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Related Experiment Video

Updated: Jul 12, 2025

Fibroblast Derived Human Engineered Connective Tissue for Screening Applications

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Published on: August 20, 2021

Tissue Forge: Interactive biological and biophysics simulation environment.

T J Sego¹, James P Sluka², Herbert M Sauro³

¹Department of Medicine, University of Florida, Gainesville, Florida, United States of America.

Plos Computational Biology

|October 23, 2023

Summary

This summary is machine-generated.

Tissue Forge is an open-source simulation environment for particle-based modeling across physics, chemistry, and biology. It enables real-time exploration of complex biophysical systems from molecular to multicellular scales.

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Area of Science:

Computational Biology
Biophysics
Soft Condensed Matter Physics

Background:

Modeling complex biological systems requires versatile simulation tools.
Existing platforms may lack flexibility across multiple scales (molecular to multicellular).
Bridging physics, chemistry, and biology simulations is challenging.

Purpose of the Study:

Introduce Tissue Forge, an open-source interactive environment for particle-based modeling.
Provide a unified platform for simulating biophysical systems from molecular to multicellular levels.
Support diverse applications from molecular dynamics to agent-based multicellular systems.

Main Methods:

Utilizes a particle-based approach with a focus on soft condensed matter physics.
Offers an interactive, real-time environment for model building and simulation.
Supports both built-in and user-specified models with extensive Python, C, and C++ APIs.

Main Results:

Tissue Forge facilitates the creation, simulation, and exploration of virtual experiments.
Enables real-time interaction with simulations and modification of parameters during execution.
Supports high-performance computing environments for off-screen and remote simulations.

Conclusions:

Tissue Forge simplifies complex biophysical problem-solving across subcellular, cellular, and tissue levels.
Its flexible architecture supports a wide range of applications and custom model development.
The environment is accessible on major operating systems and installable via conda.