# Competitive Renewal of Development, Improvement and Extension of the Tissue Simulation Environment - CompuCell3D

> **NIH NIH R01** · TRUSTEES OF INDIANA UNIVERSITY · 2020 · $434,997

## Abstract

Summary: We propose to transform our CompuCell3D virtual tissue simulator into a bona-fide computer aided
engineering (CAE) system for bio-medical research focused on the biologically-intuitive description and design of multi-
cell models of tissues and organs (Virtual Tissues). This will include descriptions of biological mechanisms, components,
processes and outcomes. Mechanism-based models of this type will allow researchers to explore the systemic outcomes
of molecular and cellular perturbations (characterized using in vitro and high-throughput experiments) to extract
mechanistic understanding of normal and disease states. CAE programs allow engineers to construct virtual
representations (computational models) of components, assemble them into complex devices, and simulate their
behaviors and interactions in virtual experiments. CAE programs allow engineers to evaluate the performance,
reliability and failure modes of proposed devices without actually having to physically build those devices. CAE platforms
enable the capture of domain knowledge in validated, sharable and reusable components and composite models and to
leverage big-data to abstract knowledge, increasing the speed, efficiency and reliability of experiment and design.
Significance: A key impediment to adoption of CAE simulation approaches in biology and medicine is not the speed or
efficiency of simulation software, but rather the lack of appropriate human-computer interaction between life-science
researchers and simulation software. Increasing the uptake of CAE tools in biomedicine requires the development of
biologically motivated languages and interfaces that facilitate the creation of mechanism-based models of biological
systems, and embed biological knowledge within these models in a way that promotes knowledge validation, mining,
recovery and reuse.
Innovation: We will create a platform for building modular, sharable and reusable virtual-tissue models (including
patient-specific models that integrate patient-derived measurements) that capture and integrate biological and
mechanistic knowledge and experimental observations. Building virtual-tissue models requires combining and
integrating a range of components from different scales. We develop a new hybrid programming language based on
biological rather than computational concepts that naturally expresses the complex multi-scale objects and dynamic
interactions in a unified way. To our knowledge, this language is the first if its kind to allow biological components and
models to be visually created and composite and enables the capture, search, formalization, extraction and reuse of
domain knowledge. Our platform will transform these models into executable simulations, creating virtual experiments
which allow direct comparison with laboratory experiments. We will also develop tools to optimize virtual-tissue models
against qualitative and semi-quantitative experimental data, providing robust techniques to explore diverse hy...

## Key facts

- **NIH application ID:** 9856463
- **Project number:** 5R01GM122424-04
- **Recipient organization:** TRUSTEES OF INDIANA UNIVERSITY
- **Principal Investigator:** James Alexander Glazier
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $434,997
- **Award type:** 5
- **Project period:** 2017-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9856463

## Citation

> US National Institutes of Health, RePORTER application 9856463, Competitive Renewal of Development, Improvement and Extension of the Tissue Simulation Environment - CompuCell3D (5R01GM122424-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9856463. Licensed CC0.

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