Systems biology model repository for macrophage pathway simulation | Zendy

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

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Systems biology model repository for macrophage pathway simulation

Author(s) -

Masao Nagasaki,

Ayumu Saito,

André Fujita,

Georg Tremmel,

Kazuko Ueno,

Emi Ikeda,

Euna Jeong,

Satoru Miyano

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr173

Subject(s) - markup language , xml , computer science , license , systems biology , pathway analysis , sbml , macrophage , world wide web , computational biology , software engineering , database , biology , operating system , biochemistry , gene expression , gene , in vitro

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 24 009 entities and 12 774 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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