REVIEWER: Philip Papadopoulous, program director, Grid and Cluster Computing, San Diego Supercomputer Center.
BACKGROUND: The California Institute for Telecommunications and Information Technology (Calit2) is a partnership between UC San Diego and UC Irvine that includes more than 1,000 researchers organized around more than 50 projects on the future of telecommunications and IT and how these technologies will transform a range of applications.
PLATFORMS: Kognitio WX2 on a Sun cluster system on Linux.
PROBLEM SOLVED: CAMERA stands for Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis. The aim of the project is to serve the needs of the global research community by creating a rich, distinctive data repository and a bioinformatics tools resource that will address many of the unique challenges of metagenomic analysis. The challenge for Calit2 and the CAMERA project is to consistently and continuously provide a cost-effective, high-performance environment where researchers from around the world have unlimited access to the existing genomics data for unfettered and unlimited access and analysis capabilities to aid in their metagenomics projects. Another challenge is to provide an open access repository for all researchers to deposit sequenced genomics data to share with the global research community. Calit2 had been developing the CAMERA repository on Sun cluster system with a PostgreSQL database. The load time for the initial batch of genomics data was 36 hours, and query times were widely variable, with the most complex queries being difficult to measure.
PRODUCT FUNCTIONALITY: The Calit2 staff downloaded the WX2 software from an FTP server and brought the system up without assistance from Kognitio. The Calit2 staff went on to provision the system and load the CAMERA data without a single call to Kognitio support. During a subsequent training session, I intentionally crashed the system and erased the database. I reconstructed the WX2 system and database in just over two hours while my team and the staff from Kognitio looked on. Today, the CAMERA repository can be loaded in under 50 minutes. The data management workload is substantially lessened due to the lack of need for traditional data enhancement such as indexing, aggregates or partitioning of the data to achieve acceptable performance levels. All of this has been achieved by utilizing existing hardware that Calit2 had been using in its existing Rocks cluster.
STRENGTHS: The products main strengths are robustness, flexibility and speed of performance above all else. The time to load data and begin analysis as well as the time to response has been virtually obliterated. We were also impressed by WX2s ease of installation and administration.
WEAKNESSES: Initially, while the product met all our requirements, we were concerned about Kognitio because the company had little presence in North America. We expressed that to Kognitio officials, and they demonstrated to us that they were moving to establish the company in the U.S. They have followed through on that promise.
SELECTION CRITERIA: WX2s performance was substantially better than other products we evaluated, both integrated appliances and software only. Coupled with its ease of use and its resilience, we became convinced that WX2 would best serve our needs.
DELIVERABLES: By using WX2, our data can be loaded in less than 50 minutes, which is of significant importance when compared to the 36 hours it took with our previous database. Furthermore, the most complex queries resolve in subsecond response times (typically 0.2 to 0.3 seconds). WX2 is now the central repository of genomic data that can be queried by analysts and researchers around the world.
VENDOR SUPPORT: Kognitio support staff was there to aid us with any installation queries; since we downloaded the software from its FTP site and installed the product ourselves, there was no need to call on the vendor for support. Any time that we have been in contact with Kognitios client services team, we found them to be very responsive, rapidly providing us with answers to our questions.
DOCUMENTATION: Although technical documentation exists on the use of Kognitio WX2 that is easy to follow, the software is intuitive enough for system administrators to load and run the database themselves without in-depth referral to the documentation.
Kognitio WX2 Analytical Database
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