Systems biology model repository for macrophage pathway simulation

Masao Nagasaki; Ayumu Saito; André Fujita; Georg Tremmel; Kazuko Ueno; Emi Ikeda; Euna Jeong; Satoru Miyano

doi:10.1093/bioinformatics/btr173

Systems biology model repository for macrophage pathway simulation

Masao Nagasaki, Ayumu Saito, André Fujita, Georg Tremmel, Kazuko Ueno, Emi Ikeda, Euna Jeong, Satoru Miyano

Tohoku Medical Megabank Organization (ToMMo)

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

The Macrophage Pathway Knowledgebase (MACPAK) is a computational system that allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways. It integrates the knowledge of 230 reviews that were carefully checked by specialists for their accuracy and then converted to 230 dynamic mathematical pathway models. MACPAK comprises a total of 24009 entities and 12774 processes and is described in the Cell System Markup Language (CSML), an XML format that runs on the Cell Illustrator platform and can be visualized with a customized Cytoscape for further analysis.

Original language	English
Article number	btr173
Pages (from-to)	1591-1593
Number of pages	3
Journal	Bioinformatics
Volume	27
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btr173
Publication status	Published - 2011 Jun

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr173

Cite this

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AU - Nagasaki, Masao

AU - Saito, Ayumu

AU - Fujita, André

AU - Tremmel, Georg

AU - Ueno, Kazuko

AU - Ikeda, Emi

AU - Jeong, Euna

AU - Miyano, Satoru

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AB - The Macrophage Pathway Knowledgebase (MACPAK) is a computational system that allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways. It integrates the knowledge of 230 reviews that were carefully checked by specialists for their accuracy and then converted to 230 dynamic mathematical pathway models. MACPAK comprises a total of 24009 entities and 12774 processes and is described in the Cell System Markup Language (CSML), an XML format that runs on the Cell Illustrator platform and can be visualized with a customized Cytoscape for further analysis.

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Systems biology model repository for macrophage pathway simulation

Abstract

ASJC Scopus subject areas

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