The Gaggle: An open-source software system for integrating bioinformatics software and data sources. - Paul T. Shannon; David J. Reiss; Richard Bonneau; Nitin S. Baliga (BMC Bioinform., 2006)

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. - J. Christopher Bare; Paul T. Shannon; Amy K. Schmid; Nitin S. Baliga (BMC Bioinform., 2007)

RCytoscape: tools for exploratory network analysis. - Paul T. Shannon; Mark L. Grimes; Burak Kutlu; Jan J. Bot; David J. Galas (BMC Bioinform., 2013)