Expressive rule-based modeling and fast simulation for dynamic compartments.

Autor: Köster T; Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany., Henning P; Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany.; Institute of Medical Biochemistry and Molecular Biology, University Medicine Rostock, Rostock, Germany., Warnke T; Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany.; Limbus Medical Technologies GmbH, Rostock, Germany., Uhrmacher A; Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2024 Oct 31; Vol. 19 (10), pp. e0312813. Date of Electronic Publication: 2024 Oct 31 (Print Publication: 2024).
DOI: 10.1371/journal.pone.0312813
Abstrakt: Compartmentalization is vital for cell biological processes. The field of rule-based stochastic simulation has acknowledged this, and many tools and methods have capabilities for compartmentalization. However, mostly, this is limited to a static compartmental hierarchy and does not integrate compartmental changes. Integrating compartmental dynamics is challenging for the design of the modeling language and the simulation engine. The language should support a concise yet flexible modeling of compartmental dynamics. Our work is based on ML-Rules, a rule-based language for multi-level cell biological modeling that supports a wide variety of compartmental dynamics, whose syntax we slightly adapt. To develop an efficient simulation engine for compartmental dynamics, we combine specific data structures and new and existing algorithms and implement them in the Rust programming language. We evaluate the concept and implementation using two case studies from existing cell-biological models. The execution of these models outperforms previous simulations of ML-Rules by two orders of magnitude. Finally, we present a prototype of a WebAssembly-based implementation to allow for a low barrier of entry when exploring the language and associated models without the need for local installation.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Köster et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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