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

Front Genet. 2019 Oct 22:10:1027. doi: 10.3389/fgene.2019.01027. eCollection 2019.

Authors

Kaito Ii¹, Kota Mashimo¹, Mitsunori Ozeki¹, Takahiro G Yamada¹, Noriko Hiroi^{1

2}, Akira Funahashi¹

Affiliations

¹ Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
² Laboratory of Physical Chemistry for Life Science, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda City, Japan.

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.