Tissue Forge: Interactive biological and biophysics simulation environment.

Autor: Sego TJ; Department of Medicine, University of Florida, Gainesville, Florida, United States of America., Sluka JP; Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America., Sauro HM; Department of Bioengineering, University of Washington, Seattle, Washington, United States of America., Glazier JA; Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2023 Oct 23; Vol. 19 (10), pp. e1010768. Date of Electronic Publication: 2023 Oct 23 (Print Publication: 2023).
DOI: 10.1371/journal.pcbi.1010768
Abstrakt: Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.
Competing Interests: No competing interests.
(Copyright: © 2023 Sego et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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