Mechanistic Modeling of Cellular Systems

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PROJECT SUMMARY This parent R24 award establishes a National Resource for Mechanistic Modeling of Cellular Systems to serve the large community of cell and systems biologists. The Resource encompasses COPASI and Virtual Cell (VCell) software platforms, which are arguably the most comprehensive and widely used tools for computational modeling of the biophysical mechanisms controlling cell function. VCell and COPASI each boast thousands of active users. Collectively, their users produce >100 papers per year relying on these software systems. Both VCell and COPASI are hosted at the University of Connecticut School of Medicine and the Resource benefits from a common High Performance Computing (HPC) facility that serves the computationally intensive needs of users and a coordinated training and outreach to the user community. It actively engages with the software standards community to assure the reproducibility and reusability of both the software and the models it generates. A key component is the continuous enhancement of HPC support for increased portability, scalability and cloud compatibility (Specific Aim 2 of the parent grant). As stated in this aim, we strive to maintain and update the software infrastructure to meet this goal. Nevertheless, modern software engineering technologies are changing at breath-taking pace in this domain and some recent paradigm-shifting advances could not be foreseen and cannot be addressed within the limitations of the current funding. This supplement proposal focuses on three such emerging needs for the VCell framework that can be properly addressed only with additional resources and expertise: (i) transition the HPC/cloud architecture from Docker Swarm to Kubernetes, (ii) implement identity and access management using third-party authentication providers, and (iii) port and update the Restlet-based API to OpenAPI.