iDynoMiCS Release 1.2 (June 2013)

We are proud to release the latest update to iDynoMiCS - which includes additional simulation functionality, enhanced methods of documentation, and improved procedures for collaboration. 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.

Changes Introduced in Version 1.2

New Species Attachment Method

This is the highlight of the new functionality in terms of simulating microbiology. In previous versions of iDynoMiCS, a specific number of species are created in a specified birth area (all controlled by parameters in the protocol file). From 1.2 onwards, iDynoMiCS can model the injection of species in an additional manner. Now a number of agents (per hour) of the specified species can be introduced on the top of the boundary layer. These agents then perform a 'run and tumble' motion until they (a) attach to the solid surface, (b) attach to forming biofilm, or (c) return to the bulk. This run and tumble motion works by choosing a random angle. The agent moves through the domain in that direction for a certain amount of time until it 'tumbles', or changes direction. This continues until one of the three conditions are met. Full instructions on using this method of attachment can be found in the iDynoMiCS Github Wiki.
This is offered as an additional method of agent attachment, alongside the traditional method which can also be used in iDynoMiCS v1.2.

iDynoMiCS Automatic Update Facility

iDynoMiCS is under constant development by several different teams working in the realm of microbial ecology, and we encourage collaborators to get involved in the simulator's future development. We feel it is vital that when new features are added to iDynoMiCS, we release these to the field as soon as is appropriate. With this in mind, iDynoMiCS 1.2 includes a new automatic update feature that will check for updates and inform you if a new version has been released. The simulator then provides the user with the option of updating iDynoMiCS to the latest version. If the user wishes to do this, the latest version is downloaded and replaces your current iDynoMiCS code on your file system.
This update check is initiated by checking the 'checkForUpdates' tag in the simulation XML protocol file. Should you not wish to check for updates, this tag can be set to 'false' or removed from the protocol file.

Enhanced Documentation

The development of iDynoMiCS has always been driven by the objective that the code is open-source and accessible to anyone who wishes to assist in the development of the tool. Over the last few months we have been working to improve the documentation of the Java code, and have moved to code documentation using doxygen. Doxygen has the ability to produce HTML and PDF manuals directly from the code, producing clear documentation detailing the role of each class and parameter in the code, and showing relationships between the included classes. From Version 1.2 onwards, code documentation will be undertaken using doxygen and the code reference manual made available online. The doxygen code reference manual for version 1.2 can be viewed here.

For Version 1.2, nearly 90% of the classes have been recommented such that doxygen can be adopted. This documentation will evolve over the next few versions. If you have any comments on this documentation please do let us know via the mailing list

Improved Procedures for Collaboration

iDynoMiCS is now available from a repository on Github. Making this change offers us many opportunities:

Small Code Fixes and Improvements

The release of a new version has provided us with the opportunity to address small problems in 1.1 that have emerged via the mailing list. These are:

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