iDynoMiCS Developer team

Jan-Ulrich Kreft, University of Birmingham

Jan is a Lecturer at the University of Birmingham and has pioneered the use of Individual-based Models for microorganisms rather than higher animals or plants. Microbes were considered to be too stupid to warrant IbM. Jan has been developing BacSim, a sort of precursor of iDynoMiCS, the first IbM of biofilms, and is mainly interested in social and metabolic interactions between microbes.

Brian Merkey, Danish Technical University (DTU), now Northwestern University, USA

Brian has been developing iDynoMiCS as a postdoc with Barth at the DTU and is now a postdoc with David Chopp at Northwestern. Brian is a mathematician who developed continuum models for biofilms during his PhD with David Chopp, before doing IbM.He wrote substantial parts of the code for iDynoMiCS and used iDynoMiCS for a metabolic switching and a horizontal gene transfer research projectfor which the publications are on the way.

Cristian Picioreanu, TU Delft

Cristian is a Universitair Docent at the TU Delft and has pioneered the use of quantitative multidimensional and multispecies biofilm models based on first principles. He is internationally recognized for his contributions to biofilm modelling.

Barth F Smets, Danish Technical University (DTU)

Barth is a Professor at the DTU in Environmental Engineering. He has produced numerous interesting publications in the area of biofilms and applications of biofilms in waste water treatment, such as nitrification and anammox. Apart from the N-cycle, he is interested in horizontal gene transfer and using IbM to shed light on plasmid transfer in biofilms. His former postdocs Laurent Lardon and Brian Merkey have written most of the iDynoMiCS code and applied it to study plasmid transfer in biofilms.

Laurent Lardon, Danish Technical University (DTU), now Laboratory of Environmental Biotechnology, INRA, Narbonne (France)

Laurent started the code development of iDynoMiCS in 2006, designing the structure and writing the core code, using design ideas and code from previous models,such as Jan's BacSim and Joao's framework. He went back to theLaboratory of Environmental Biotechnology, Narbonne, INRAof Jean-Philippe Steyer, where he did his PhD.

Joao Xavier, TU Delft, Universidade Nova de Lisboa, Harvard University, Memorial Sloan-Kettering Cancer Center, New York

Joao, among other work, developed algorithms for the analysis of confocal biofilm images during his PhD with Jonas Almeida,before joining Cristian Picioreanu in Mark van Loosdrecht's group at the TU Delft as a postdoc. There he made a number of contributions to biofilm modelling,e.g. a detachment algorithm based on the level set method and the framework model, before moving back to Portugal and then toKevin Foster's group at Harvard where he has made numerous interesting contributions to the evolution of social behaviour.In 2010, he took up a position at the Memorial Sloan-Kettering Cancer Center, New York. Joao's detachment code has been adopted in iDynoMiCS,and he has been teaching in our PhD courses.

Andreas Dötsch, Theoretical Biology, University of Bonn, now Chronic Pseudomonas Infections Group, Helmholtz Centre for Infection Research, Germany

Andreas was a student of Jan Kreft while he was in the Theoretical Biology group at the University of Bonn. During this time, Andreas made some additions to the iDynoMiCS code to solve reaction-diffusion equations in the non-steady state case. Andreas also taught in the PhD course.

Sónia Martins, University of Birmingham

Sónia is a PhD student in Jan's group and has been working on modelling plasmid dynamics in biofilms and chemostats,looking at the effects of a trade-off between host range and fitness cost on the competitiveness of broad host range plasmids.She has contributed the stochastic chemostat simulation option to iDynoMiCS and been helping to organize and teach the PhD courses.

Susanne Schmidt, University of Birmingham

Susanne obtained a Marie Curie Fellowship to join Jan's group in Birmingham and work on modelling microbial microcolonies in groundwater. To be able to simulate larger domains with convective and diffusive transport in porous media, she has been working on the combination of Comsol Multiphysics with iDynoMiCS, which could be of interest for various other projects as well. Susanne has also been teaching in the PhD courses and organized the 2010 course in Birmingham..

Chinmay Kanchi, University of Birmingham

Chinmay is a PhD student in Jan's group working on gut microbial ecology.While not using iDynoMiCS, he has helped the others with advice on programming and software issues and written a few things here and there.He has also helped organize and teach the PhD courses, and is therefore an honorary member of the development team.

Robert Clegg, University of Birmingham

Rob has joined Jan's group in 2010 as a PhD student and started to use iDynoMiCS to study aging in biofilms. Apart from developing new routines for aging,he has made a few improvements here and there and helped in producing the web pages.

Edward Miles, University of Birmingham

Edd was a Bioinformatics student using iDynoMiCS in his final year project in Jan's group in 2009/10. He has written some scripts to launch iDynoMiCS automatically so he could run simulations on the Linux cluster and various Windows PCs. He also helped with the PhD course in 2010.

A bit of history

The idea to develop a common platform for individual-based modelling of biofilms for use by several groups for consistency, easier exchange of code,and to facilitate comparison of results goes back to 2006 when Jan Kreft organized a meeting at the TU Delft to forge this team.Present at this inaugural meeting over a weekend in September 2006 were:Cristian Picioreanu, Barth F Smets with postdoc Laurent Lardon, Joao Xavier, and Jan Kreft with PhD student Andreas Dötsch.

Barth F Smets' postdoc Laurent Lardon started the development of iDynoMiCS in 2006 with a stint from April-June as guest of Jan Kreft at the group of Theoretical Biology at the University of Bonn, a sort of stopover in his move from Montpellier to the DTU in Lyngby. Then Laurent went back to France to take up a permanent position in the Laboratory of Environmental Biotechnology, Narbonne, INRA.

After Laurent left in 2008, Brian Merkey, who did his PhD with David Chopp at Northwestern, took over the further development of iDynoMiCS,and has continued to work on the code and publication after returning to Northwestern in March 2010.