The PathSBML plugin allows researchers to visualize and overlay data on the same pathway models they use in simulation experiments. Exporting these models as GPML would also allow them to be uploaded to Wikipathways for community curation.
PathVisioRPC is an XML-RPC interface for PathVisio. It allows users to use PathVisio functionality directly in their favourite analytical environment,
License: Apache License
This plugin allows users to create pathway diagrams in the Systems Biology Graphical Notation (SBGN). A description of this standard notation can be found here: http://www.sbgn.org/Main_Page.
Basic GeneOntology plugin to create GO pathways visualizing all genes annotated with a specific term or its one of its subterms. The terms are structured hierarchically. All genes are annotated and data can be automatically visualized on them.
The MAPPBuilder plugin helps you get started quickly on creating a new pathway. Given a list of gene identifiers, MAPPBuilder will build a simple prototype pathway for you containing those genes, eliminating the step of manual searching for each gene/gene product you want to include.