Integrating biopathway databases for large-scale modeling and simulation

• Authors: Masao Nagasaki;Atsushi Doi;Hiroshi Matsuno;Satoru Miyano
• Venue: APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
• Year: 2004

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, SBML and CellML are subsets of GONML. Thus, BPE can bridge major biopathway databases and major modeling and simulating softwares. To demonstrate the effectiveness/usability of BPE, four examples are created and simulated on Genomic Object Net which is based on the HFPN architecture; (i) executable KEGG maps while keeping the features of original maps, (ii) executable BioCyc maps while keeping the features of original maps, (iii) large-scale editable and simulatable KEGG metabolic pathways, (iv) a metabolic pathway with gene regulatory networks. These examples show that BPE is a useful tool for integrating biopathway databases for largescale modeling and simulation.