iDynoMiCS Release 1.3 (June 2015)
We are proud to release the latest update to iDynoMiCS - which includes additional simulation functionality and enhanced methods of analysis & visualisation. 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 using the button below. 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 using the Github button below. 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.
We strongly encourage users to upgrade their Java version to 1.8
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Changes Introduced in Version 1.3
Aging Bacteria
Agent classes that "age" (AgingBac, etc), as described in this paper.
Runnable Jar File
A runnable jar version of iDynoMiCS: just double click on iDynoMiCS_v1_3.jar to launch a simulation. It may be convenient to make a shortcut to this on your desktop. The console output can now be diverted to a pop-up window by ticking a box on the file chooser window. Thanks to Bastiaan Cockx (DTU Copenhagen) for this improvement.
Python Analysis Tools
New simulation analysis tools in Python 2, including a number of plotting scripts that use the package Matplotlib. Windows users are encouraged to install WinPython, as this includes the necessary packages. Please remember to install Python 2, not Python 3.
Image made using the example protocol file multi_species_multi_substrate_nitrification_2D.xml and the analysis script results_analysis_python/idyno_plot_biofilm.py with options -b -f -i 720 -t -T.
Small Code Fixes and Improvements
The release of a new version has provided us with the opportunity to address small problems in 1.2 that have emerged on the via the mailing list. These are:- Number Format Change. In Agent and ExtraMath classes, genealogy is now a BigInteger to prevent running out of numbers in long simulations.
- Moran process. Option of choosing a maximum population size in constant environment.
- Species Defaults
If a one or more parameters are common to multiple species, the user can now specify them in the protocol file using the tag
. Added by Kieran Alden so that these parameters need only be specified once. Note that if any parameters are given in the markup, these will override the values. - SimpleInhibition. Fred Phillips (Edinburgh) fixed a bug in the ReactionKinetic SimpleInhibition.
Changes in Release 1.3.1 (March 2016)
- Tutorial updated to reflect changes in the Eclipse IDE.
- Bug fixed for halting the simulation early in competitive biofilm simulations.