure field, and (iv) switching metabolism according to internal or external signals. In comparison to former simulators, we aim to improve accessibility to non programmers and to provide a backbone to future developments proposed by any interested contributor. iDynoMiCS is therefore an open-source software developed under the GPL-like CeCILL license.
iDynoMiCS originally was the result of years of work mainly by Laurent Lardon and Brian Merkey, with code contributions from Joao Xavier and others and design decisions by all members of the team. Later, Sonia Martins, Kieran Alden, Katrin Bohl, Max Adolph and Bastiaan Cockx made a number of additions and improvements. Recently, Rob Clegg has taken over the role of chief programmer. For more information on iDynomics, visit our dedicated iDynomics site.
We strongly encourage users to upgrade their Java version to 1.8
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 the Github repository wiki, and contact Jan Kreft
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, Bastiaan Cockx, Max Adolph, Kieran Alden, Jan-Ulrich Kreft and others.
From this section you can download previous versions of iDynoMiCS.
|iDynoMiCS Version 1.2.1 - June 2013|
|iDynoMiCS Version 1.1 - October 2012|
|iDynoMiCS Version 1.0 - June 2011|