Months-long cancer gene analysis in an evening: using CycleCloud on Google Compute Engine Preemptible VMs

Cycle’s mission is to enable our customers to easily access the Big Compute resources required to solve problems and meet deadlines. Over the years our software has orchestrated workloads both internally and externally while accelerating the move to cloud. This is why we were ready when the Broad Institute came to us with a problem: Their cancer researchers saw value in a highly-complex genome analysis, but even though they already had powerful processing systems in-house, running the analysis would take months or more. We thought this would be a perfect opportunity to utilize Google Compute Engine’s Preemptible VMs to further their cancer research, which was a natural part of our mission. And now that Preemptible VMs are generally available, we’re excited to tell you about this work.   The Science: The search for understanding cancer The Broad Institute’s Cancer Program has data sets that include hundreds of cancer cell lines, information on the genetic mutations present in each cell line, gene expression data showing which genes are more or less active under various conditions, as well as  information about how various small molecules interact with the cell lines at both large and small scales. Each of these data sets is massively complex in its own right.  Combining them to explore the interactions between these layers of knowledge quickly creates a vast landscape of interrelated data to explore.   One of the Cancer Program’s goals is to intelligently direct future research using these datasets. This particular workload used machine learning techniques to infer  relationships among and between these cell line and gene/expression data sets. This map provides scientists that are...

BioIT World – Time to Test Cloud & to Beat Those Computational Traffic Jams

This year, unlike any previous BioIT World Conference and Expo, attendees have the opportunity to try out some of our push-button cloud clusters live on the showroom floor. Because many of our customers have paved the way in demanding their Life Science application are deployed on cloud, it means much of the heaving lifting has been done for those ready to start using cloud. By stopping by the Cycle Computing booth #360, you can: Discuss Scientific Computing & BigData on the cloud with one of our solutions architects and Cycle Computing’s leading tools running in a Cloud Computing Test Drive. Some of the Life Science workload & applications Cycle Computing has helped customers deploy on cloud include: Computational Chemistry Big Data workloads Intel Lustre File System Internet of Things data collection and processing Genomics PK / PD Proteomics Clinical Trial Simulation We hope you’ll stop by to also discuss Cloud Cost optimization, including Spot Instances, and multi-data center workloads. Keep Calm & Compute On   We also will have a limited number of KEEP CALM & COMPUTE ON t-shirts we’ll be handing out to those who take a short survey in our booth. Finally – don’t miss our CEO in his two conference speaking sessions: Conference session – Wed., April 22, 5 p.m. Creating Customized Research Computing Environments on Cloud, While Addressing Needs for Faster Data Transfer, and a High Performance Parallel File System Jason Stowe, CEO, Cycle Computing Cloud provides researchers the ability to create customized computing environments for drug design and life sciences. But with that flexibility, come challenges. This session will review successful enterprise & start-up use cases to highlight how people...

OpenSSL Vulnerabilities Announced, Cycle Computing Products Unaffected

On March 19, 2015, the OpenSSL developers announced a set of releases to address some high-priority security issues. Because OpenSSL is an important part of secure communication on the Internet, Cycle Computing has paid close attention to these vulnerabilities. Cycle Computing products (including CycleCloud and DataMan) do not rely on these libraries, and are therefore unaffected. The OpenSSH package used to provide remote login access to Linux instances does make use of OpenSSL, however the announced vulnerabilities to not appear to affect SSH. Customers who run other software on cloud instances that make use of OpenSSL (for example, the Apache web browser), should update the OpenSSL package as soon as it becomes available from the operating system vendor. Amazon has indicated that services provided by Amazon Web Services are not impacted or have mitigation plans in...

Extending Your Data Center to the Cloud for Faster Time to Market

There is a great event at Harvard University this Thursday, the Equinix Evolution event, which still has some seats available. Attending CIOs/Directors of IT will be gathering to discuss how dramatically and rapidly cloud is extending the power and capability of their data center. Among others, David Neitz, the CIO of CDM Smith will be giving a great talk on his organization’s Evolution in the datacenter and cloud, as will our CEO Jason Stowe, on how  evolved, cloud technical computing workloads can accelerate time to market and optimize cost. There will be a lot of great discussion at this event, so if you’re in the Boston area reserve a spot here: Date: Thurs., March 19, 2015 Time: 11:30 a.m. – 5:45 p.m. Location: Harvard University, The Loeb House RSVP Here If you can’t attend, this recent article in CIO Review, titled How CIOs Can Be the Corporate Hero in Accelerating Time to Market with Cloud Cluster Computing, outlines some of the concepts that will be presented. Hope to see you...
The Quiet Revolution: How Cloud Cluster Computing Has Defined the New Speed & Agility of Business

The Quiet Revolution: How Cloud Cluster Computing Has Defined the New Speed & Agility of Business

Recently, Cycle Computing CEO Jason Stowe was featured among four other business leaders and innovators in an online book published by Chef, called The Quiet Revolutionaries. Chef, a software automation platform company, and the other people featured in the book, called Quiet Revolutionaries, all share a vision for serving up a better customer experience, faster. Cycle Computing has worked with Chef for more than five years. In the book, Jason celebrates the innovative spirit & leadership of several of Cycle Computing’s customers. These customers, like Novartis, and Compendia, are motivated to move fast; more directly driven to shorten time to market. To meet these demands, researchers needed more computing power, and corporate IT needed to be innovative. But innovative companies aren’t doing this to be innovative – they are doing it to achieve better results, faster. Compendia & Novartis highlighted some of their results while speaking at recent AWS events. In both cases, the companies are leveraging Cloud cluster computing in a fight against cancer. The results speak for themselves: As part of its gene detection project, Compendia BioScience evaluated more than 4,000 DNA and RNA samples, 19 cancer types. Working with Cycle, Compendia accomplished 15.6 years of computing analysis in just a few day. Novartis Institutes for Biomedical Research completed 39 years of computing in just hours! More importantly, they identified three compounds that are now being explored further in the fight against cancer. Customers like Compendia, and Novartis achieve this new agility by working working with Cycle Computing software to dynamically provision hundreds, to thousands, to hundreds of thousands of cores to create on-demand clusters in the...