Maastricht University, The Netherlands

Software Tools and Services

High-throughput data analysis pipelines:

  • ArrayAnalysis: Quality Control, pre-processing, normalization and statistics of Affymetrix microarrays

Semantic Web tools using RDF, ontologies and SPARQL:

  • Open PHACTS: Platform to reduce barriers in drug discovery
  • WikiPathways RDF: SPARQL endpoint of WikiPathways to query pathway data
  • rrdf: a R package to handle RDF data
  • ops4j: java Client library for Open PHACTS servers
  • ropenphacts: a R package to interact with Open PHACTS servers

Cheminformatics software:

Interoperability of Biological data:

  • BridgeDb: database identifier mapping framework for bioinformatics applications
  • BridgeDbR: R package that exposes BridgeDb functionality
  • Metabolite identifier mapping database (HMDB + ChEBI)
  • Interaction identifier mapping database (EBI-Rhea)

Structuring and collecting biological processes in WikiPathways:

Pathway and network analysis in PathVisio and Cytoscape:

  • GoElite: extended pathway and Gene Ontology analysis
  • Apps for Cytoscape:
    • CyTargetLinker: a generic Cytoscape app to build regulatory networks
    • SemScape: Visualizes Semantic Data Landscapes (Google Summer of Code project 2012)