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 journalArticlepeer-review

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

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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