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Derek Wright, Tim Angus and Tom C. Freeman (The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG. Scotland)
BioLayout Express3D 3.2 adds parser for BioPAX Level 3 community standard pathway language and Pathway Commons CPath2 web service client.We developed the mEPN graphical notation scheme to depict complex pathways.Existing mEPN glyphs were mapped to BioPAX equivalents and new glyphs were added for compatibility.BioLayout parses BioPAX RDF/OWL using PaxTools library and constructs a network of BioPAX Entities represented by mEPN glyphs,providing consistent visualization with existing mEPN pathways.We adapted the Fast Multipole Method force-directed layout algorithm to 3D (FM3).This provides superior performance compared to Fruchterman-Reingold,rapidly producing elegant and structured networks.FM3 produces excellent layouts for BioPAX,allowing large networks to be informatively visualized.Class Viewer provides detailed information about BioPAX features. Pathway Commons is a linked dataset combining pathway and interaction data from a range of databases.BioLayout searches and performs graph queries across this dataset and downloads BioPAX as RDF/OWL.Interoperability with BioPAX and data import enhances BioLayout Express3D as a fully featured pathway-modelling suite.Available April 2014.