Microbiomes are governed by processes that occur at multiple scales, from molecules and cells to
interacting populations and changing environments. In order to better understand and predict these
processes, we need mechanistic models that can integrate information from the simpler levels and
generate accurate predictions at the community and systems level.
ModelMEMS is a tutorial cycle organised by Daniel Garza, Akshit Goyal, and Bram van Dijk,
where we will explore diverse microbiome modeling frameworks with the guidance of their proponents. If you
have (some) experience with a specific modelling technique, but wish to learn more about what other researchers
are doing in this field, then this tutorial cycle is for you!
Tutorials will be online, approximately once every two months, starting on April 6th. The tutorials
will consist of using / comparing models, discussion of published modelling work, and hands-on tours
of the models in question.
Overal, it will be
a great opportunity to exchange information about diverse microbiome modelling frameworks and
how they may be combined and refined with experimental data.
Tutorials
Tutorial II (Aug 17th 2021): Exploring bacterial and phage interactions with dynamic models
In our second tutorial, Hilje Doekes will discuss modeling of phage/bacterial dynamics. Hilje is an expert in eco-evolutionary dynamical systems modelling.
She has recently published a beautiful paper about modelling a viral small-molecule communication system which governs the switch
between lytic and lysogenic decisions. Her model has a number of intriguing implications for the ecological and evolutionary
dynamics of the phage-host system. Hilje will first cover the broader question of how to model phage dynamics and how to
address the many important questions about the detailed ecological and evolutionary dynamics that are governed by phages.
She will first give a historical and current overview of previous models. Next, she will talk about her own work and finalize
it with a practical hands-on tutorial of her model.
Seminar by Hilje Doekes
15:00 - 16:20 (CET) | 8:00 - 9:20 (CT)
Coffee break
16:20 – 16 :30 (CET) | 9:20 – 9:30 (CT)
Hands-on tutorial
16:30 – 17:45 (CET) | 9:30 – 10:45 (CT)
Wrap-up session
17:45 - 18:00 (CET) | 10:45 - 11:45 (CT)
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Register here
Tutorial I (April 6th 2021): recording and materials
We have explored consumer-resource models with Veronika Dubinkina, but you can still watch the recording and play with the community simulator package.
Recording of the workshop is available
here
Workshop material is available
here
Seminar by Veronika Dubinkina
15:00 - 16:20 (CET) | 8:00 - 9:20 (CT)
Coffee break
16:20 – 16 :30 (CET) | 9:20 – 9:30 (CT)
Hands-on tutorial
16:30 – 17:45 (CET) | 9:30 – 10:45 (CT)
Wrap-up session
17:45 - 18:00 (CET) | 10:45 - 11:45 (CT)
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About
ModelMEMS is a (virtual) tutorial cycle organised by
Daniel Garza,
Akshit
Goyal, and
Bram van Dijk, with the goal of bringing together modellers from different backgrounds to
discuss techniques and insights.
Daniel Garza
Microbial Systems Biology
Rega Institute, KU Leuven
danielriosgarza [at] gmail [dot] com
Akshit Goyal
Physics of Living Systems
Massachusetts Institute of Technology
akshitg [at] mit [dot] edu
Bram van Dijk
Max Planck Institute for Evolutionary Biology
Microbial Populations biology
vandijk [at] evolbio [dot] mpg.de