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.
Highlights
With the recent development of imaging technologies, we can quantitatively analyze spatial localization and concentration gradients of biochemicals within living cells (Chen et al, 2014; Keller and Ahrens, 2015)
The JSBML application programming interface (API) converts the processed images to a spatial SBML model, which is converted to an SBML Level 3 Version 1 object that can be modified through the XitoSBML graphical user interface (GUI)
We present the result of a spatial model simulation with a spatial model exported from XitoSBML to validate the usefulness of the obtained spatial model
Summary
With the recent development of imaging technologies, we can quantitatively analyze spatial localization and concentration gradients of biochemicals within living cells (Chen et al, 2014; Keller and Ahrens, 2015). The importance of biochemical spatial localization and concentration gradients has become apparent. The effect of dynamics related to biochemical spatial distribution and cellular shape can be analyzed by using spatial model simulations (Rangamani et al, 2013). In most spatial model simulations, cellular regions are defined as two- or threedimensional spatial models based on simple mathematical equations. Because cell shape in such models differs from actual cells, these simulations will not produce appropriate results. It is crucial to perform three-dimensional spatial model simulations by using spatial models with the actual cellular shape
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