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Martijn van Iersel PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University.

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Presentation on theme: "Martijn van Iersel PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University."— Presentation transcript:

1 Martijn van Iersel PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University

2 Pathway editor

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

4 PathVisio Pathway editor –High-throughput data visualization –Plugin framework –Compatible with Van Iersel et al., BMC Bioinformatics Sep 25;9(1):399.

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

6 1.Visualization of models (SBGN) 2.Visualization of (dynamic) data inside models 3.Creation of models (Explicit MIM) 4.Model comparison & Exchange (MIRIAM) Applications for Modeling

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  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  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


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