Map builder
Overview
Map builder window create XML files for FCModeler. It is a Java version of MapBuilder.
Build new XML files
First, the user click "retrieve pathway" button. The program will display all pathway names in MetNetDB. The user can check those pathways that need to be exported in XML files. Then the user need click "retrieve trivial node" to get a list of small molecular compounds. Since those compounds will be involved in many chemical reactions, it is better to duplicate them to prevent distorted graph layout of pathways. The user check those compounds need to be duplicate in layout. Finally, the user choose the mode of building. By default, the program export the network without transcriptions. "Simple mode" only exports metabolite networks. "Gene mode" exports all information including transcription. "Keep XML" will not remove the intermediate XML files. Normally, the program only export compressed XML files in zip format. When all setting are determined, the user can click "build" button to generate XML files for FCModeler.