iDynoMiCS workshop at Biofilms6 Vienna - 14 May 2014

Biofilms6 Post-Conference Workshop:
Individual-based modelling of biofilms using iDynoMiCS

14 May 2014 (the day after Biofilms6)

NEW: Download slides from the workshop

Click here to download the flyer

The workshop is part of the Biofilms6 conference

Morning Session (9:00-13:00):
Brief introduction to individual-based modelling using iDynoMiCS
Then we will demonstrate how to install and run iDynoMiCS, and how to use our new Protocol File Generator Tool to produce a description of the system to be simulated that iDynoMiCS will read in. A simple one-species one-substrate biofilm will serve as example. You will also learn how to analyse the simulation output with the statistical software R (or Matlab or Python). Afternoon session (14:00-17:00):
Building on the morning session, we will guide and help you how to make the biofilm more complex, e.g. by adding another species or process such as detachment or EPS formation, depending on your choice. There will be an opportunity to discuss your own ideas and plans for modelling of biofilms.

We will also brief you on progress with our ongoing development of eGUT, a generic tool or platform for simulation the gut microbiota and how the microbes interact with the human or other animal host. The eGUT project is funded by the NC3Rs because it will help to reduce and replace animal experiments with computer simulations.

More info on iDynoMiCS can be found on our iDynoMiCS lab pages or (which needs some updating but has useful info).

Who should attend?
The workshop is mainly for researchers who are thinking of using individual-based modelling of biofilms or have just started. Programming experience is not required but useful, as is experience with handling, visualising and analysing data.

The workshop will take place in one of the computer teaching rooms of the University of Vienna in the city centre, the location will be confirmed in due course.

The course will be run by Rob Clegg and Jan Kreft

The workshop is free of charge thanks to support from the University of Vienna and the NC3Rs.

Registration: Places are limited to 20 and will be allocated on a first come, first served basis.
Registration deadline is 10 May 2014, the same as for the conference, but please register early to avoid disappointment.

Contact: For registration or further info, please email Jan Kreft (j.kreft at

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