Python-based geometry preparation and simulation visualization toolkits for STEPS

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scient...

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Detalles Bibliográficos
Autores principales: Chen, Weiliang, De Schutter, Erik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2014
Materias:
Neuroscience
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990042/
https://www.ncbi.nlm.nih.gov/pubmed/24782754
http://dx.doi.org/10.3389/fninf.2014.00037
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author Chen, Weiliang
De Schutter, Erik
author_facet Chen, Weiliang
De Schutter, Erik
author_sort Chen, Weiliang
collection PubMed
description STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations.
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spelling pubmed-39900422014-04-29 Python-based geometry preparation and simulation visualization toolkits for STEPS Chen, Weiliang De Schutter, Erik Front Neuroinform Neuroscience STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations. Frontiers Media S.A. 2014-04-11 /pmc/articles/PMC3990042/ /pubmed/24782754 http://dx.doi.org/10.3389/fninf.2014.00037 Text en Copyright © 2014 Chen and De Schutter. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Neuroscience
Chen, Weiliang
De Schutter, Erik
Python-based geometry preparation and simulation visualization toolkits for STEPS
title Python-based geometry preparation and simulation visualization toolkits for STEPS
title_full Python-based geometry preparation and simulation visualization toolkits for STEPS
title_fullStr Python-based geometry preparation and simulation visualization toolkits for STEPS
title_full_unstemmed Python-based geometry preparation and simulation visualization toolkits for STEPS
title_short Python-based geometry preparation and simulation visualization toolkits for STEPS
title_sort python-based geometry preparation and simulation visualization toolkits for steps
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990042/
https://www.ncbi.nlm.nih.gov/pubmed/24782754
http://dx.doi.org/10.3389/fninf.2014.00037
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