Integrating Biopathway Databases for Large-scale Modeling and Simulation

Biopathway databases have been developed, such as KEGG and EcoCyc, that compile interaction structures of biopathways together with biological annotations. However, these biopathways are not directly editable and simulatable. Thus, we have made an application, the Biopathway Executer (BPE), that reconstructs these two major biopathway databases to XML formats of modeling and simulation platforms. BPE is developed with JAVA and has a database of executable biopathways that integrates some parts of biopathway information, KEGG and BioCyc, and other databases, e.g. MIPS and BRENDA. Currently, BPE employs the XML format (GONML) of a Hybrid Functional Petri net (HFPN) for the output. The features of HFPN are: (i) biopathways that contain discrete and continuous processes can be modeled, (ii) all biopathways that are modeled with ordinary differential equations (ODEs) can be remodeled, (iii) biopathways can be modeled while keeping readability by human. Other XML formats of biopathways, SBM...

• Type: Conference
• Year: 2004
• Where: APBC
• Authors: Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
• Keywords: APBC 2004, APBC 2007, Biopathway Databases, Major Biopathway Databases, XML Formats