The BiGCaT core projects each have their own project page, which can be found here.
There are several tutorials available for these tools and software, which can be found here.
High-throughput data analysis pipelines
ArrayAnalysis: Quality Control, pre-processing, normalization and statistics of Affymetrix microarrays. ArrayAnalysis offers user-friendly solutions for gene expression data analysis, from raw data to biological pathways. It contains modules of three types that can be lauched individually or successively as an integrated workflow.
BridgeDb: identifier mapping framework for bioinformatics applications.
- Open PHACTS: Bringing together pharmacological data resources in an integrated, interoperable infrastructure. Open PHACTS started as an IMI-funded project to integrate data sources like ChEMBL, WikiPathways, Uniprot, and DisGenet to support drug discovery by the pharmaceutical industry.
The Phenotype Data Infrastructure
- DBNP: An open source application suite to store biological studies. The central module (GSCF) stores the study design, which links out to modules that contain the measurements of specific measurement platforms.
Semantic Web tools using RDF and SPARQL
Open PHACTS: drug discovery in industry, academia and for small businesses
WikiPathways RDF: SPARQL endpoint of WikiPathways to query pathway data
Structuring and collecting biological processes in WikiPathways
WikiPathways: Pathways for the People
Pathway analysis in PathVisio
PathVisio: a tool to edit and analyze biological pathways
Facilitating PathVisio use in familiar analytical environments :
GoElite: extended pathway and Gene Ontology analysis
Network Analysis with Cytoscape
CyTargetLinker: a generic Cytoscape app to build regulatory networks
SemScape: Visualizes Semantic Data Landscapes (Google Summer of Code project 2012)