Expressive rule-based modeling and fast simulation for dynamic compartments
Year: 2024
Type: article
Abstract: 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.
Source: PLoS ONE
Institutions: University of Rostock, Universitätsmedizin Rostock
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,290
Funder: Deutsche Forschungsgemeinschaft
OpenAlex ID: W4403938727