Tissue Forge: Interactive biological and biophysics simulation environment.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
Oct 2023
Oct 2023
Historique:
received:
28
11
2022
accepted:
25
09
2023
revised:
02
11
2023
medline:
6
11
2023
pubmed:
23
10
2023
entrez:
23
10
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37871133
doi: 10.1371/journal.pcbi.1010768
pii: PCOMPBIOL-D-22-01734
pmc: PMC10621971
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1010768Informations de copyright
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.
Déclaration de conflit d'intérêts
No competing interests.
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