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NimbleGen, DNAStar, University of Arizona, Agilent, Denver Research Hospital

NimbleGen to Distribute DNAStar's New Gene Expression Software
NimbleGen customers will receive a free trial of DNAStar’s latest gene-expression software as part of a new distribution agreement between the companies, DNAStar said this week.
Under terms of the agreement, NimbleGen customers will be provided with a free trial version of ArrayStar v.2.0 when they receive either their chip data or product from NimbleGen.
DNAStar said ArrayStar is the first gene expression analysis software product designed specifically for data files from NimbleGen microarrays.
The company said the software enables users to determine gene-expression levels, gene relationships and class discoveries, and it offers visualization capabilities such as heat maps, k-means clustering, and other statistical analysis options.
The deal is an extension of an agreement the companies signed two years ago to distribute an early prototype version of ArrayStar. 

University of Arizona Installs SGI Altix with RASC; Sees 20X Blast Speedup
The Center for Computing and Information Technology at the University of Arizona has installed an SGI Altix 4700 with 512 cores, 1 terabyte of shared memory, and the SGI RASC RC100 blade based on field-programmable gate-array technology, SGI said this week.
Among other applications, UA is using the new system for bioinformatics research. 
Michael Bruck, assistant director of research computing at the UA CCIT, said that the RASC blades have accelerated Blast searches by 20-fold — a capability that enables researchers to “complete jobs 16 to 20 times faster than on the systems they were running before.”
UA installed two SGI Altix 4700 systems with a total of 1.136 terabytes of memory. The main system is configured with 512 Intel Itanium 2 processors and 1 terabyte of memory, and runs Novell SUSE Enterprise Linux 10 with SGI ProPack 5. The second SGI Altix 4700 runs 56 Intel Itanium 2 processors and has 112 gigabytes of memory. The University also purchased two SGI RASC RC100 blades with four FPGAs.
Financial terms of the agreement were not provided.

Agilent Contributes Software, other Omics Tools to Denver Research Hospital for Systems Bio Training Courses
Agilent Technologies and the National Jewish Medical and Research Center will provide educational training focused on systems biology applications, Agilent said this week.
The training programs, which will be open to the public, include e-seminars, classroom courses, and hands-on instruction on life-science hardware, the company said.
Agilent will provide a number of its genomics, proteomics, and metabolomics technology platforms, including its GeneSpring GX and MS software for statistical analysis of array and mass spectrometry data and SpectrumMill software for analysis of peptides and proteins.
"Agilent's integrated collection of mass spectrometers, DNA microarrays, and informatics software allows us to teach coherent, comprehensive 'omics' techniques in our lab," said Nichole Reisdorph, assistant professor of immunology and director of the National Jewish mass spectrometry facility. Reisdorph will lead the training programs, Agilent said.

The courses include the new "Hands-on Metabolomics and Proteomics Workshop" to be held Aug. 27-31, as well as database-searching and clinical-proteomics programs.

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The Scan

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Study Looks at Parent Uncertainties After Children's Severe Combined Immunodeficiency Diagnoses

A qualitative study in EJHG looks at personal, practical, scientific, and existential uncertainties in parents as their children go through SCID diagnoses, treatment, and post-treatment stages.

Antimicrobial Resistance Study Highlights Key Protein Domains

By screening diverse versions of an outer membrane porin protein in Vibrio cholerae, researchers in PLOS Genetics flagged protein domain regions influencing antimicrobial resistance.

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.