Core Facilities

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

Center technology development is driven by the increasing biological complexity of scientific inquiry. Each Core is a venue for collaborative technology development and application in a variety of biological systems: Genomics, Proteomics, Microfluidics and Imaging and Informatics Cores.

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

Below are Center resources. A list of Institute for Systems Biology resources can be found on the Institute website.

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