Tools

Prequips connects to a wide range of systems biology tools through the flexible Gaggle interface and to a collection of proteomics mass spectrometry software through its data providers. Below we list a few of the tools that we found useful in our work with Prequips and provide links to the relevant webpages.

Trans-Proteomic Pipeline

The Trans-Proteomic Pipeline (TPP) is a data analysis pipeline for the analysis of LC/MS/MS proteomics data. The TPP includes modules for validation of database search results, quantitation of isotopically labeled samples, and validation of protein identifications, as well as tools for viewing raw LC/MS data, peptide identification results, and protein identification results.

Prequips connects to the TPP through the mzXML, pepXML and protXML file formats.

• TPP Website

The Gaggle

The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data.

• Gaggle Website

Cytoscape

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

• Cytoscape Goose on the Gaggle Website
• Cytoscape Project Website

R

R is an open source software environment for statistical computing and graphics that includes a large variety of packages for data analysis in computational and systems biology.

• R Goose on the Gaggle Website
• R Project Website

MeV

TIGR MeV (Multiexperiment Viewer) is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. It's part of the TM4 software suite.

• MeV Goose on the Gaggle Website
• TM4 Software Suite Website

DAVID

DAVID (Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of tools for investigators to visually summarize annotation from large list of genes. Dozens of annotation types are available for analysis including Gene Ontology categories, KEGG and BioCarta pathway maps.

Lists of functional categories associated with a set of genes in a gene list can be sorted based on gene count or term co-occurrence probability, a method that has been shown to identify biological processes closely associated with a given experimental condition.

DAVID is accessed through the Firegoose, a Firefox plug-in that allows the Gaggle to exchange information with certain websites.

• Firegoose on the Gaggle Website
• DAVID website