Speaker
Description
Collaborative modeling and simulation become increasingly important to study complex developmental processes across molecular to organism scales. To support interdisciplinary workflows in quantitative multicellular biology we designed the extensible open-source modeling framework Morpheus. It is centered around the cellular Potts model (cell behavior), allows for tight integration with intra-cellular regulation models (e.g. SBML) and fluently couples cells to neighboring cells and their extracellular environment (1,2,3).
A user-friendly GUI allows to formulate the multiscale models in an accessible modular modeling language (MorpheusML), rendering Morpheus applicable for a broad scientific community, beyond skilled programmers. Numerical simulations are automatically composed by extracting the graph of model components from the MorpheusML model definitions and scheduling suitable solvers in the simulator. The associated FitMultiCell toolbox supports parameter estimation for stochastic Morpheus models (4,5).
MorpheusML models can easily be exchanged, versioned, extended and shared through a FAIR model repository (6). It already presents more than 100 hundred models in valuable detail, the majority published in peer-reviewed journals.
(1) Starruß et al. (2014). Bioinformatics 30, 1331.
(2) Morpheus homepage: https://morpheus.gitlab.io
(3) Open source code: https://gitlab.com/morpheus.lab/morpheus
(4) Alamoudi et al. (2023). Bioinformatics 39, btad674.
(5) FitMultiCell toolbox: https://gitlab.com/fitmulticell/fit
(6) Model repository: https://morpheus.gitlab.io/models
