| Genome Informatics 14: 296--297 (2003) BPE: Biopathway Executer for Large-Scale Biopathway (2004) | |||||||||||||||
Abstract | |||||||||||||||
| Introduction Biopathway databases have been developed, such as KEGG [6] and EcoCyc [3], that compile interaction structures of biopathways together with biological annotations. However, these biopathways are not directly editable and simulatable. Thus, we are developing an application, the Biopathway Executer (BPE) [5], 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 di#erential equations (ODEs) can be remodeled, (iii) biopathways can be modeled while keeping readability by human. Other XM | |||||||||||||||
Publication details | |||||||||||||||
| |||||||||||||||