Department of Bioinformatics – BiGCaT

Tools/Software


This a list of BiGCaT core projects. Click here for a comprehensive list of projects.

High-throughput data analysis pipelines

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

Identifier Mapping

  • BridgeDb: identifier mapping framework for bioinformatics applications

Arrayanalysis.org

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.

Website

http://www.arrayanalysis.org/

The Phenotype Data Infrastructure

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.

Website

http://www.dbnp.org/

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

Open PHACTS

Bringing together pharmacological data resources in an integrated, interoperable infrastructure

About

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.

Website

Structuring and collecting biological processes in WikiPathways

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)