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Shared Data and Resources

Pacific Northwest National Laboratory (PNNL) offers resources to facilitate research conducted by members of the systems biology community. Our single-chain antibody library is available to scientists whose research or teaching is U.S. Government related. We also provide free proteomics and bioinformatics tools for all researchers to download.

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Biological & Environmental Research

With the support of DOE's Genomics:GTL program, PNNL staff are developing, operating, and building on existing high-throughput proteomics measurement capabilities to support a growing set of DOE/Office of Biological and Environmental Research scientists.

Learn more about PNNL's Biological & Environmental Research and available software, such as Time-Course Analysis, as well as datasets, such as for Shewanella oneidensis.

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Biological MS Data and Software Distribution Center

The Biological MS Data and Software Distribution Center at PNNL provides information and software tools related to mass spectrometry and separations projects.

Learn more about the Biological MS Data and Software Distribution Center and register to download featured tools, fasta file/protein sequence/protein database-related software, MS/MS analysis tools, MS analysis tools, data analysis and data presentation tools, mass spectrometry auxiliary tools, and MS data file utilities.

Bioinformatics Resource Manager

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The BRM architecture; BRM was highlighted in the March 2006 issue of Scientific Computing.

Contact: Katrina Waters

Bioinformatics Resource Manager (BRM) seamlessly connects researchers; data sources, including data in private, publicly available, and custom in-house formats; and commercial and private bioinformatic tools. BRM allows biologists to use efficiently analytic techniques that are otherwise costly, time-consuming, require expertise in bioinformatics and statistics, and require knowledge of data sources.

An article on BRM was featured in the March 2006 issue of Scientific Computing.

Learn more about BRM, and download the software for free.

Collective Analysis of Biological Interaction Networks

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CABIN uses interactive visual interfaces.

Contact: Mudita Singhal

The Collective Analysis of Biological Interaction Networks (CABIN) was developed as a plug-in to Cytoscape, which is an open source network visualization and analysis tool. CABIN promotes analytical reasoning for integrating evidence of interaction data from multiple sources by the use of interactive visual interfaces. It facilitates integration and analysis of evidence from multiple prediction and experimental sources, such as Gene Neighborhood-GN, Gene Cluster-GC, Phylogenetic Profiles-PP, Rosetta Stones-RS, BIND, and DIP. Multiple coordinated views within CABIN foster exploratory data analysis by users, accommodating expert domain knowledge.

Learn more about CABIN, and download the software for free.

Experimental Data Management System (EDMS)

The EDMS is a web-based portal for the storage, organization, and management of high-throughput biological data. EDMS has been developed as a part of internal research initiatives in Systems Biology and Data Intensive Computing at the Pacific Northwest National Laboratory (PNNL).

Learn more about EDMS and how to access the database.


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ProMAT was spotlighted by Science magazine's NetWatch in June 2006.

Contact: Amanda White

The Protein Microarry Analysis Tool (ProMAT) was designed for use with enzyme-linked immunosorbent assays to analyze protein microarray data. ProMat yields protein concentration values and statistically significant information about data quality in HTML format for researchers to view and share data easily.

ProMAT was featured in Science magazine's NetWatch in June 2006, and an article about ProMAT was published in the May 2006 edition of Bioinformatics.

Learn more about ProMAT, and download the software for free.

Proteomics Research Resource for Integrative Biology Software

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Tools developed as part of the Resource enhance LC-MS data analysis.

The Proteomics Research Resource for Integrative Biology is a national user facility established and funded by the National Center for Research Resources component of the National Institutes of Health. The Resource is housed in the Environmental Molecular Sciences Laboratory (EMSL) at PNNL.

As part of the Resource, many sophisticated Software and Tools for proteomics have been developed and are available for download. Software and tools developed as part of the Resource manage and process high-throughput proteomic data, interpret mass spectra, visualize and characterize features detected during liquid chromatography-mass spectrometry (LC-MS) analysis, as well as calculate molecular weights of chemical formulas and amino acids.

Antibody Library
The antibody library is a 2004 R&D100 Award Winner!

Single-Chain Antibody Library

Contact: Cheryl Baird

PNNL researchers cloned a library of 109 human antibody scFv fragments expressed on the surface of yeast cells using a platform designed by collaborator Dane Wittrup of the Massachusetts Institute of Technology. This yeast library is the first nonimmune antibody library to be cloned, expressed, and screened on the yeast surface, and it is the largest reported yeast expression library of any kind.

Learn more about the single-chain antibody library.

Software Environment for Biological Network Inference (SEBINI)

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The start of a SEBINI table.

Contact: Ron Taylor

Researchers at PNNL created a the SEBINI software platform that provides an interactive environment for the deployment and evaluation of algorithms used to reconstruct the structure of biological regulatory and interaction networks.

Learn more about SEBINI and visit the demonstration web site.

Support Vector Machine (SVM)-based tool to detect Homology Using Semi-supervised iTerative LEarning(SVM-HUSTLE)

Contact: Anuj Shah

The Support Vector Machine (SVM)-based tool to detect Homology Using Semi-supervised iTerative LEarning (SVM-HUSTLE) identifies significantly more remote homologs than current state-of-the-art sequence or cluster-based methods.

Learn more about SVM-Hustle and download the free software.

Systems Biology at PNNL

Research & Capabilities