Summary of ssbd-repos-00013

SSBD:database
URL

Name
ssbd-repos-00013 (13-Watabe-MolDyn)
URL
DOI
-

Title
-
Description
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Submited Date
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Release Date
2016-01-18
Updated Date
2018-11-15
License
Funding information
-
File formats
Data size
151.4 GB

Organism
D. discoideum, R. norvegicus
Strain
PC-12
Cell Line
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Genes
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Proteins
ERK, PTEN

GO Molecular Function (MF)
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GO Biological Process (BP)
cellular protein localization
GO Cellular Component (CC)
NA
Study Type
-
Imaging Methods
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Method Summary
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Related paper(s)

Masaki Watabe, Satya N V Arjunan, Seiya Fukushima, Kazunari Iwamoto, Jun Kozuka, Satomi Matsuoka, Yuki Shindo, Masahiro Ueda, Koichi Takahashi (2015) A Computational Framework for Bioimaging Simulation., PloS one, Volume 10, Number 7, pp. e0130089

Published in 2015 (Electronic publication in July 6, 2015, midnight )

(Abstract) Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of biomolecules. However, there still remain formidable challenges in bridging the gap between bioimaging and mathematical modeling. Generally, measurements using fluorescence microscopy systems are influenced by systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics. Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages. Computational tools for such a comparison are still unavailable. Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems. Simulation using this framework can generate digital images of cell simulation results after accounting for the systematic effects. We then demonstrate that such a framework enables comparison at the level of photon-counting units.
(MeSH Terms)

Contact(s)
Koichi Takahashi
Organization(s)
RIKEN , Quantitative Biology Center , Laboratory for Biochemical Simulation
Image Data Contributors
Quantitative Data Contributors

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