Since 1986 - Covering the Fastest Computers
in the World and the People Who Run Them
Visit additional Tabor Communication Publications
July 30, 2012
TimeLogic FPGAs Help Power Rothamstead Research
Rothamsted Research has added TimeLogic’s latest J1-series Field Programmable Gate Array (FPGA) hardware to their computational tools platform. This sophisticated technology will help Rothamsted scientists deliver the knowledge and innovation for environmentally sustainable solutions for food and energy agriculture, for example the 20:20 Wheat Programme.
TimeLogic’s DeCypher systems greatly increase the speed of sequence comparison by combining custom field programmable gate array (FPGA) circuitry with optimized implementations of BLAST, Smith-Waterman, Hidden Markov Model and gene modeling algorithms. With the inclusion of this additional TimeLogic hardware, Rothamsted researchers now have a sizeable DeCypher system in-house, which significantly enhances their high-throughput genome annotation efforts.
According to Michael Murray, Manager of Sales & Marketing for TimeLogic products at Active Motif, “We have a long standing relationship with Rothamsted Research and their funding agency, the Biotechnology and Biological Sciences Research Council (BBSRC). This particular system represents an upgrade to an existing DeCypher system and we’re very proud of the fact that Rothamsted Research, like so many of our TimeLogic customers, continues to utilize our latest FPGA hardware revisions. Our recently announced J1-series FPGA platform will run Tera-BLAST, our accelerated BLAST implementation, over 960 times faster than running BLAST in software.” Ted DeFrank, President of Active Motif added, “Recent advances in next- generation DNA sequencing technology have created great opportunities for our TimeLogic division and, as a result, Active Motif is investing heavily in this portion of our business. In addition to a major hardware revision, TimeLogic has several additional projects ongoing and we are excited about their continuation as we strive to further strengthen our position as the leader in the field of FPGA-accelerated Biocomputing solutions.”
Dr. Jan Taubert, a Senior Bioinformatician in the Department of Computational and Systems Biology at Rothamsted - Harpenden added, “We are really excited about the latest products from TimeLogic and are going to use them to assist with our analysis of the recently sequenced wheat genome, process next generation DNA sequencing data from our studies of the microbial biodiversity of soils and to compare crop pathogen genomes” Prof. Christopher Rawlings, Head of the Department of Computational and Systems Biology at Rothamsted - Harpenden summarized, “The DeCypher system at Rothamsted is popular with our scientists because of its great performance and the simple web-based user interface. The increasing influx of next-generation DNA sequencing data and newly sequenced genomes from species relevant to our research in sustainable agriculture has led to our decision to expand in-house analysis capacity with the new DeCypher system. We are grateful to the support from the BBSRC that allowed us to make this new investment in our research e-infrastructure.”
About Rothamsted Research
Rothamsted Research, the longest running agricultural research station in the world, providing cutting-edge science and innovation for over 160 years. It receives strategic funding from BBSRC to deliver the knowledge and new practices to increase crop productivity and quality and to develop environmentally sustainable solutions for food and energy production.
For further information, please contact Dr Darren Hughes, Head of Communications, on +44 (0) 1582 763 133 ext 2673, email darren.hughes@rothamsted.ac.uk
About BBSRC
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, and with an annual budget of around £445M (2011-2012), we support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
For more information about BBSRC, our science and our impact see: www.bbsrc.ac.uk.
For more information about BBSRC strategically funded institutes see: www.bbsrc.ac.uk/institutes.
