Speaker
Description
Modeling and simulation become increasingly important to study complex developmental processes across scales and thus constitute an indispensable component of interdisciplinary workflows in quantitative multicellular biology.
Along the lines of a data driven study of collective migration in early zebrafish development, that revealed a novel concept termed ‘guidance by followers’ \cite{Boutillon_2022,Model_repo}, I will recapitulate how the dynamic cell shape representation in the cellular Potts model allows us to account for membrane-local sensing and active behavior (e.g. motility). The fluent composability of the CPM with other paradigms simplified the development and implementation of multiple concurrent hypotheses about the underlying coordinating mechanisms, obscured in complex biological scenario.
To infer the best mechanism we employed the FitMultiCell workflow: implement the concurrent models in the multi-scale modelling framework Morpheus and perform model selection for stochastic models using FitMultiCell and PyABC \cite{Morpheus, FitMultiCell}.
Bibliography
@article{Boutillon_2022, title={Guidance by followers ensures long-range coordination of cell migration through α-catenin mechanoperception}, volume={57}, ISSN={15345807}, DOI={10.1016/j.devcel.2022.05.001}, number={12}, journal={Developmental Cell}, author={Boutillon, Arthur and Escot, Sophie and Elouin, Amélie and Jahn, Diego and González-Tirado, Sebastián and Starruß, Jörn and Brusch, Lutz and David, Nicolas B.}, year={2022}, pages={1529-1544.e5} }
@misc{Model_repo, title={Guidance by Followers}, url={https://morpheus.gitlab.io/model/m0006/}, author={Boutillon, Arthur and Escot, Sophie and Elouin, Amélie and Jahn, Diego and González-Tirado, Sebastián and Starruß, Jörn and Brusch, Lutz and David, Nicolas B.}, year={2022} }
@article{Morpheus, title={Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology}, volume={30}, rights={http://creativecommons.org/licenses/by/3.0/}, ISSN={1367-4811, 1367-4803}, url={https://morpheus.gitlab.io/}, DOI={10.1093/bioinformatics/btt772}, number={9}, journal={Bioinformatics}, author={Starruß, Jörn and De Back, Walter and Brusch, Lutz and Deutsch, Andreas}, year={2014}, pages={1331–1332} }
@article{FitMultiCell, title={FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes}, volume={39}, rights={https://creativecommons.org/licenses/by/4.0/}, ISSN={1367-4803, 1367-4811}, url={https://gitlab.com/fitmulticell/fit}, DOI={10.1093/bioinformatics/btad674}, number={11}, journal={Bioinformatics}, author={Alamoudi, Emad and Schälte, Yannik and Müller, Robert and Starruß, Jörn and Bundgaard, Nils and Graw, Frederik and Brusch, Lutz and Hasenauer, Jan}, editor={Martelli, Pier Luigi}, year={2023}, pages={btad674} }
