HIGH PERFORMANCE COMPUTING g


developing a prototype that can stream data from the vehicles back to their cloud system, which will be used for processing and running analytics on the data that has been collected. ‘That was not a field that we started building vScaler for, but as a result of all the capabilities that we are able to deploy and configure, and the performance of the system, means that it is actually quite a good fit for these AI applications,’ stated Power. ‘HPC nowadays means a lot more than just the traditional scientific workloads. The technologies that we use for HPC are applicable to a lot more of the market today,’ Power concluded.


Precision medicine Medicine and healthcare is one discipline that has adopted cloud technology, especially for management of informatics data and sharing information between multiple sites or laboratories. However, the use of cloud-based HPC is gaining traction for heavy workloads such as the development of initiatives for precision medicine. Precision medicine and the concept


of predictive medicine that came before it focus on the use of using targeted personal data about individual patients in order to make more accurate, rapid diagnoses. Generally, this involves the use of genetic screening of individual patients in order to build up a comprehensive genetic picture of a patient, but this can also include data from other areas, such as pollution data for the area where the patient lives. Earlier this year, two companies that


are partnered with Amazon Web Services (AWS) announced a partnership to combine their technologies to create a platform that can deliver the performance and security needed to drive precision medicine research. The partnership combines the


DNAnexus platform-as-a-service (PaaS) to create custom workflows and Edico Genome, which specialises in accelerating genome sequencing analysis for precision medicine using FPGAs. DNAnexus has architected its platform


to align with key security and compliance frameworks, such as HIPAA, 21 CFR Part 11, CLIA, and FedRAMP to provide security and ease of use through the service-based platform. Edico Genome uses FPGAs in its Dynamic Read Analysis for GENomics (DRAGEN) software. By optimising the FPGA logic for this specific application, Edico can deliver results much faster than CPU implementations. The company


6 Scientific Computing World October/November 2017


has released a white paper detailing how it sequenced the entire genome of a newborn baby in 26 hours, to demonstrate the speed of its technology. DNAnexus and Edico Genome announced a joint partnership to integrate Edico Genome’s DRAGEN solution, deployed on Amazon EC2 F1 instance, into the DNAnexus platform. This integration gives customers the ability to use the combined capabilities of the two companies. This provides the speed of DRAGEN to analyse genomes coming from high-throughput sequencers, while also making use of the security and compliance controls that DNAnexus has implemented through AWS.


genome-powered precision medicine is available to every child who needs it. To do this, we needed a rapid research- to-bedside pipeline and be able to scale it and make it accessible to hospitals around the world’. Kingsmore also added: ‘DNAnexus has


the technology and expertise to facilitate this ambitious project, Edico Genome’s rapid testing capability allows for rapid diagnosis of critically ill newborns.’


Open technology As the number of applications for cloud computing grows, so too does the number of implementations. The traditional choice of whether to set up an in-house deployment, use hosting services, or to use a public cloud infrastructure still persists, but now this is further complicated by the number of cloud providers. Selecting some technologies can lock


you into a specific technology as the effort and investment required rewriting code for a new architecture or GPU can be prohibitively expensive. Some cloud providers, such as vScaler,


“While we have invested in our public infrastructure and put a load of HPC technology in there, we are really using that more as a burst facility for customers or as a prototyping facility”


This new platform has been adopted by the Rady Children’s Institute for Genomic Medicine in San Diego, USA. The institute aims to advance genetic screening and precision medicine for infants and children with the aim of developing rapid diagnosis and targeted treatment for critically ill patients. The institute adopted the DNAnexus


platform to gain a secure, flexible, and scalable environment for local and distributed sequencing and analysis. Stephen Kingsmore, president and


chief executive officer at Rady Children’s Institute for Genomic Medicine, commented in a blog post by AWS, that the institute’s ‘goal is to ensure that


are trying to alleviate the problem by using OpenStack for its cloud technology. ‘There is a little bit of resistance in putting all your eggs into one basket and getting locked in to a single vendor. It is good for us, because we are an OpenStack based product. All of the APIs that we expose are completely open standard, so if you can push and burst into our cloud, you have the flexibility to use other OpenStack clouds,’ said Power. Power added that the Linux implementation of OpenStack made developing the vScaler product easier, as the HPC specialists had considerable experience with Linux-based systems. ‘We have spent years tuning and building HPC systems, so we were immediately able to go in and optimise the OpenStack platform,’ stated Power. As the use cases for cloud computing


increase, many new users are beginning to take up the technology. In the opinion of vScaler’s David Power,


we will continue to see growth in demand for cloud computing. ‘It started off as just a prototype with a single customer, but over the years it has developed into more of a comprehensive product as we have been building and adding additional features and capabilities. ‘Cloud addresses a need, certainly, and I do not see that need going away. Nearly everyone that I go and see, now has some form of ambition or strategy towards enabling a cloud technology within their HPC infrastructure,’ Power concluded.


@scwmagazine | www.scientific-computing.com


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