About TimeLogic
TimeLogic, a division of Active Motif, Inc, is the world leader in hardware accelerated bioinformatics search tools which accelerate genome annotation by combining optimized bioinformatics applications with powerful FPGA-based PCIe accelerator cards. This blend of specialized hardware and optimized software provides a perfect combination of performance, accuracy and value. Furthermore, these systems are simple to maintain and scale easily. Utilizing a TimeLogic system reduces pressure on over-used CPU-clusters by off-loading BLAST, Smith- Waterman (SW) and Hidden Markov Model (HMM) tasks to a highly time and energy efficient solution. From the earliest genome sequencing projects in the 1990’s to the largest Metagenomics projects undertaken to date, TimeLogic has provided the enabling technology to make this research possible. Active Motif/TimeLogic operates globally through its corporate headquarters in Carlsbad, California, European headquarters in Rixensart, Belgium and Japanese headquarters in Tokyo, Japan. Active Motif/TimeLogic applies a multi-disciplinary approach to create new and modify existing technologies to meet the current and future needs of life science researchers.
Find out more by visiting us at http://www.timelogic.com or contact Michael Murray at tlsales@activemotif.com.
-----
Source: TimeLogic
Discussion
There are 0 discussion items posted.
|
Join the Discussion |
Sponsored Links
Businesses that want to be on the cutting edge of their industries are increasingly turning to high-performance computing (HPC) solutions to handle complex compute processes and speed up their rate of innovation. Download this Executive Brief to see how businesses in energy, life sciences and entertainment put HPC solutions to work in their operations.
Accelerate your science with Seneca
One of the first HPC providers installing a 4X NVIDIA Kepler K-20 cluster. Invites you to a free evaluation on Seneca’s NVIDIA K20 Kepler cluster, pre-loaded with AMBER, NAMD, LAMMPS
Webinar: Programming Heterogeneous X64+GPU Systems Using OpenACC
Join Michael Wolfe as he compares the advantages and costs of using both low-level models and the directive-based OpenACC model for programming accelerated heterogeneous systems. Registration is free.
- ClusterStor™ 1500 – High Performance Efficiency
- PGI 2013: OpenMP 1.5X faster than GCC, new GNU-compatible OpenACC C++ compiler, CUDA 5 and Tesla K20 support, and more.
- Receive Higher Application Performance with end-to-end 56GbE
- The Accelerated Genomics Cloud $25,000 Giveaway
- White Paper: Building a Data-Intensive Cluster Supercomputer
- Memory Debugging Challenges in Parallel and Distributed Applications
- Acer and Altair simplify cluster computing
- Visualize Historical Usage for Optimized Returns on HPC Investments
RSS Feeds
Feeds by Topic
- Applications
- Developer Tools
- Interconnects
- Middleware
- Networks
- Processors
- Storage
- Systems
- Visualization
Feeds by Industry
Feeds by Content Type
- Features
- Blogs
- Short Takes
- Off the Wire
- Whitepapers
- Multimedia
- HPC Soundbite Podcasts
- HPCwire Job Bank
Subscribe to All Content
May 24, 2013
- IEEE TCSC Young Achievers in Scalable Computing
- Bright Computing Named Winner of 2013 Red Herring Top 100 North America Award
- Supermicro Announces New High-Density Server Solutions
May 23, 2013
- TACC to Upgrade to Internet2's Fastest Network Connection: 100 Gbps
- European Commission CoolEmAll Project Releases Prototypes
- Internet2 Establishes Direct Peering to Microsoft Cloud Services
- Model of Sun's Magnetic Field Created
- Enthought Awarded $1M Grant to Develop Python HPC Framework
- Supermicro Server Platforms to Use NVIDIA GRID Technology
