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Institute for Systems Biology Uses Complete Genomics’ Human Genome Sequencing Service to Verify Gene Responsible For Miller Syndrome; Results Published in Science PDF Print E-mail
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Written by Chris O'Neal   
Wednesday, 10 March 2010 17:20
Complete Genomics today announced that the Institute for Systems Biology (ISB) employed Complete Genomics’ human genome sequencing service to sequence a family quartet to determine the depth of genetic information possible in analyzing a full family’s sequence, and to verify the gene responsible for Miller syndrome, a rare craniofacial disorder. Results from this collaboration will be published online later today in the journal Science; the manuscript is titled “Analysis of Genetic Inheritance in a Family Quartet by Whole Genome Sequencing.”

“We are convinced that this new kind of analysis, family sequencing, will be a remarkably powerful scientific and medical tool in the future. ISB was delighted to work closely with the group at Complete Genomics to generate the data that enabled us to complete this study,” said David Galas, professor and senior vice president of ISB.

ISB used Complete Genomics’ service to sequence the genomes of a four-member nuclear family in which the two children suffer from Miller syndrome and ciliary dyskinesia, a lung disorder similar to cystic fibrosis, but neither parent is affected. The goal of this study was to identify rare genetic variations that could be responsible for Miller syndrome, and to estimate the intergenerational mutation rate.

Complete Genomics sequenced the four genomes to a depth of 51x to 88x, and 85-92% of the bases in each genome were called. A comparative analysis of the four genomes yielded four genes consistent with recessive inheritance of rare variations. One of these genes, DHODH, was concurrently identified as a cause of Miller syndrome [Nat Genet. 2010 Jan;42(1):13-4]. Mutations in a second gene, DNAH5, have previously been shown to cause primary ciliary dyskinesia.

“When we established Complete Genomics, our goal was to provide large-scale complete human genome sequencing as a service that would enable our customers to make medically relevant discoveries. We are delighted that ISB is already making breakthroughs of that caliber from its first study using our service,” said Dr. Clifford Reid, chairman, president and CEO of Complete Genomics. “This is the type of positive disruptive influence that we want our technology to have on medical research.”

By providing a turnkey, outsourced complete human genome sequencing service, Complete Genomics provides researchers with research-ready data directly from DNA samples.

Customers send their DNA samples to Complete Genomics, which handles all the genome sequencing, data management and analysis. In return, customers receive their assembled sequences and variant reports including a functional annotation report. This annotation report describes the changes to gene products that each variation had caused, as well as annotations of the detected variations against public databases (dbSNP in particular), thus enabling comparison with other data.

Last Updated on Wednesday, 10 March 2010 17:26
 
DataDirect Networks to Speak at XGen Congress, the Premier Conference for Next-Generation Genomic Technologies PDF Print E-mail
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Written by Tyler O'Neal   
Wednesday, 10 March 2010 12:57

Storage Experts to Discuss Challenges and Solutions for High-Throughput Sequencing and Next-Generation Cloud Storage Initiatives

DataDirect Networks (DDN) today announced its participation in the world's premier conference for sequencing data storage and analysis -- the Cambridge Healthtech Institute's XGen Conference, held on March 15-19 in San Diego.

Around the world, next-generation gene sequencing and analysis methods have introduced substantial data management challenges into the life sciences research center. DDN solutions answer this challenge by providing unrivaled levels of storage performance, archive capacity, energy efficiency and data protection. These challenges and solutions will be discussed by DDN at the XGen Conference. DDN is an established leader in scalable life sciences data storage solutions -- having delivered to dozens of the world's leading genomics, pharmaceutical and biotechnical research environments. More information on DDN solutions for life sciences can be found at www.ddn.com/lifesciences.

The company will participate in two key storage sessions at the conference:

Vice President of Marketing Jeff Denworth will speak on March 16 at 7:30 AM, to deliver a talk titled: "Solutions for High-throughput Sequencing, Mass Spectrometry, and Genomic Archives"

On March 17 at 8:15 AM Chris Williams, DDN product manager for cloud storage solutions, will host a roundtable titled: "Solving Performance and Availability with Content Scale-Out"

 
Research and Markets: Single-Source Reference for Market-Oriented Grid and Utility Computing PDF Print E-mail
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Written by Chris O'Neal   
Wednesday, 10 March 2010 08:04
Research and Markets has announced the addition of John Wiley and Sons Ltd's new report "Market-Oriented Grid and Utility Computing" to their offering.

Single-Source Reference for Market-Oriented Grid and Utility Computing

Divided into four main parts and with contributions from a panel of experts in the field it systematically and carefully explores:

  • Foundations presents the fundamental concepts of market-oriented computing and the issues and challenges in allocating resources in a decentralized computing environment.
  • Business models covers business models for service providers and brokers supporting different types of distributed applications, as well as business rules-based models for managing virtual organizations and accounting operations and services in grid computing environments.
  • Policies and agreements introduces policies, agreements, and specifications for the negotiation and establishment of contracts between providers and consumers. It also covers different approaches for resource allocation based on service-level agreements (SLAs) and management of risks associated with SLA violations.
  • Resource allocation and scheduling mechanisms covers economic models, such as commodity models, reciprocation, auctions, and game theory, and middleware technologies, such as Nimrod/G and Gridbus, for market-oriented grid computing and utility-oriented resource allocation.

