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

Research output: Contribution to journalArticle

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 languageEnglish
Article number1027
JournalFrontiers in Genetics
Volume10
DOIs
Publication statusPublished - 2019 Oct 22

Fingerprint

Systems Biology
Language
Software

Keywords

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

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)

Cite this

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.

In: Frontiers in Genetics, Vol. 10, 1027, 22.10.2019.

Research output: Contribution to journalArticle

@article{ebe7a90f3d3c4fccb76aca606d151940,
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 = "image processing, ImageJ, 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",
year = "2019",
month = "10",
day = "22",
doi = "10.3389/fgene.2019.01027",
language = "English",
volume = "10",
journal = "Frontiers in Genetics",
issn = "1664-8021",
publisher = "Frontiers Media S. A.",

}

TY - JOUR

T1 - XitoSBML

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

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.

KW - image processing

KW - ImageJ

KW - spatial model simulation

KW - spatial modeling

KW - systems biology markup language

UR - http://www.scopus.com/inward/record.url?scp=85074645702&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85074645702&partnerID=8YFLogxK

U2 - 10.3389/fgene.2019.01027

DO - 10.3389/fgene.2019.01027

M3 - Article

AN - SCOPUS:85074645702

VL - 10

JO - Frontiers in Genetics

JF - Frontiers in Genetics

SN - 1664-8021

M1 - 1027

ER -