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)

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)
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

Daniel Garza

Microbial Systems Biology
Rega Institute, KU Leuven

danielriosgarza [at] gmail [dot] com

Akshit Goyal

Akshit Goyal

Physics of Living Systems
Massachusetts Institute of Technology

akshitg [at] mit [dot] edu

Bram van Dijk

Bram van Dijk

Max Planck Institute for Evolutionary Biology
Microbial Populations biology

vandijk [at] evolbio [dot] mpg.de