- LG Electronics Becomes Lead Partner for ARM Cortex-A50 Family of Products
- ProximusDA Teams with STMicroelectronics to Develop Virtual Prototypes
- The Brain as a Model for Future Supercomputers
May 22, 2013
- OpenFabrics Alliance to Host Two RDMA Training Courses at University of New Hampshire
- Imperas Delivers Embedded Software Development Suite Based On ToolMorphing Technology
- University of Ulster to Host Scientific Computing Event
- ICT Investment Trends in Germany
- Skyera Adds NAS to skyHawk Enterprise Solid-State Storage Systems
- NetApp Announces Q4 Results
May 21, 2013
- Keyes and Sterling to Headline IEEE Cluster 2013 Conference
- Cyber Network Gears Up for Growth in the Cloud With IBM PureSystems
- New OMAP5432 Processor-Based Evaluation Module From Texas Instruments
- TwinStrata Introduces On-Demand Disaster Recovery as Service for VMware Users
- Weidlinger Launches PZFlexCloud Using CliQr Technologies
- "Places2Be" Project to Boost European Leadership Around FD-SOI
May 20, 2013
- Cray and VBRX to Host Event for Upstream Applications in Oil and Gas
- Dell to Deliver Public Cloud Through Partner Ecosystem
- Mentor and Tezzaron Optimize Calibre 3DSTACK for 2.5/3D-ICs
- Cloud Provider Selects Mellanox's InfiniBand as Their Cloud Interconnect
- Xyratex to Present at Barclay Telco and Media Event
May 17, 2013
May 16, 2013
- D-Wave Two Quantum Computer Selected for New AI Initiative
- Mines' Powerful New Supercomputer to Focus on Energy Research
- Kitware Develops Customizable Simulation Framework to Provide HPC for Mid-Sized Manufacturers
- Next HPC Installation Step Initiated at High Performance Computing Center Stuttgart
- HybridCluster2.0 Self-Healing, Ultra-High Availability Capabilities Unveiled
May 15, 2013
- Nominations for SC13 Cray, Fernbach and Kennedy Awards Due July 1
- Mellanox Technologies Ltd. Announces Definitive Agreement to Acquire Kotura, Inc.
- NYSERDA Awards $1.8 Million to Rensselaer Polytechnic Institute
- Bright Computing Named Finalist for the 2013 Red Herring Top 100 North America Award
- Flow Science Releases FLOW-3D/MP 5.0
- NEC Establishes NEC Ukraine to Strengthen Operations in Russia and the CIS
- Fujitsu Receives Supercomputer Order From Nagoya University
- Avere Systems Helps Framestore Create Extraordinary Visual Effects for Blockbuster Films
- Workshop on Modeling and Simulation of Exascale Systems Call for Papers
May 14, 2013
- Multimillion Pound Project to Develop Next Generation Computing Systems
- HPC Simulations Target Nanoscale Materials Under Strain
- New IBM Center in Beijing to Speed Linux Applications on Power Systems
- OpenCL Software Development Kit Fosters FPGA Exploitation
- S&P Capital IQ and Kuberre Systems Sign Data Facilitator Agreement
- Solarflare to Speak at Linux Foundation Enterprise End User Summit
May 13, 2013
- SDSC Hosts First Annual Industry Partners Research Review
- AMD Targets Server Performance with Open 3.0 Release
- BICS Selects Infinera DTN-X for 500G Pan-European Network
- Juniper Systems Celebrates its 20th Anniversary
Most Read Features
- Adapteva Shows Off $99 Supercomputer Boards
- "No Exascale for You!" An Interview with Berkeley Lab's Horst Simon
- Cray Answers Mid-Market's Call
- The Week in HPC Research
- Saddling Phi for TACC’s Stampede
- Supercomputing Vet Champions Quantum Cause
- Intel’s Big Data to HPC Interconnect
- The Week in HPC Research
- NERSC Managers Shed Light on 'Edison'
- Emerging Technologies at SC13: A Chat with the Chairs
Most Read Around the Web
- Speaking Many Languages into the MIC
- Floating Funding to Exascale Island
- New Tome Tells Modern History of Supercomputing
- Sequoia Hits Warp Speed
- HPC and the True Cost of Cloud
- Revolutionizing Tornado Prediction
- CUDA-Designed Robot: It's a Hit!
