XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images

XitoSBML is a software tool designed to create an SBML (Systems Biology Markup Language) Level 3 Version 1 document from microscopic cellular images. It is implemented as an ImageJ plug-in and is designed to create spatial models that reflect the three-dimensional cellular geometry. With XitoSBML, u...

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Detalles Bibliográficos
Autores principales: Ii, Kaito, Mashimo, Kota, Ozeki, Mitsunori, Yamada, Takahiro G., Hiroi, Noriko, Funahashi, Akira
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Genetics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842926/
https://www.ncbi.nlm.nih.gov/pubmed/31749833
http://dx.doi.org/10.3389/fgene.2019.01027
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author Ii, Kaito
Mashimo, Kota
Ozeki, Mitsunori
Yamada, Takahiro G.
Hiroi, Noriko
Funahashi, Akira
author_facet Ii, Kaito
Mashimo, Kota
Ozeki, Mitsunori
Yamada, Takahiro G.
Hiroi, Noriko
Funahashi, Akira
author_sort Ii, Kaito
collection PubMed
description XitoSBML is a software tool designed to create an SBML (Systems Biology Markup Language) Level 3 Version 1 document from microscopic cellular images. It is implemented as an ImageJ plug-in and is designed to create spatial models that reflect the three-dimensional cellular geometry. With XitoSBML, users can perform spatial model simulations based on realistic cellular geometry by using SBML-supported software tools, including simulators such as Virtual Cell and Spatial Simulator. XitoSBML is open-source and is available at https://github.com/spatialsimulator/XitoSBML/. XitoSBML is confirmed to run on most 32/64-bit operating systems: Windows, MacOS, and Linux.
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spelling pubmed-68429262019-11-20 XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images Ii, Kaito Mashimo, Kota Ozeki, Mitsunori Yamada, Takahiro G. Hiroi, Noriko Funahashi, Akira Front Genet Genetics XitoSBML is a software tool designed to create an SBML (Systems Biology Markup Language) Level 3 Version 1 document from microscopic cellular images. It is implemented as an ImageJ plug-in and is designed to create spatial models that reflect the three-dimensional cellular geometry. With XitoSBML, users can perform spatial model simulations based on realistic cellular geometry by using SBML-supported software tools, including simulators such as Virtual Cell and Spatial Simulator. XitoSBML is open-source and is available at https://github.com/spatialsimulator/XitoSBML/. XitoSBML is confirmed to run on most 32/64-bit operating systems: Windows, MacOS, and Linux. Frontiers Media S.A. 2019-10-22 /pmc/articles/PMC6842926/ /pubmed/31749833 http://dx.doi.org/10.3389/fgene.2019.01027 Text en Copyright © 2019 Ii, Mashimo, Ozeki, Yamada, Hiroi and Funahashi http://creativecommons.org/licenses/by/4.0/ 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) and the copyright owner(s) 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 Genetics
Ii, Kaito
Mashimo, Kota
Ozeki, Mitsunori
Yamada, Takahiro G.
Hiroi, Noriko
Funahashi, Akira
XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
title XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
title_full XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
title_fullStr XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
title_full_unstemmed XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
title_short XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
title_sort xitosbml: a modeling tool for creating spatial systems biology markup language models from microscopic images
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842926/
https://www.ncbi.nlm.nih.gov/pubmed/31749833
http://dx.doi.org/10.3389/fgene.2019.01027
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