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

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

JOURNAL=Frontiers in Genetics

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01027

DOI=10.3389/fgene.2019.01027

ISSN=1664-8021

ABSTRACT=<p>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 <uri xlink:href="https://github.com/spatialsimulator/XitoSBML/" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/spatialsimulator/XitoSBML/</uri>. XitoSBML is confirmed to run on most 32/64-bit operating systems: Windows, MacOS, and Linux.</p>