Proudly presenting iDynoMiCS 2.0 – a major upgrade

How It Works

iDynoMiCS 2.0 employs individual-based modelling, where microbes are treated as discrete particles with extent in continuous space, characterised by unique properties and behaviours. The software allows users to define models without programming by using a graphical user interface (GUI) or protocol files. Researchers can specify various aspects of microbial communities, such as agent properties, environmental conditions, and biological processes. The modular structure of the software facilitates flexibility and scalability—making it capable of simulating up to 10 million agents in 3D biofilms.

Key features include:

• Enhanced ease of use through a GUI and tools for data analysis and visualization.
• Support for complex kinetic functions and logic expressions for adaptive behaviours.
• A force-based mechanical interaction framework that allows for microbial morphologies such as coccoid or bacillus like shapes as well as filament formation.
• Output compatibility with tools like Matlab, python and R for post-processing simulations.

History

iDynoMiCS 2.0 builds on decades of collaborative development in individual-based microbial modeling, evolving from its predecessors BacSim and the original iDynoMiCS 1.x. Here’s how the software evolved:

Predecessors and Evolution

BacSim (1998, 2001)

Developed initially as an extension of Ginger Booth’s Gecko ecological simulator at Yale, adapted to simulate microbial communities. BacSim was one of the first individual-based biofilm models. The initial release of BacSim was developed by Jan-Ulrich Kreft, Ginger Booth and Julian W. T. Wimpenny, and later extended with the help of Cristian Picioreanu, Hermann Eberl, and Mark van Loosdrecht. The platform was written in Objective-C and later Java. BacSim enabled 2D biofilm simulations but had limited scalability and required programming expertise. It pioneered representing agents as particles in continuous space in contrast to Cellular Automata (CA) models, the shoving algorithm for mechanical agent interactions and representing extracellular polymeric substances (EPS) as capsules surrounding the producing cell or as independent particles.

iDynoMiCS 1.x (2011)

Launched in 2011, the first version of iDynoMiCS merged features from BacSim and other platforms into a unified open-source tool under the CeCILL licence. The development efforts were led by Laurent A. Lardon, Brian V. Merkey, Sónia Martins, Andreas Dötsch, Cristian Picioreanu, Barth F. Smets and Jan-Ulrich Kreft. Later improvements were made by Kieran Alden, Katrin Bohl, Max Adolph, Bastiaan J. R. Cockx, Robyn Wright and Rob J. Clegg. The platform introduced XML-based input files, stochastic chemostat modes, and biomass pressure-driven spreading and was capable to simulate 2D and 3D biofilms. While more accessible than BacSim, it still required manual coding for complex scenarios and had computational limits (up to ~100,000 agents).

iDynoMiCS 2.0 (2024)

The overhauled 2.0 version, developed by Bastiaan J. R. Cockx, Tim Foster, Robert J. Clegg, Kieran Alden, Sankalp Arya, Dov J. Stekel, Barth F. Smets, Jan-Ulrich Kreft, and others, addressed key limitations:

• Ease of use: GUI, unit conversion, protocol files, and live visualization tools eliminate programming needs.
• Scalability: Simulates up to 10 million agents in 3D biofilms.
• Modularity: Agents and processes are assembled from reusable modules (morphology, metabolism, interactions, etc).
• Flexibility: Custom kinetic and mechanical functions and adaptive behaviours (e.g., metabolic switching) via arithmetic and logic expressions.

This evolution reflects a shift toward democratizing individual-based modelling, enabling researchers to focus on biological questions rather than coding. The software remains open-source, with ongoing contributions from the Kreftlab and collaborators.