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

Department of Biosciences and Informatics

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

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.

Original language	English
Article number	1027
Journal	Frontiers in Genetics
Volume	10
DOIs	https://doi.org/10.3389/fgene.2019.01027
Publication status	Published - 2019 Oct 22

Keywords

ImageJ
image processing
spatial model simulation
spatial modeling
systems biology markup language

ASJC Scopus subject areas

Molecular Medicine
Genetics
Genetics(clinical)

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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.",

keywords = "ImageJ, image processing, spatial model simulation, spatial modeling, systems biology markup language",

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",

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journal = "Frontiers in Genetics",

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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.

AB - 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 - spatial model simulation

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KW - systems biology markup language

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

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Keywords

ASJC Scopus subject areas

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