ACCELERATE: ACADEMIC RESEARCH - Researching the Genetic Basis of Behavior, Cognition and Aff ect, USC Needed a High Performance, Scalable Infrastructure to Support Next-Gen Genomics Sequencing
Customer Company Size
Large Corporate
Region
- America
Country
- United States
Product
- GRIDScaler® File Storage Appliance
- Illumina® HiSeq2000 instruments
Tech Stack
- GRIDScaler parallel file system
- SFA10K-E
- Burrows-Wheeler Aligner (BWA)
Implementation Scale
- Enterprise-wide Deployment
Impact Metrics
- Productivity Improvements
- Innovation Output
Technology Category
- Infrastructure as a Service (IaaS) - Cloud Storage Services
- Analytics & Modeling - Big Data Analytics
Applicable Industries
- Healthcare & Hospitals
- Life Sciences
Applicable Functions
- Product Research & Development
Use Cases
- Predictive Maintenance
- Process Control & Optimization
Services
- System Integration
- Cloud Planning, Design & Implementation Services
About The Customer
The Zilkha Neurogenetic Institute is an integral part of a broader USC neuroscience initiative, promoting collaboration between researchers from diverse disciplines. It was designed to foster interaction among the best and brightest. Scientists at the Institute reach across boundaries to embrace methods and techniques from other fields of study, identifying new approaches to examine nervous system function, so we may all better understand the underlying causes of neurological and psychiatric disorders. The Laboratory of Dr. James Knowles is interested in understanding the genetic basis of behavior, cognition and affect. At present, most of the lab's efforts are directed to understanding the transcriptional program of brain development and the genetics of schizophrenia, bipolar disorder and obsessive-compulsive disorder. The lab is leveraging high throughput sequencing technology to look for genetic factors that have an etiological role in psychiatric illness. With this knowledge, they aim to improve diagnostic methods and possibly develop therapies to improve the quality of life for that population.
The Challenge
The Laboratory of Dr. James Knowles at the Zilkha Neurogenetic Institute, Keck School of Medicine at the University of Southern California (USC) was facing a significant challenge. The lab, which is focused on understanding the genetic basis of behavior, cognition, and affect, was struggling with a legacy SAN storage server that was nearing capacity and could not keep up with data access requirements. The storage throughput was hobbled by the network and by the performance limitations of NFS. The storage bottleneck caused by slow uploads was delaying time to discovery. The lab needed a new storage solution that could serve in excess of Gigabyte per second throughput and scale to petabytes in a single name space. The Knowles Lab had a data storage performance problem. They needed to sequence 1,400 full human genomes to support their ongoing studies. This work would generate several terabytes of raw data per day that needed to be transferred, inspected, and aligned to the human genome. Their legacy storage system could only output enough data to the CPU cluster to run a single instance of their Burrows-Wheeler Aligner (BWA) under the Pegasus MPI workflow. Furthermore, they could only upload data to that system at 30-50 MB/second, nowhere near the 100MB/second peak theoretical capacity of the GbE network. This bottleneck was not only an inconvenience, but it was slowing their time to discovery.
The Solution
The Knowles lab and USC’s HPCC team worked with DDN to identify a high-performance, scalable, cost-effective solution. USC selected a solution based on DDN’s Storage Fusion Architecture®, running an embedded image of DDN GRIDScaler parallel file system on the SFA10K-E. This solution appeared to meet both parties’ needs, supporting a high performance parallel file system, and NFS, simultaneously. Additional research groups with large amounts of data at the Keck School of Medicine learned about the impending storage deployment. They added their resources to the purchase of GRIDScaler, which then doubled the raw system capacity to over 1PB. GRIDScaler is a large, high-performance storage appliance with a shared architecture - capable of delivering in excess of 800 million IOPS continuously to the USC HPCC cluster. This provided a clear advantage over the use of smaller, lower performance units, which would also entail more HPCC management. The storage array is connected to the computer resources via multiple 10Gb-E. There’s a separate 10Gb-E connection to the head node that runs an image of the GRIDScaler client software and acts as an NFS server. The caching server in the Knowles Lab provides the long-haul connection to the head node in the HPCC and acts as a data transfer gateway for the Windows/Linux terminals and instruments located in the Knowles Lab.
Operational Impact
Quantitative Benefit
Case Study missing?
Start adding your own!
Register with your work email and create a new case study profile for your business.
Related Case Studies.
Case Study
Hospital Inventory Management
The hospital supply chain team is responsible for ensuring that the right medical supplies are readily available to clinicians when and where needed, and to do so in the most efficient manner possible. However, many of the systems and processes in use at the cancer center for supply chain management were not best suited to support these goals. Barcoding technology, a commonly used method for inventory management of medical supplies, is labor intensive, time consuming, does not provide real-time visibility into inventory levels and can be prone to error. Consequently, the lack of accurate and real-time visibility into inventory levels across multiple supply rooms in multiple hospital facilities creates additional inefficiency in the system causing over-ordering, hoarding, and wasted supplies. Other sources of waste and cost were also identified as candidates for improvement. Existing systems and processes did not provide adequate security for high-cost inventory within the hospital, which was another driver of cost. A lack of visibility into expiration dates for supplies resulted in supplies being wasted due to past expiry dates. Storage of supplies was also a key consideration given the location of the cancer center’s facilities in a dense urban setting, where space is always at a premium. In order to address the challenges outlined above, the hospital sought a solution that would provide real-time inventory information with high levels of accuracy, reduce the level of manual effort required and enable data driven decision making to ensure that the right supplies were readily available to clinicians in the right location at the right time.
Case Study
Gas Pipeline Monitoring System for Hospitals
This system integrator focuses on providing centralized gas pipeline monitoring systems for hospitals. The service they provide makes it possible for hospitals to reduce both maintenance and labor costs. Since hospitals may not have an existing network suitable for this type of system, GPRS communication provides an easy and ready-to-use solution for remote, distributed monitoring systems System Requirements - GPRS communication - Seamless connection with SCADA software - Simple, front-end control capability - Expandable I/O channels - Combine AI, DI, and DO channels
Case Study
Driving Digital Transformations for Vitro Diagnostic Medical Devices
Diagnostic devices play a vital role in helping to improve healthcare delivery. In fact, an estimated 60 percent of the world’s medical decisions are made with support from in vitrodiagnostics (IVD) solutions, such as those provided by Roche Diagnostics, an industry leader. As the demand for medical diagnostic services grows rapidly in hospitals and clinics across China, so does the market for IVD solutions. In addition, the typically high cost of these diagnostic devices means that comprehensive post-sales services are needed. Wanteed to improve three portions of thr IVD:1. Remotely monitor and manage IVD devices as fixed assets.2. Optimizing device availability with predictive maintenance.3. Recommending the best IVD solution for a customer’s needs.
Case Study
HaemoCloud Global Blood Management System
1) Deliver a connected digital product system to protect and increase the differentiated value of Haemonetics blood and plasma solutions. 2) Improve patient outcomes by increasing the efficiency of blood supply flows. 3) Navigate and satisfy a complex web of global regulatory compliance requirements. 4) Reduce costly and labor-intensive maintenance procedures.
Case Study
Cloud-based healthcare solution for Royal Philips
Royal Philips wanted to launch its cloud-based healthcare solution HealthSuite Digital Platform in China to deliver services to help cope with challenges related to urbanization and population growth. Philips wanted to achieve this goal by combining mobile, cloud computing and big data technologies. To bring this platform and product to market, Philips required cloud computing and local technical service capabilities in China, in addition to a flexible IT infrastructure that could handle user requests.
