Core Facilities

The NIGMS award has funded the development of the Microfluidics and Imaging and Informatics Cores.

Publicly Available Resources

Gaggle	Database and software integration framework - The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data.	PMID: 18021453 Nitin Baliga
Peptide Atlas	Information resource - Atlas for human, mouse; yeast peptides from large set of tandem mass spectrometry data. Results processed through Trans-Proteomic Pipeline	PMID: PMC2373374 Eric Deutsch
Trans-Proteomic Pipeline	Data analysis software - a suite of software tools for the analysis of tandem mass spectrometry data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios.	PMID: 18212004 Eric Deutsch
NRC-1: Peptide Atlas	Data analysis software - A peptide atlas for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments.	PMID: PMC2643335 Nitin Baliga
Cytoscape	Data analysis - An open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.	PMID: PMC2478690 Ilya Shmulevich
Addama	Data management - An adaptable data management system designed to support the mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, and flow cytometry).	PMID: 19265554 Ilya Shmulevich
Simcluster	Data analysis - Designed to perform clustering analysis for data on the simplex space. Simcluster is a stand-alone command-line C package and user-friendly on-line tool.	PMID: PMC2147035 Ilya Shmulevich
ProbCD	Data analysis - An open source analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques, and (ii) probabilistic gene annotation.	PMID: PMC2169266 Ilya Shmulevich
ProbTF	Data analysis - A flexible, probabilistic framework to predict transcription factor binding from multiple data sources.	PMID: PMC2268002 Ilya Shmulevich