Faculty Mentor(s)

Dr. Matthew DeJongh, Hope College

Document Type


Publication Date



This material is based upon work supported by the National Science Foundation under grant No. MCB-0745100.


The goal of our research is to develop a plug-in for Cytoscape that will be used in tandem with the Model SEED Viewer to help biologists better understand and visualize the metabolic pathways of bacteria. The Model SEED is an online resource at www.theseed.org/models that provides biologists with a static but very detailed view of metabolic models. It uses KEGG (www.genome.jp) metabolic pathway maps which cannot be edited by users. This ability to edit metabolic pathways is one of our primary focuses in creating the plug-in – in particular, adding, removing, and moving reaction and compound nodes. Additionally, we want to fully integrate the plug-in with the Model SEED, including the ability to link back to the Model SEED via hyperlinks and laying out the model’s maps as they are seen in the Model SEED viewer so the user may easily recognize them and quickly find what they are looking for. To get the KEGG representation of these maps, we use the KGML reader for Cytoscape in addition to some of our own code to read KGML files containing the positions of each node and edge of the map. Another priority has been to limit the amount of information displayed to the user to just those compounds and reactions represented in the current organism’s metabolic model. Lastly, we have worked to implement a large variety of features aimed at improving the plug-in’s user friendliness, such as loading and saving of user-defined metabolic pathway map layouts, showing the user which nodes are connected to a node and whether or not they are in the current map, and a large number of smaller additions that work to simplify navigation and the appearance of the user interface.