Speaker
Description
Collaborative modeling and simulation become increasingly important to study complex disease processes across molecular to organism scales. To support collaborations and construction of digital twins in a modular way, we present Morpheus (https://morpheus.gitlab.io) - an extensible open-source software framework with user-friendly GUI to develop multiscale models in a modular manner and in a standardized language, enabling model exchange, versioning and sharing through a public model repository (https://morpheus.gitlab.io/models) \cite{Morpheus}.
A numerical simulation is automatically composed by parsing the MorpheusML model definition and scheduling of solvers in the simulator. Moreover, Morpheus is SBML-compliant, it supports simulations based on experimental data, e.g. segmented cell configurations, and offers a broad set of analysis tools to extract features right during simulation. The associated FitMultiCell toolbox supports parameter estimation for stochastic Morpheus models (https://gitlab.com/fitmulticell/fit) \cite{FMC}.
We demonstrate the use of Morpheus for liver systems medicine and regenerative processes in tissues and organs.
Bibliography
@article{Morpheus,
title = {Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology},
author = {Starruß, Jörn and de Back, Walter and Brusch, Lutz and Deutsch, Andreas},
journal = {Bioinformatics},
year = {2014},
volume = {30},
number = {9},
pages = {1331--1332},
doi = {10.1093/bioinformatics/btt772},
}
@article{FMC,
author = {Alamoudi, Emad and Schälte, Yannik and Müller, Robert and Starruß, Jörn and Bundgaard, Nils and Graw, Frederik and Brusch, Lutz and Hasenauer, Jan},
title = {FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes},
journal = {Bioinformatics},
volume = {39},
number = {11},
pages = {btad674},
year = {2023},
doi = {10.1093/bioinformatics/btad674},
}
