PhysiCellModelManager.jl: A database-backed manager of PhysiCell simulation campaign inputs and outputs.

作者：Daniel Bergman · 发表于：Zenodo (CERN European Organization for Nuclear Research) · 年份：2026 · DOI：10.5281/zenodo.21281749 · 研究领域：Computer science、Human–computer interaction、Simulation、Distributed computing、Real-time computing、Software engineering、Database、Embedded system

PhysiCellModelManager.jl (PCMM) is a Julia package for managing PhysiCell simulation workflows—from input preparation to output analysis. Using a database-driven approach, PCMM organizes simulation inputs, tracks parameter values, and manages outputs in a structured hierarchy, allowing users to focus on modeling rather than bookkeeping. This system supports efficient reuse of previously run simulations and simplifies the process of extending simulation scripts and campaigns. PCMM enables both scripted analysis in Julia and interactive visualization in PhysiCell Studio, made simple by its structured database design. PCMM also facilitates reproducibility by capturing simulation inputs and outputs in a centralized database that supports tracking, reuse, and extension. Altogether, PCMM reduces the cognitive and logistical overhead of agent-based modeling workflows, enabling faster iteration, easier collaboration, and a clearer path from model development to insight.