# Mechanistic Modeling of Cellular Systems

> **NIH NIH R24** · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · 2022 · $1,277,350

## Abstract

Project Summary
This proposal aims to establish a National Resource for Mechanistic Modeling of Cellular
Systems to serve the large community of cell and systems biologists. The Resource will
encompass 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 supports a number of key biophysical mechanisms,
including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion,
electrophysiology and rule-based models of multi-state/multimolecular interactions. Simulations
can be based on 0D, 1D, 2D or 3D analytical or experimental image-based geometries. Users
may choose among multiple available simulation approaches: ordinary differential equations,
partial differential equations, stochastic reaction kinetics, network-free simulations, spatial
particle-based simulations and spatial hybrid stochastic/deterministic simulations. COPASI
enables the simulation and analysis of complex biochemical reaction networks either
deterministically or stochastically. It offers a broad range of analysis tools including parameter
estimation/optimization, steady state analysis, stoichiometric analysis, sensitivity analysis and
metabolic control analysis. 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 will be hosted at the University of Connecticut School of Medicine. Thus, the
Resource will benefit from: (1) the common institutional organization under which it will operate;
(2) a joint website; (3) a common high performance computing facility that will serve the
computationally intensive needs of users; (4) coordinated training and outreach to the user
community in the form of web-based documentation and tutorials, a yearly Computational Cell
Biology Workshop and numerous roadshows at national and international meetings.
Additionally, VCell and COPASI will be leveraged by external systems biology software
developers as user-friendly platforms for the wide dissemination of their third party algorithms,
software and databases. Finally, the Resource will actively engage with the software standards
community to assure the reproducibility and reusability of both the software and the models it
generates.

## Key facts

- **NIH application ID:** 10455477
- **Project number:** 5R24GM137787-03
- **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:** 2022
- **Award amount:** $1,277,350
- **Award type:** 5
- **Project period:** 2020-08-01 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10455477

## Citation

> US National Institutes of Health, RePORTER application 10455477, Mechanistic Modeling of Cellular Systems (5R24GM137787-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10455477. Licensed CC0.

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