This book expertly captures the state of the art in the field while also identifying potential research directions and technologies that will facilitate the creation of global commercial grid and utility computing systems. It is an indispensable reference for systems architects, practitioners, developers, new researchers, and graduate students.

This book presents the first coordinated and integrated single-source reference on market-oriented grid computing. The need for this book is supported by the increasing number of initiatives aiming to interconnect or globalize current grid systems. Researchers have built many research Grid infrastructures, mostly with support from funding agencies. As soon as the projects terminate and funding ends, there is general concern that the infrastructure and the results will not survive. The main reason for this is the lack of proven models for sustainability, including market strategies, grid economy, service level agreements and business models. These are the topics that are presented in this book by leading experts in these fields.

Key Topics Covered:

PART I FOUNDATIONS. 1 Market-Oriented Computing and Global Grids: An Introduction (Rajkumar Buyya and Srikumar Venugopal). 2 Markets, Mechanisms, Games, and Their Implications in Grids (Yibo Sun, Sameer Tilak, Ruppa K. Thulasiram, and Kenneth Chiu). 3 Ownership and Decentralization Issues in Resource Allocation Mechanisms (Tiberiu Stef-Praun). 4 Utility Functions, Prices, and Negotiation (John Wilkes). 5 Options and Commodity Markets for Computing Resources (Dan Cristian Marinescu, John Patrick Morrison, and Howard Jay Siegel).

PART II BUSINESS MODELS. 6 Grid Business Models, Evaluation, and Principles (Steve Taylor and Paul McKee). 7 Grid Business Models for Brokers Executing SLA-Based Workflows (Dang Minh Quan and Jorn Altman). 8 A Business-Rules-Based Model to Manage Virtual Organizations in Collaborative Grid Environments (Pilar Herrero, Jose Luis Bosque, and Maria S. Perez). 9 Accounting as a Requirement for Market-Oriented Grid Computing (Andrea Guarise and Rosario M. Piro).

PART III POLICIES AND AGREEMENTS. 10 Service-Level Agreements (SLAs) in the Grid Environment (Bastian Koller, Eduardo Oliveros, and Alfonso Sanchez-Macian). 11 SLAs, Negotiation, and Challenges (Paul McKee, Steve Taylor, Mike Surridge, and Richard Lowe). 12 SLA-Based Resource Management and Allocation (Jordi Guitart, Mario Macias, Omer Rana, Philipp Wieder, Ramin Yahyapour, and Wolfgang Ziegler). 13 Market-Based Resource Allocation for Differentiated Quality Service Levels (H. Howie Huang and Andrew S. Grimshaw). 14 Specification, Planning, and Execution of QoS-Aware Grid Workflows (Ivona Brandic, Sabri Pllana, and Siegfried Benkner). 15 Risk Management In Grids (Karim Djemame, James Padgett, Iain Gourlay, Kerstin Voss, and Odej Kao).

PART IV RESOURCE ALLOCATION AND SCHEDULING MECHANISMS. 16 A Reciprocation-Based Economy for Multiple Services in a Computational Grid (Nazareno Andrade, Francisco Brasileiro, Miranda Mowbray, and Walfredo Cirne). 17 The Nimrod/G Grid Resource Broker for Economics-Based Scheduling (Rajkumar Buyya and David Abramson). 18 Techniques for Providing Hard Quality-of-Service Guarantees in Job Scheduling (Pavan Balaji, Ponnuswamy Sadayappan, and Mohammad Islam). 19 Deadline Budget-Based Scheduling of Workflows on Utility Grids (Jia Yu, Kotagiri Ramamohanarao, and Rajkumar Buyya). 20 Game-Theoretic Scheduling of Grid Computations (Yu-Kwong Kwok). 21 Cooperative Game-Theory-Based Cost Optimization for Scientific Workflows (Radu Prodan and Rubing Duan). 22 Auction-Based Resource Allocation (Bjorn Schnizler). 23 Two Auction-Based Resource Allocation Environments: Design and Experience (Alvin AuYoung, Phil Buonadonna, Brent N. Chun, Chaki Ng, David C. Parkes, Jeff Shneidman, Alex C. Snoeren, and Amin Vahdat). 24 Trust in Grid Resource Auctions (Kris Bubendorfer, Ben Palmer, and Wayne Thomson). 25 Using Secure Auctions to Build a Distributed Metascheduler for the Grid (Kyle Chard and Kris Bubendorfer). 26 The Gridbus Middleware for Market-Oriented Computing (Rajkumar Buyya, Srikumar Venugopal, Rajiv Ranjan, and Chee Shin Yeo).

