Martijn van Iersel PathVisio & WikiPathways BiGCaT Bioinformatics Maastricht University

Pathway editor

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

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

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

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

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

2. Visualization of (Dynamic) Data

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

4. Model Comparison & Exchange

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