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Technology and Code ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01027

XitoSBML: a modeling tool for creating spatial SBML models from microscopic images

Kaito Ii1, Kota Mashimo1, Mitsunori Ozeki1,  Takahiro G. Yamada1,  Noriko F. Hiroi2 and  Akira Funahashi3*
  • 1Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Japan
  • 2Laboratory of Physical Chemistry for Life Science, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Japan
  • 3Dept. of Biosciences and Informatics, Keio University Shonan Fujisawa Campus, Japan

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 XitoSBML is confirmed to run on most 32/64-bit operating systems: Windows, MacOS, and Linux.

Keywords: Spatial Model Simulation, spatial modeling, SBML, ImageJ, image processing

Received: 25 Mar 2019; Accepted: 24 Sep 2019.

Copyright: © 2019 Ii, Mashimo, Ozeki, Yamada, Hiroi and Funahashi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Akira Funahashi, Keio University Shonan Fujisawa Campus, Dept. of Biosciences and Informatics, Kanagawa, 223-8522, Kanagawa, Japan,