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PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University

PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University. Martijn van Iersel. Pathway editor. WikiPathways. Resource for biological pathways Free and open source Wiki, editable by users. Pico, Kelder et al., PLoS Biology, 2008. PathVisio. Pathway editor

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PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University

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  1. PathVisio & WikiPathwaysBiGCaT BioinformaticsMaastricht University Martijn van Iersel

  2. Pathway editor

  3. WikiPathways • Resource for biological pathways • Free and open source • Wiki, editable by users Pico, Kelder et al., PLoS Biology, 2008

  4. PathVisio • Pathway editor • High-throughput data visualization • Plugin framework • Compatible with http://www.pathvisio.org Van Iersel et al., BMC Bioinformatics. 2008 Sep 25;9(1):399.

  5. BridgeDb for ID mapping Entrez Gene 3643 BridgeDb Affymetrix probeset 100234_at Van Iersel et al., BMC Bioinformatics. Jan 2010;11:1.

  6. Applications for Modeling • Visualization of models (SBGN) • Visualization of (dynamic) data inside models • Creation of models (Explicit MIM) • Model comparison & Exchange (MIRIAM)

  7. 1. Visualization of Models Systems Biology Graphical Notation (SBGN) Graphical companion to SBML Glycolysis in SBGN

  8. 2. Visualization of (Dynamic) Data

  9. 3. Creation of Models (explicit MIM) AKT-Cyclin D1 Interactions as MIM in Pathvisio

  10. 4. Model Comparison & Exchange

  11. Contributors • NIH • Mirit Aladjem • Margot Sunshine • Augustin Luna • Pharmgkb • Mark Woon • Rebecca Tang • Summer of code • Jianjiong Gao • Adem Bilican • TNO Food & Nutrition • Susan Wopereis • Jildau Bouwman • Ben van Ommen • Gladstone Institutes • Alexander Pico • Kristina Hanspers • Nathan Salomonis • Bruce Conklin • Oregon State University • Pankaj Jaiswal • Justin Elser • Maastricht University • Chris Evelo • Susan Coort • Andra Waagmeester • Stan Gaj • Thomas Kelder • Martijn van Iersel

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