TOPAS - nBio, a Monte Carlo tool for radiation biology research

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The parent project, TOPAS-nBio, focuses on developing a Monte Carlo simulation toolkit specifically designed to connect research disciplines. TOPAS-nBio simulates the initial energy deposition events (physics), then follows the diffusion and reaction of chemical species (chemistry) to infer biological ob- servables at the cell and organelle scale (biology). For the Administrative Supplement to TOPAS-nBio in response to NOT-OD-23-073, we propose to carry out three supplemental tasks which, acting together, enhance TOPAS-nBio for Open Science: 1. Develop an automated cloud-based system for users to build simulation executables from the TOPAS kernel plus any set of user-provided TOPAS extensions. The new system will generate executables suitable for standard desktop, cluster and cloud systems including containerized versions suitable for entry into tool registries. 2. Redesign TOPAS-nBio GitHub setup from current ad-hoc design to instead follow current best-prac- tices for open science. The improved design will make it possible for standard cloud tools to install TOPAS-nBio. 3. Provide tools to launch, monitor and collate results from TOPAS-nBio simulations on cluster and cloud systems. The new tools will be provided as new features within the existing TOPAS Graphical User Interface, removing the need for users to have scripting or other computing expertise to make use of cloud re- sources.