# Mechanistic Modeling of Cellular Systems

> **NIH NIH R24** · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · 2023 · $239,392

## Abstract

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.

## Key facts

- **NIH application ID:** 10839683
- **Project number:** 3R24GM137787-04S1
- **Recipient organization:** UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
- **Principal Investigator:** LESLIE M LOEW
- **Activity code:** R24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $239,392
- **Award type:** 3
- **Project period:** 2020-08-01 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10839683

## Citation

> US National Institutes of Health, RePORTER application 10839683, Mechanistic Modeling of Cellular Systems (3R24GM137787-04S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10839683. Licensed CC0.

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