Blue Gene is an IBM Research project dedicated to exploring the
frontiers in supercomputing: in computer architecture, in the software required to program and control massively parallel systems, and in the use of computation to advance our understanding of important biological processes such as protein folding.

The Blue Gene/L machine was designed and built in collaboration with the Department of Energy's NNSA/Lawrence Livermore National Laboratory in California, and the LLNL system has a peak speed of 596 Teraflops. Blue Gene systems occupy the #4 (LLNL Blue Gene/L) and #5 (Argonne Blue Gene/P) positions in the TOP500 supercomputer list announced in November 2008.

IBM now offers a Blue Gene Solution. IBM and its collaborators are currently exploring a growing list of applications including hydrodynamics, quantum chemistry, molecular dynamics, climate modeling and financial modeling.

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The Proteomics Research Center at the University of Toronto involves the close interdisciplinary collaboration of a team of highly skilled and motivated investigators who are expert in model organism biology, protein biochemistry, protein mass spectrometry, functional genomics, computational biology and informatics.

The focus and long-term objectives of the Proteomics Research Center (PRC), are to develop a fully integrated experimental framework for researchers to systematically address the complexities of protein function and cellular networks using advanced and complimentary experimental approaches and technologies.

The Computational Proteomics Laboratory (CPL) at Fred Hutchinson Cancer Research Center (FHCRC) develops and uses computational approaches for protein and proteomics research. As Principal Investigator, Dr. Martin McIntosh leads the CPL's substantive research, which centers on serum proteomics for disease detection and classification. The CPL also collaborates with other researchers at the FHCRC and around the world on a variety of bioinformatics projects.

The Australian Proteome Analysis Facility (APAF Ltd) is Australia’s premier proteomics institution.

APAF Ltd was the birthplace of the term proteomics in 1995 and the first high throughput lab worldwide. APAF research and development has continued in all areas of technology development and industry, providing world leading advances and services for over a decade.

Proteomics is the study and identification of the thousands of types of proteins found in humans, plants, animals, bacteria and other life forms, and the expression of particular proteins can be used as “biomarkers” of health, disease and/or quality.

APAF is the leading proteomics service provider nationally. Additionally APAF is a developer of new technologies for protein discovery - continually forming new collaborations with research groups throughout the Australian and international biotechnology communities.

APAF is a member of Proteomics Australia (PA) and is one of five (5) nodes. Each node possess synergistic technologies and expertise enabling the consortium to offer a far broader range of services to our collaborators and returning maximum return on the investment of Australians in this venture. PA includes nodes located at:

• Macquarie University
• Monash University
• Queensland Institute of Medical Research
• TGR BioSciences Pty Ltd (Adelaide)
• University of New South Wales

The computational mass spectrometry group, headed by Professors Vineet Bafna and Pavel Pevzner, focuses on developing algorithms to process mass spectrometry data. In our lab we have developed a number of tools for computational proteomics. Each one has it's own purpose and setting. These tools are free for download, or are also integrated into a web server.

The Proteome Exploration Laboratory (PEL) at the Beckman Institute at the California Institute of Technology was founded with a grant from the Moore Foundation to Prof. Deshaies in 2006. After a nationwide search Dr. Sonja Hess from NIDDK was appointed to direct the PEL.

The PEL is performing state-of-the-art research in proteomics-based mass spectrometry. We plan to collaborate with California Institute of Technology scientists from various backgrounds. By nature, the level of collaboration varies from project to project. However, to achieve best results, we encourage you to contact us as early as possible to delineate the best avenues for a particular project.

New and existing users, please visit our User sites.

The Proteome Informatics group is part of the Swiss Institute of Bioinformatics (SIB). The group focuses its activities on the development of software tools and databases for proteomics. Besides teaching activities of the PIG members, in particular within the Master's Degree in Proteomics and Bioinformatics, three axes of research and services have been pursued since the creation of the SIB. Some of these activities have been ongoing since 1984.

We are a bioanalytical laboratory that develops separation science and mass spectrometric methods to solve biological problems of interest to us and our collaborators. In general we seek to use mass spectrometry to extract the maximum amount of information with a minimum of fractionation prior to MS analysis, which we refer to as Indolent Driven Science. Our primary tool is mass spectrometry and specifically Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). We have upgraded an older Bruker APEX III FTICRMs instrument to allow electron capture dissociation (ECD) with infrared multi-photon dissociation (IRMPD) as well as collision induced dissociation of ions in quadrupoles located prior to the ICR cell. Additionally, we have implemented a simple version of Dynamic Range Expansion Applied to Mass Spectrometry (DREAMS) developed by the R.D. Smith laboratory on this instrument. We are currently pursuing data-independent analysis of complex mixtures using a protocol we refer to as Precursor Acquisition Independent From Ion Count (PAcIFIC; see Panchaud Anal Chem 2009) that is related to a type of data produced by a novel tandem mass spectrometer (see Wang RCMS 2007). Most recently we implemented an ion funnel on our Thermo LTQ-FT instrument (see Kelly et al. Mass Spectrom Rev 2009). Other work horse instruments in the laboratory include a Waters SYNAPT, a Thermo LTQ-Velos and a Thermo LTQ-Orbitrap all fitted with Waters NanoAcquity HPLCs. We are applying these and other technologies with our collaborators who are in the fields of microbiology, prostate cancer, urinary track disorders, HIV and fatigue, acute respiratory distress syndrome, and pediatric medulloblastomas. Finally, we are part of the University of Washington's Proteomics Resource**** (UWPR) consortium developed to aid proteomics research on campus.

The Institute for Systems Biology was co-founded in 2000 by Alan Aderem, Ruedi Aebersold, and Leroy Hood. In just 10 years it has grown to more than 300 staff members, including 13 faculty members and their laboratory groups. This pioneering approach to the study of biological systems takes place in the institute's 65,000-square-foot facility in Seattle.

Building a new kind of research institute — one that can tackle the multi-disciplinary challenges of systems biology – requires a strategy that itself integrates many sciences including biology, chemistry, physics, computation, mathematics and medicine. Because the field of systems biology requires the seamless integration of these disciplines, ISB has developed a philosophy, an environment, and an administrative structure that transcends traditional organizational and disciplinary barriers. Scientists collaborate across their specialties to leverage knowledge and expertise with others at the Institute and in academia and industry.

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