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

Kaito Ii; Kota Mashimo; Mitsunori Ozeki; Takahiro G. Yamada; Noriko Hiroi; Akira Funahashi

doi:10.3389/fgene.2019.01027

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

Kaito Ii
, Kota Mashimo
, Mitsunori Ozeki
, Takahiro G. Yamada
, Noriko Hiroi
, Akira Funahashi

生命情報学科

研究成果: Article › 査読

3 被引用数 (Scopus)

抄録

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.

本文言語	English
論文番号	1027
ジャーナル	Frontiers in Genetics
巻	10
DOI	https://doi.org/10.3389/fgene.2019.01027
出版ステータス	Published - 2019 10月 22

ASJC Scopus subject areas

分子医療
遺伝学
遺伝学（臨床）

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10.3389/fgene.2019.01027

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

abstract = "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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author = "Kaito Ii and Kota Mashimo and Mitsunori Ozeki and Yamada, \{Takahiro G.\} and Noriko Hiroi and Akira Funahashi",

note = "Funding Information: The authors thank Ryuichi Tanimoto, Keio University, and Yuta Tokuoka, Keio University for providing the three-dimensional SH-SY5Y cell images and for productive discussions on recent segmentation algorithms. Funding Information: This work was supported by JSPS KAKENHI Grant-in-Aid for Scientific Research (B) (Grant Number 24300112) and the Imaging Science Project of the Center for Novel Science Initiatives (CNSI), National Institutes of Natural Sciences (NINS) (Grant Number IS271002). Publisher Copyright: {\textcopyright} Copyright {\textcopyright} 2019 Ii, Mashimo, Ozeki, Yamada, Hiroi and Funahashi.",

year = "2019",

month = oct,

day = "22",

doi = "10.3389/fgene.2019.01027",

language = "English",

volume = "10",

journal = "Frontiers in Genetics",

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T2 - A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images

AU - Ii, Kaito

AU - Mashimo, Kota

AU - Ozeki, Mitsunori

AU - Yamada, Takahiro G.

AU - Hiroi, Noriko

AU - Funahashi, Akira

N1 - Funding Information: The authors thank Ryuichi Tanimoto, Keio University, and Yuta Tokuoka, Keio University for providing the three-dimensional SH-SY5Y cell images and for productive discussions on recent segmentation algorithms. Funding Information: This work was supported by JSPS KAKENHI Grant-in-Aid for Scientific Research (B) (Grant Number 24300112) and the Imaging Science Project of the Center for Novel Science Initiatives (CNSI), National Institutes of Natural Sciences (NINS) (Grant Number IS271002). Publisher Copyright: © Copyright © 2019 Ii, Mashimo, Ozeki, Yamada, Hiroi and Funahashi.

PY - 2019/10/22

Y1 - 2019/10/22

N2 - 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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KW - ImageJ

KW - image processing

KW - spatial model simulation

KW - spatial modeling

KW - systems biology markup language

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SN - 1664-8021

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JO - Frontiers in Genetics

JF - Frontiers in Genetics

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

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