Research Paper#Systems Biology, Multiscale Modeling, Process Bigraphs🔬 ResearchAnalyzed: Jan 3, 2026 16:24
Process Bigraphs for Composing Multiscale Biological Models
Published:Dec 27, 2025 13:19
•1 min read
•ArXiv
Analysis
This paper introduces Process Bigraphs, a framework designed to address the challenges of integrating and simulating multiscale biological models. It focuses on defining clear interfaces, hierarchical data structures, and orchestration patterns, which are often lacking in existing tools. The framework's emphasis on model clarity, reuse, and extensibility is a significant contribution to the field of systems biology, particularly for complex, multiscale simulations. The open-source implementation, Vivarium 2.0, and the Spatio-Flux library demonstrate the practical utility of the framework.
Key Takeaways
- •Process Bigraphs provides a framework for composing and simulating multiscale biological models.
- •The framework emphasizes clear interfaces, data structures, and orchestration patterns.
- •Vivarium 2.0 is an open-source implementation of the Process Bigraph framework.
- •Spatio-Flux demonstrates the utility of the framework for microbial ecosystem simulations.
Reference
“Process Bigraphs generalize architectural principles from the Vivarium software into a shared specification that defines process interfaces, hierarchical data structures, composition patterns, and orchestration patterns.”