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Nuclea Establishes Compute Clusters at Three Massachusetts Colleges to Support Regional Research


By Uduak Grace Thomas

Nuclea Biotechnologies this week said it will establish compute clusters at three East Coast institutions that aim to advance scientific research in western and central Massachusetts by enabling researchers to analyze complex mathematical, biological, and chemical information.

Nuclea said the colleges in question, Berkshire Community College, Clark University, and Massachusetts College of Liberal Arts, will use the new clusters for educational research while Nuclea will have access to them for commercial research efforts to supplement its in-house compute clusters.

Patrick Muraca, Nuclea's president and CEO, told BioInform that the firm decided to install the clusters in order to tap into the varied research interests and bioinformatics knowledge of students and staff at the universities as well as to provide a teaching resource.

Muraca said that Nuclea selected the three colleges because they had prior relationships with the company, including a summer internship program hosted by Nuclea.

The Pittsfield, Mass.-based company will provide more than $300,000 to reimburse the schools for the purchase of the computer servers. In addition, the Massachusetts Life Sciences Center has provided a matching grant.

Furthermore, Nuclea has right of first refusal on any new methods and approaches developed on the clusters, Muraca said.

Students and researchers at the schools will have access to the compute infrastructure for 60 percent of operational time while Nuclea's researchers will have 40 percent access. The new clusters will boost Nuclea's computing capacity by roughly 50 percent.

Muraca said the additional compute power will help support the firm's genomics and proteomics programs.

Nuclea, founded in 2005, uses its DecisionDx platform to develop in vitro companion diagnostic assays based on corresponding gene and protein expression profiles associated with an individual's tumor or specific disease state.

Among its technologies is its Y-Bio- gene analysis suite, a proprietary algorithm and database-driven interface to common gene and protein sequence analysis programs. In addition, the firm has access to a biorepository of 150,000 highly characterized clinical patient samples along with corresponding gene and protein expression data for each specimen.

The company has developed data-mining toolkits and statistical analysis methods to process the extensive amount of data involved in gene and protein expression analysis, Muraca said.

"As you look at gene-based chips from Affymetrix or mass spectrometry-related protein profiles, [the data] is massive and to be able to sort through hundreds of thousands of samples along with that specific data, you need a high-performance computing cluster," he explained.

Nuclea has developed companion diagnostics for use in therapeutic and medical imaging applications in colon, stomach, leukemia, lung, and prostate cancer, as well as in cardiovascular, neurological, inflammation, and metabolic disorders.

Muraca said the new clusters will "strengthen" Nuclea's in-house hardware, which provides compute power equal to 465 servers. It includes a 10-gigabit ethernet switch and 10-gigabit ethernet network interface cards, with Twinax cabling.

It boasts Apple server head nodes and cluster nodes, each with dual-core Xeon 2.5 gigahertz chips with 4 gigabytes of memory; HP DL4x170hG6 cluster nodes, with dual Xeon quad-core E5520 chips providing 16 GB of memory; an HP DL360R06 head/login node, with dual Xeon quad-core E5520 chips providing 8 GB of memory; and an HP DL360R06 storage node, with quad-core Xeon E5504 chips and 6 GB of memory.

A cluster has already been installed at Clark University and is up and running, according to Muraca.

The cluster, which includes some of the same hardware that’s part of Nuclea's in-house infrastructure, comprises a 10 GbE switch and a10 GbE network interface card as well as HP DL4x170hG6 cluster nodes, with dual Xeon quad-core E5520 chips providing 16 GB of memory; an HP DL360R06 head/login node, with dual Xeon quad-core E5520 chips providing 8 GB of memory; and an HP DL360R06 storage node, with quad-core Xeon E5504 chips and 6 GB of memory.

Similar clusters will are planned for both BCC and MCLA.

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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