Vendors Demo Next-Gen Sequencing Platforms for Pharma

By Robert Gelber

May 14, 2012

Three teams developed and demonstrated platforms to supply cloud-based, next-generation sequence (NGS) data during the second annual Pistoia Alliance conference. Projects were aimed at assisting research and development in the pharmaceutical industry. The groups consisted of HP and the Swiss Life Science Center; Eagle Genomics and Cycle Computing; and Constellation Technologies and Genestack. BioInform reported on the event.

Pistoia Alliance logoEach team was responding to a request for proposals [PDF] made by the Pistoia Alliance Sequence Services working group last year, asking for a hosted data services platform that “can solve scientific problems based on DNA/RNA sequence information.” Out of ten submissions received, the alliance selected three proposals. Pharmaceutical companies GlaxoSmithKline, AstraZeneca, Roche, Novartis, and Lundbeck provided shared funding for the project.

The platforms are part of a larger plan to build a fully-functional system for NGS storage and analysis to assist the pharmaceutical industry. The first phase, completed last year, resulted in the creation of an infrastructure focused on performance, scalability and availability.

This second phase required open source tools for analysis while accounting for scalability and security concerns. The platform are required to host Ensembl, a genome browser and PlasMapper, an application that builds and annotates plasmid maps.

Each team had its own ideas when it came to implementing the project requirements. For example, Constellation Technologies and Genestack kept flexibility in mind when developing their platform. Rob Gill, Constellations CTO discussed this point: What we want to do is build a platform that anybody’s tool can go on and thus they can do their science…not our science,” adding that users would also have their choice of cloud offerings. Constellation plans to work with multiple providers, including Amazon Web Services, Microsoft Azure and others.

Although Gill’s group focused on building a versatile platform, he mentioned the other teams as having similar concepts regarding workflow and cloud computing.

Not looking to reinvent the wheel, Cycle Computing and Eagle Genomics focused more on standards. Will Spooner, founder and CTO of Eagle Genomics, spoke with BioInform about their platform: “The way we have put it together is very flexible in terms of tying these different components together using industry standard protocols and web services.”

HP, on the other hand, used its foothold in academia to promote a single platform approach. Joel Jankow, Life Science Business Development Manager for HP, seemed confident about the company’s offering. He claimed that users could do anything they wanted and followed up by saying “there is a very clear delineation between what we do and what our partners do, [and] that didn’t come across as clear with the other [groups].”

All three teams have plans to commercialize their platforms. HP is expecting to integrate its offering into the company’s cloud infrastructure in January 2013. Eagle Genomics hopes to launch it product this summer with a pay-as-you-go model, and Constellation Technologies says it will make its platform available in the next six months.

On a related note, the winner of the Pistoia Alliance Sequence Squeeze Competition was announced during the Pistoia Alliance Conference on April 24, 2012. James Bonfield of the Sanger Institute received the $15,000 prize for developing the best new algorithm for compressing next-generation sequencing (NGS) data. The contest was hosted on Amazon servers.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

NSF Project Sets Up First Machine Learning Cyberinfrastructure – CHASE-CI

July 25, 2017

Earlier this month, the National Science Foundation issued a $1 million grant to Larry Smarr, director of Calit2, and a group of his colleagues to create a community infrastructure in support of machine learning research Read more…

By John Russell

DARPA Continues Investment in Post-Moore’s Technologies

July 24, 2017

The U.S. military long ago ceded dominance in electronics innovation to Silicon Valley, the DoD-backed powerhouse that has driven microelectronic generation for decades. With Moore's Law clearly running out of steam, the Read more…

By George Leopold

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in 2017 with scale-up production for enterprise datacenters and Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE Servers Deliver High Performance Remote Visualization

Whether generating seismic simulations, locating new productive oil reservoirs, or constructing complex models of the earth’s subsurface, energy, oil, and gas (EO&G) is a highly data-driven industry. Read more…

