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Tissue Forge: Interactive biological and biophysics simulation environment

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...

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Detalles Bibliográficos
Autores principales: Sego, T. J., Sluka, James P., Sauro, Herbert M., Glazier, James A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621971/
https://www.ncbi.nlm.nih.gov/pubmed/37871133
http://dx.doi.org/10.1371/journal.pcbi.1010768
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author Sego, T. J.
Sluka, James P.
Sauro, Herbert M.
Glazier, James A.
author_facet Sego, T. J.
Sluka, James P.
Sauro, Herbert M.
Glazier, James A.
author_sort Sego, T. J.
collection PubMed
description 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.
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spelling pubmed-106219712023-11-03 Tissue Forge: Interactive biological and biophysics simulation environment Sego, T. J. Sluka, James P. Sauro, Herbert M. Glazier, James A. PLoS Comput Biol Research Article 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. Public Library of Science 2023-10-23 /pmc/articles/PMC10621971/ /pubmed/37871133 http://dx.doi.org/10.1371/journal.pcbi.1010768 Text en © 2023 Sego et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sego, T. J.
Sluka, James P.
Sauro, Herbert M.
Glazier, James A.
Tissue Forge: Interactive biological and biophysics simulation environment
title Tissue Forge: Interactive biological and biophysics simulation environment
title_full Tissue Forge: Interactive biological and biophysics simulation environment
title_fullStr Tissue Forge: Interactive biological and biophysics simulation environment
title_full_unstemmed Tissue Forge: Interactive biological and biophysics simulation environment
title_short Tissue Forge: Interactive biological and biophysics simulation environment
title_sort tissue forge: interactive biological and biophysics simulation environment
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621971/
https://www.ncbi.nlm.nih.gov/pubmed/37871133
http://dx.doi.org/10.1371/journal.pcbi.1010768
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