Author:

Dr. Rajkumar Buyya is an Associate Professor of Computer Science and Software Engineering and Director of the Cloud Computing and Distributed Systems (CLOUDS) Laboratory at the University of Melbourne, Australia. Dr. Buyya has contributed to the creation of high-performance computing and communication system software for Indian PARAM supercomputers and has pioneered the economic paradigm for service-oriented grid and cloud computing. He currently serves as the founding CEO of Manjrasoft, a company producing software systems for utility-oriented grid and cloud computing.

Dr. Kris Bubendorfer lectures in computer science at the Victoria University of Wellington, New Zealand. He teaches courses in networking, operating systems, algorithms, mobile systems, and advanced distributed systems.

Last Updated on Wednesday, 10 March 2010 08:11
 
Imec, Synopsys Collaborate on 3D Stacked IC Development PDF Print E-mail
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Written by Chris O'Neal   
Tuesday, 09 March 2010 14:19

Synopsys TCAD Tools Accelerate Development of Through-Silicon Via Technology

Synopsys and the Belgian nanoelectronics research center, imec, today announced they have entered into a collaboration to use Synopsys TCAD (Technology Computer-Aided Design) finite-element method tools for characterizing and optimizing the reliability and electrical performance of through-silicon vias (TSVs). The collaboration will accelerate the development of 3D stacked IC technologies.

While considered an emerging technology, 3D stacked IC complements conventional transistor scaling and allows multiple chips to be stacked and integrated into a single package. This technology reduces form factor and power consumption, and increases bandwidth of inter-chip communication by minimizing connections through the circuit board with high parasitic capacitance. As with other innovative technologies, 3D stacked IC introduces a number of new issues that can potentially affect its reliability and performance. The collaborative research to address these issues will take place at imec, where silicon wafers with test structures will be manufactured and tested, and Synopsys' TCAD tools will be used to model the TSVs in the chip stacks to optimize 3D stacked IC performance and reliability.

"We consider the availability of Synopsys' silicon-proven finite-element method tools to be an integral part of deploying 3D stacked IC technology. This collaboration will speed up the development of through-silicon via technologies and will in turn facilitate the adoption of 3D stacked ICs in the semiconductor industry," said Luc Van den hove, president and chief executive officer of imec.

"This collaboration with imec affords us the opportunity to validate Synopsys' industry-leading TCAD simulation tools for addressing the emerging 3D stacked IC technology. Imec is an ideal collaboration partner for this effort given its excellent research facilities, industry focus and expertise," said Howard Ko, general manager and senior vice president of the Silicon Engineering Group at Synopsys.

Last Updated on Tuesday, 09 March 2010 14:19
 
Scale Computing Secures $9 Million Series B Investment PDF Print E-mail
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Written by Tyler O'Neal   
Tuesday, 09 March 2010 13:13

Benchmark Capital General Partner Bill Gurley to Join Scale Computing Board of Directors

Scale Computing has announced Series B investment totaling $9.0 million. Led by Benchmark Capital, with participation from existing investors Blue Chip Venture Company, CID Equity and Spring Mill Venture Partners, the funding will be used to support the long-term development of Scale Computing’s product line, international expansion and company growth.

“We are thrilled by the tremendous investor support which will help us not only continue to improve our product line, but also aggressively expand into international markets,” said Jeff Ready, CEO, Scale Computing. “Benchmark Capital’s experience and expertise in helping to build market-leading companies will certainly help us significantly to advance our offerings and continue growing the company - both of which are key to meeting the accelerating demand we're experiencing. Our pipeline growth is accelerating at a 50 percent rate per quarter.”

With the announcement, Benchmark Capital general partner, Bill Gurley, will also join Scale Computing board members Jeff Ready, Scott Loughmiller, Rick Thau, and Don Aquilano. Since joining the venture industry 10 years ago after a successful stint as a research analyst on Wall Street, Gurley has invested in such companies as de-dupe pioneer Avamar (acquired By EMC), as well as OpenTable, one of last year’s most successful IPOs.

“We are thrilled to be leading an investment in Scale,” said Gurley. “This is what I would consider to be an investment trifecta - a team of repeat entrepreneurs connected with a disruptive product targeted at a massive growth industry.”

Recently awarded Best New Product Infrastructure Category by PC Mall, Scale’s storage portfolio is based on the company’s Intelligent Clustered Storage (ICS) technology, which enables users to add storage hardware, known as storage nodes, as necessary without suspending services or migrating data. IT managers are able to build out storage clusters, starting with just three usable terabytes up to the multiple petabyte range on a single file system. As a unified storage platform, Scale’s Starter Cluster line of products provides for simultaneous SAN and NAS services from a single pool of storage, providing enterprise-class, truly clustered, and highly scalable storage at a fraction of the price of competing solutions.

For more information on Scale Computing, contact Scale at 877-SCALE-59 or visit www.scalecomputing.com.

Last Updated on Tuesday, 09 March 2010 14:06
 
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