Tools and Resources

Tools & Resources



PathVisio is a free open-source pathway analysis and drawing software that allows drawing, editing, and analyzing biological pathways. This tool is developed in Java and can be extended with plugins. PathVisio is the pathway editor for WikiPathways, a community-curated pathway database enabling collaborative pathway editing.

Collaboration: PathVisio is maintained by the Department of Bioinformatics (BiGCaT) at Maastricht University. 

Project architects: Martina Summer-Kutmon (MaCSBio, former BiGCaT)


BridgeDb is a framework to map identifiers between various biological databases and related resources. These mappings are provided for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. BridgeDb includes a Java library that provides an API for programmatic access.

Collaboration: PathVisio is maintained by the Department of Bioinformatics (BiGCaT) at Maastricht University, Gladstone Institutes, Heriot Watt University, University of Manchester.

Project architects: Egon Willighagen, Denise Slenter, Luc de Meyer, Marvin Martens, Tooba Abbassi-Daloii, Helena Basaric (BiGCaT)

Chemistry Development Kit (CDK)

The Chemistry Development Kit (CDK) is a open science cheminformatics toolkit founded in 2000 and written in the Java programming language. It provides cheminformatics functionality for 2D and 3D structure, various input/output formats like molfiles and SMILES, and can be used in multiple languages, including Python.

Collaboration: The CDK PathVisio is an international open science project with more than 100 contributors from academia and industry.

Project architects: Egon Willighagen


CyTargetLinker is a Cytoscape app that allows extending networks with additional nodes. In biomedical research context, these nodes can be transcription factors (Linkset: ENCODE), miRNA (Linksets from MirTarBase, TransMir, TargetScan or MirBase), chemical compounds (Linksets: DrugBank, CTD, ChEMBL), molecular pathways (Linksets: WikiPathways, REACTOME), or diseases (Linkset: Orphanet, OMIM)

BiGCaT members involved:

- Martina Kutmon

- Susan Coort

- Friederike Ehrhart

- Egon Willighagen