Trinity Supercomputer’s Haswell and KNL Partitions Are Merged

July 19, 2017

Trinity supercomputer’s two partitions – one based on Intel Xeon Haswell processors and the other on Xeon Phi Knights Landing – have been fully integrated are now available for use on classified work in the Nationa Read more…

By HPCwire Staff

NSF Project Sets Up First Machine Learning Cyberinfrastructure – CHASE-CI

July 25, 2017

Earlier this month, the National Science Foundation issued a $1 million grant to Larry Smarr, director of Calit2, and a group of his colleagues to create a comm Read more…

By John Russell

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

Fujitsu Continues HPC, AI Push

July 19, 2017

Summer is well under way, but the so-called summertime slowdown, linked with hot temperatures and longer vacations, does not seem to have impacted Fujitsu's out Read more…

By Tiffany Trader

Researchers Use DNA to Store and Retrieve Digital Movie

July 18, 2017

From abacus to pencil and paper to semiconductor chips, the technology of computing has always been an ever-changing target. The human brain is probably the com Read more…

By John Russell

The Exascale FY18 Budget – The Next Step

July 17, 2017

On July 12, 2017, the U.S. federal budget for its Exascale Computing Initiative (ECI) took its next step forward. On that day, the full Appropriations Committee Read more…

By Alex R. Larzelere

Women in HPC Luncheon Shines Light on Female-Friendly Hiring Practices

July 13, 2017

The second annual Women in HPC luncheon was held on June 20, 2017, during the International Supercomputing Conference in Frankfurt, Germany. The luncheon provid Read more…

By Tiffany Trader

Satellite Advances, NSF Computation Power Rapid Mapping of Earth’s Surface

July 13, 2017

New satellite technologies have completely changed the game in mapping and geographical data gathering, reducing costs and placing a new emphasis on time series Read more…

By Ken Chiacchia and Tiffany Jolley

Intel Skylake: Xeon Goes from Chip to Platform

July 13, 2017

With yesterday’s New York unveiling of the new “Skylake” Xeon Scalable processors, Intel made multiple runs at multiple competitive threats and strategic Read more…

By Doug Black

Google Pulls Back the Covers on Its First Machine Learning Chip

April 6, 2017

This week Google released a report detailing the design and performance characteristics of the Tensor Processing Unit (TPU), its custom ASIC for the inference Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Just how close real-wo Read more…

By John Russell

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its a Read more…

By Tiffany Trader

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the cam Read more…

By John Russell

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

In this contributed perspective piece, Intel’s Jim Jeffers makes the case that CPU-based visualization is now widely adopted and as such is no longer a contrarian view, but is rather an exascale requirement. Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

Facebook Open Sources Caffe2; Nvidia, Intel Rush to Optimize

April 18, 2017

From its F8 developer conference in San Jose, Calif., today, Facebook announced Caffe2, a new open-source, cross-platform framework for deep learning. Caffe2 is the successor to Caffe, the deep learning framework developed by Berkeley AI Research and community contributors. Read more…

By Tiffany Trader

Leading Solution Providers

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

MIT Mathematician Spins Up 220,000-Core Google Compute Cluster

April 21, 2017

On Thursday, Google announced that MIT math professor and computational number theorist Andrew V. Sutherland had set a record for the largest Google Compute Engine (GCE) job. Sutherland ran the massive mathematics workload on 220,000 GCE cores using preemptible virtual machine instances. Read more…

By Tiffany Trader

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

Groq This: New AI Chips to Give GPUs a Run for Deep Learning Money

April 24, 2017

CPUs and GPUs, move over. Thanks to recent revelations surrounding Google’s new Tensor Processing Unit (TPU), the computing world appears to be on the cusp of Read more…

By Alex Woodie

Six Exascale PathForward Vendors Selected; DoE Providing $258M

June 15, 2017

The much-anticipated PathForward awards for hardware R&D in support of the Exascale Computing Project were announced today with six vendors selected – AMD Read more…

By John Russell

Top500 Results: Latest List Trends and What’s in Store

June 19, 2017

Greetings from Frankfurt and the 2017 International Supercomputing Conference where the latest Top500 list has just been revealed. Although there were no major Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This