Process bigraphs and the architecture of compositional systems biology.

Process Bigraph enables effective integration of diverse biological processes in multiscale models, demonstrated by spatially organized microbial ecosystem simulations.

• Why it matters: Current tools lack comprehensive specifications for variable sharing, translation, and synchronization in multiscale biological modeling, hindering model reuse and understanding.
• What they did: The authors developed Process Bigraph, a framework that formalizes process interfaces, data structures, and orchestration patterns, implemented in Vivarium 2.0 with tools like bigraph-schema and viva-superpowers, and demonstrated with the Spatio-Flux library.
• The result: The framework facilitates the integration of heterogeneous biological processes, leading to emergent spatial population dynamics, and supports the development of multiscale modeling standards.