XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images
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Updated: Jan 3, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Kaito Ii1, Kota Mashimo1, Mitsunori Ozeki1
1Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, 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.

