Martijn van Iersel

PathVisio & WikiPathways

BiGCaT BioinformaticsMaastricht 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. 2008 Sep 25;9(1):399.

http://www.pathvisio.org

BridgeDb for ID mapping

BridgeDb

Entrez Gene 3643

Affymetrix probeset 100234_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