The Computational Genomics Resource Laboratory is part of the QB3 at the University of California Berkeley.
The CGRL aims to provide:
• Computational infrastructure for data analysis
• Training in analytical tools for next-generation sequence data
• Project-specific consultation on experiment design and analysis
CGRL facilitate research programs employing computational biology with computational infrastructure for data analysis, training in analytical tools for next-generation sequence data, and project-specific consultation on experiment design and analysis. The cluster hardware capabilities include Centos 5.6 using Perceus and has various analysis software for next gen sequencing including packages for RNASeq, CHIPSeq, De Novov Asssembly – Galaxy, Cutadapt, Trim Galore, FastQC, FastX, BWA, Bowtie, Tophat, MAQ, Bismark, BLAST, BLAT, QiimeUSEARCH, GMAP, MUMmer.
The National Center for Supercomputing Applications (NCSA) is a hub of interdisciplinary research and digital scholarship. The Center provides computing, data, networking, and visualization resources and services that help scientists, engineers, and scholars at the University of Illinois at Urbana-Champaign and across the country better understand our world.
Established in 1986 as one of the original sites of the National Science Foundation's Supercomputer Centers Program, NCSA is supported by the state of Illinois, the University of Illinois, the National Science Foundation, and grants from other federal agencies.
The High Performance Biological Computing Center (HPCBio) is a collaborative effort between multiple partners in the University of Illinois Urbana-Champaign community. It is administratively attached to the Roy J. Carver Biotechnology Center, and incorporates the Center’s Bioinformatics Unit. It is strongly anchored in the genomics research agenda of the Institute for Genomic Biology (IGB), and in particular in its Genomic Technology program area. It builds on the research expertise of IGB faculty and affiliates. The National Center for Supercomputing Applications (NCSA) provides high-level technical expertise in high-performance computing.
The primary mission of the Illinois Simulator Laboratory at the University of Illinois Urbana-Champaign is to support the integration of advanced technologies so that Institute researchers can conduct experiments in human multi-modal perception and cognition. To facilitate this mission, the Illinois Simulator Laboratory maintains discrete laboratories allowing the incorporation of individualized multimodal control and monitoring technologies into advanced visualization environments, both immersive and ultra-high resolution. In fulfilling that mission, the Illinois Simulator Laboratory has become a world-recognized leader in creating and applying pc cluster-based computer technologies to graphics-intensive applications. As a core facility of the Beckman Institute, the Illinois Simulator Laboratory provides fertile environments for interdisciplinary research across the four Main Research Themes
The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory is the largest facilities in the world devoted to providing computational resources and expertise for basic scientific research, NERSC is a world leader in accelerating scientific discovery through computation. Edison is NERSC's newest supercomputer, a Cray XC30, with a peak performance of 2.57 petaflops/sec, 133,824 compute cores, 357 terabytes of memory, and 7.56 petabytes of disk-based storage.
The Pitzer Center for Theoretical Chemistry at the University of California Berkeley contains state-of-the-art computer resources that serve the needs of the 7 theory groups. These are typically Linux or Unix clusters that consist of between 30 and 70 processors. A survey of the groups in summer 2004 showed that in aggregate, we have well over 500 processors in total.
The Center for Computational Biology at University of California Berkeley was established in 2003 through the Chancellor’s New Ideas Initiative, an outgrowth of the 2002 Strategic Academic Plan, to expand the research base at the University and produce the next generation of leaders in the fundamental and applied biological sciences. Administratively housed in the Berkeley component of the California Institute for Quantitative Biosciences (QB3), the mission of CCB is to support interdisciplinary research on the broad array of subjects that cover the interface between computation and biology, and to foster graduate and undergraduate education in the field.
Computational Research Division at Lawrence Berkeley National Laboratory conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. They collaborate directly with scientists across the Berkeley Lab, the Department of Energy and industry to solve some of the world’s most challenging computational and data management and analysis problems in a broad range of scientific and engineering fields, including materials science, biology, climate modeling, astrophysics, fusion science, and many others.
The Biosciences Computing Group is part of the Computational Research Division. BCG's mission is to address key data management challenges caused by the massive increase in the amount and range of biological data, the difficulty of quantifying the quality of data generated using inherently imprecise tools and techniques, and the high complexity of integrating data residing in diverse and sometimes poorly correlated repositories. BCG's strategy involves using existing database technologies and analysis methods, adapted as needed to a specific application, in order to address immediate biological data management and bioinformatics requirements.
Computational Chemistry, Materials & Climate is part of the Computational Research Division. The goal of this group is to enable scientific discovery through the development of advanced software applications, tools, and libraries in key research areas, as well as the development of scientific computing applications and capabilities for the integration and analysis of complex data from simulation and experiment
AMPLab is located at University of California Berkeley. Working at the intersection of three massive trends: powerful machine learning, cloud computing, and crowdsourcing, the AMPLab is integrating Algorithms, Machines, and People to make sense of Big Data. They are creating a new generation of analytics tools to answer deep questions over dirty and heterogeneous data by extending and fusing machine learning, warehouse-scale computing and human computation. They validate these ideas on real-world problems including participatory sensing, urban planning, and personalized medicine with their application and industrial partners.
The Statistical Computing Facility at University of California Berkeley is a unit of the academic Department of Statistics, formally organized in 1986. We provide computing, networking, and information resources to the community of students, faculty, and staff of the Statistics Department and the Econometrics Laboratory of the Department of Economics in support of the University's mission of teaching, research, and public service. It is staffed by a Systems Manager, a Statistical Computing Consultant, and UNIX System Administrator.
The Parallel Computing Institute at the University of Illinois Urbana-Champaign aims to build powerful and efficient infrastructure for computation-heavy applications, such as the ability to read MRI results in real-time, weather and disease prediction tools, individualized genomic analysis tools for targeted treatments, design tools for new nano-scale materials, ultra-realistic video gaming and videoconferencing, immersive reality and others.
Researchers from a variety of disciplines are collaborating to build new hardware and software that will enable more powerful and efficient computing for everything from multicore processors in commodity electronics to supercomputers with nearly a million processing elements.
PCI is developing solutions with greater impact for:
The Geospatial Innovation Facility (GIF) at the University of California Berkeley's College of Natural Resources provides leadership and training across a broad array of integrated mapping technologies. Our goal is to help people better understand the changing world through the analysis and visualization of spatial data. We develop engaging applications that leverage and build upon state-of-the-art geospatial and web technologies, and provide opportunities for researchers to learn how they can use spatial data to answer critical questions.