This article presents a conceptual framework for a compositional approach to systems biology, focusing on multiscale cellular modeling. It is not a research paper with specific findings, but rather a proposal for a new way of thinking about and conducting systems biology research.
The article begins by highlighting the limitations of traditional systems biology models, which often focus on isolated subsystems and struggle to integrate data and models across different scales. It proposes "compositionality" as a guiding principle, drawing inspiration from category theory and software design.
The core of the proposed framework is "process bigraphs," a graphical and conceptual tool for representing complex systems as compositions of interacting processes. The article outlines key features of this framework:
The article then applies this framework to cellular modeling, proposing templates for representing cells and their environments:
The article emphasizes the importance of self-organization and coarse-graining in bridging scales, allowing for the representation of emergent properties while maintaining computational tractability. It also discusses how the framework can be used to model cellular growth, division, development, and evolution.
Finally, the article advocates for a collaborative approach to systems biology, emphasizing the need for standardized schemas and protocols to facilitate data and model sharing, ultimately leading to a more integrated and scalable understanding of complex biological systems.
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by Eran Agmon о arxiv.org 11-25-2024
https://arxiv.org/pdf/2408.00942.pdfГлибші Запити