Building Sustainable ShapeWorks: Performance, Scalability, and User-Friendly Deployment for Open Science - Project Summary ShapeWorks is an open-source software suite that transforms medical imaging data into quantitative, population- level models of anatomical shapes, providing researchers with tools to uncover and study links between morphol- ogy and function across diverse biomedical applications. Previously supported by NIH funding, ShapeWorks has been adopted across fields such as orthopedics, cardiology, psychology, and biological phenotyping, demonstrat- ing its utility for biomedical research. This project, in response to NIH's “RFA-OD-24-010: Building Sustainable Software Tools for Open Science,” will modernize ShapeWorks to improve its scalability, usability, and reliability, ensuring its long-term utility for biomedical research. The proposed improvements will integrate best practices in software engineering, enabling ShapeWorks to meet the evolving demands of biomedical research. By enhanc- ing its functionality and accessibility, the project will ensure sustained adoption and adaptability to emerging user needs, supporting reproducible and impactful research into anatomical shape variations and their implications for health and disease. To achieve these goals, the project focuses on three aims. Aim 1 will improve ShapeWorks' ability to handle large-scale biomedical datasets by implementing internal monitoring tools to track performance metrics, using profiling to identify and analyze bottlenecks, and developing targeted optimizations to improve ef- ficiency. These improvements will enable efficient operation across diverse computing environments, including cloud infrastructures. Aim 2 will enhance ShapeWorks' usability and accessibility by overhauling its installa- tion and dependency management, removing technical barriers, and simplifying deployment to accommodate a broader range of users. Aim 3 will establish a robust foundation of reliability by implementing a comprehensive suite of automated testing, including integration and user interface (UI) testing, to ensure consistent performance and foster long-term community use. Integration testing will ensure seamless functionality across all compo- nents, while UI testing will enhance user experience by improving interface reliability and ease of use. Our interdisciplinary team includes expert computer scientists, senior research software engineers, and experienced developers with extensive expertise in professional programming, code refactoring, and scientific computing. This expertise ensures the proposed improvements are executed with technical rigor and align with best practices in software engineering. This project aligns with the RFA's focus on creating sustainable, scalable, and repro- ducible biomedical research tools by improving ShapeWorks' ability to handle large-scale datasets, enhancing its usability and accessibility, and establishing a robust foundation for reliability. By addressing key challenges in performance, deployment, and testing, these improvements will ensure ShapeWorks remains a versatile and adaptable tool for advancing biomedical discoveries through precise, reproducible analysis of anatomical shape variations and comprehensive evaluation of organ and bone deformities across diverse medical conditions.
