Regulatory network operations in the Pathway Tools software

BMC Bioinformatics

Table 1 Major new features

Ontology classes	Compound-Mediated-Translation-Regulation (riboswitches)
	Allosteric-Regulation-of-RNAP
Visualizations	Regulation Summary Diagram (section The regulation summary diagram)
	Specialized Signaling Pathway display and editing (section Pathway diagrams)
	Port of Regulatory Overview (section Regulatory overview) to BioCyc website
Computational Analyses	Object Group Operations and Regulation Enrichment Analysis (section Object group operations and regulation-enrichment analysis) Export of Regulatory Network
	to XGMML (Cytoscape) (section Export to cytoscape) Ranking Genes According
	to Regulatory Influence (section Ranking genes according to regulatory influence)
	Web services access to regulatory data

Regulation-related features or capabilities described in this paper that are new in Pathway Tools since the last major Pathway Tools paper [1].