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Sources of ‘Pathway Data’ the literature (reviews) pathway databases • KEGG • NetPath • Upstate • Panther • Reactome • WikiPathways • GenMapp……. for comprehensive list see: http://www.pathguide.org/ interaction databases • BIND • String • Ingenuity…… gene lists • pathway membership – databases/array designs/reviews
4 views of apoptosis need for a standardised approach for presenting and modelling biological pathways
Page 1 and 2: BioLayout Express 3D visualisation
Page 3 and 4: PLoS Comp Biol. 3:2032-42 (2007) Na
Page 5 and 6: current capabilities • OS-indepen
Page 8 and 9: http://www.macrophages.com/pig-atla
Page 12 and 13: http://www.sbgn.org
Page 14 and 15: IFNB Pathway Diagram Interferon B (
Page 16 and 17: Framework Map of Macrophage Signall
Page 18 and 19: Integrated View of Macrophage Activ
Page 20 and 21: Petri nets • Petri nets were firs
Page 22 and 23: Conversion of mEPN concepts to Petr
Page 24 and 25: starting assumptions •the ‘rate
Page 26 and 27: Screenshot 2
Page 28: BioLayout Express 3D Team Roslin In

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