- Finnish Researchers Welcome New Cray Super
- Running Computational Fluid Dynamics in the Cloud
- Blue Waters: Security at Scale
Most Read This Just In
- IBM and Forrester Webinar to Discuss New Ways to Reduce Cost in HPC and Big Data
- Altera Opens FPGAs to Programmers with SDK, Off-the-Shelf Boards for OpenCL
- D-Wave Two Quantum Computer Selected for New AI Initiative
- New Simulation Speed Record Achieved with Sequoia Supercomputer
- AMD Targets Server Performance with Open 3.0 Release
- Brain Outperforms Supercomputers
- Vicor's ChiP Power Component Packaging to Make European Debut at PCIM Europe 2013
- Mines' Powerful New Supercomputer to Focus on Energy Research
- Commercial Quantum Computing Company D-Wave Systems Launches
- XSEDE13 Student Programming Contest Registration Opens April 30
Feature Articles
Exascale Advocates Stand on Nuclear Stockpiles
In quieter times, sounding the bell of funding big science with big systems tends to resonate further than when ears are already burning with sour economic and national security news. For exascale's future, however, the time could be ripe to instill some sense of urgency....
Read more...
NSF Forges Further Beyond FLOPs
In a recent solicitation, the NSF laid out needs for furthering its scientific and engineering infrastructure with new tools to go beyond top performance, Having already delivered systems like Stampede and Blue Waters, they're turning an eye to solving data-intensive challenges. We spoke with the agency's Irene Qualters and Barry Schneider about..
Read more...
CERN, Google Drive Future of Global Science Initiatives
Large-scale, worldwide scientific initiatives rely on some cloud-based system to both coordinate efforts and manage computational efforts at peak times that cannot be contained within the combined in-house HPC resources. Last week at Google I/O, Brookhaven National Lab’s Sergey Panitkin discussed the role of the Google Compute Engine in providing computational support to ATLAS, a detector of high-energy particles at the Large Hadron Collider (LHC).
Read more...
Short Takes
NASA Builds 'Climate in a Box'
May 23, 2013 |
The study of climate change is one of those scientific problems where it is almost essential to model the entire Earth to attain accurate results and make worthwhile predictions. In an attempt to make climate science more accessible to smaller research facilities, NASA introduced what they call ‘Climate in a Box,’ a system they note acts as a desktop supercomputer.
Read more...
Building Supercomputers with Raspberries
May 22, 2013 |
At some point in the not-too-distant future, building powerful, miniature computing systems will be considered a hobby for high schoolers, just as robotics or even Lego-building are today. That could be made possible through recent advancements made with the Raspberry Pi computers.
Read more...
Running Computational Fluid Dynamics in the Cloud
May 16, 2013 |
When it comes to cloud, long distances mean unacceptably high latencies. Researchers from the University of Bonn in Germany examined those latency issues of doing CFD modeling in the cloud by utilizing a common CFD and its utilization in HPC instance types including both CPU and GPU cores of Amazon EC2.
Read more...
Computing the Physics of Bubbles
May 15, 2013 |
Supercomputers at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) have worked on important computational problems such as collapse of the atomic state, the optimization of chemical catalysts, and now modeling popping bubbles.
Read more...
Sponsored Whitepapers
Best Practices in Big Data Storage
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
Progress in Parallel: the Bull Parallel Programming Center
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
Sponsored Multimedia
SGI DMF ZeroWatt Disk Solution
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
Cray CS300-AC Cluster Supercomputer Air Cooling Technology Video
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.
HPC Job Bank
Featured Events
- June 13, 2013
- June 14, 2013
Think Beyond Plastics Conference
Berkeley, CA
United States
- June 16, 2013
- June 20, 2013
ISC'13
Leipzig,
Germany
.gif)
- June 17, 2013
- June 18, 2013
Forecast 2013
San Francisco, CA
United States
- June 20, 2013
- June 21, 2013
CIO North America
Marina Del Rey, CA
United States
- June 24, 2013
- June 25, 2013
The Trading Show Chicago
Chicago, IL
United States
- June 25, 2013
- June 26, 2013
TERATEC 2013 Forum
Paris,
France
