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SeqCruncher PCIe, RefSeq Release 32, dbGaP, Symyx Draw 3.1, Volocity 5, RPro, Mathematica 7

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Active Motif’s TimeLogic division said this week that its SeqCruncher PCIe accelerator card enables a single server to search hidden Markov model databases with the equivalent performance of 471 Xeon CPU-cores.
 
Search tests were run to compare the performance range, flexibility and scalability of the new SeqCruncher field programmable gate array hardware and improved DeCypherHMM software against the established standard open-source software, HMMER from Sean Eddy. SeqCruncher provided 471x, 863x, and 1151x faster performance per CPU core with 1, 2, and 3 cards when searching an HMM database.
 
A full report of the SeqCruncher HMM performance details is available here.  
 

 
The National Center of Biotechnology Information has released RefSeq Release 32, which is available here.
 
This release includes genomic, transcript, and protein data as of Nov. 10, 2008, and includes 9,501,764 records, 6,042,750 proteins, and sequences from 5,726 different organisms.
 
This release includes a new accession format and an update for variation feature annotation for human records.
 
A problem with redundant SNP annotations on RefSeq 31 in which two different coordinates might be given for the same SNP on a single RefSeq mRNA has been fixed, NCBI said. Only the best mRNA to assembly alignment hit is used to place a SNP uniquely on mRNA.
 
A list of SNPs and the sequences containing the redundant annotations in RefSeq31 are
available here.  
 

 
NCBI has also added new data to dbGaP from the GAIN: Major Depression study. The database now includes provisional analysis results performed as part of the GAIN quality control process.
 
The component name is: pha002850.v1.p1.tgz.
 
It includes genome-wide genotyping data produced from the Perlegen 600K platform that was filtered to result in a set of 1,754 cases and 1,800 controls genotyped over 438,129 markers.
 
Additionally, 43 controls and 81 cases were removed due to status as population outliers detected using principle component analysis. The genome-wide association scan has been pre-computed by NCBI.
 

 
Symyx Technologies has released Symyx Draw 3.1, a chemical drawing application that replaces industry-leading ISIS/Draw, at no charge for academic and non-commercial personal use, available here.
 
Symyx Draw 3.1 lets scientists draw and edit complex chemical structures and reactions, and facilitates collaborative searching, viewing, registering, and archiving of scientific information, the company said.
 

 
PerkinElmer has launched the Volocity 5 high-performance imaging software suite, developed by Improvision, a PerkinElmer company.
 
Volocity 5 is a solution for 3D and 4D image acquisition, allowing data visualization, deconvolution, publication, object measurement, tracking, and charting.
 
Using Volocity, cell images can either be directly acquired or the data can be imported from a diverse range of fluorescence microscopy systems. Acquired images are then analyzed in 3D and 4D, delivering both qualitative and quantitative information.
 
The Volocity suite comprises four core software products, all of which are available for Windows and Mac OS:
  • Volocity Acquisition: Designed for high-speed image capture, ranging from simple 2D image capture to multi-channel 4D experiments.
  • Volocity Visualization: For rapid, interactive high-resolution 4D rendering of multi-channel 3D and 4D data sets.
  • Volocity Quantitation: For measurement, tracking and analysis structure and function in 3D and 4D image data.
  • Volocity Restoration: For conversion of standard wide field fluorescence microscope images into confocal quality data.

 
Revolution Computing has added Windows HPC Server 2008 as a supported platform for RPro and all RPro modules.
 
Revolution’s RPro programs can now use the multiple microprocessors inside Microsoft computer clusters. RPro focuses on providing the computational benefits of a cluster with little programmer or system administration overhead, the company said.
 
The RPro module that enables cluster computing, ParallelR, runs in interactive mode on Windows HPC Server 2008. Revolution has also integrated RPro with the Windows HPC Server 2008's scheduler, allowing users to queue RPro batch jobs.
 

 
Wolfram Research has released Mathematica 7, which supports image processing and parallel high-performance computing, and includes on-demand curated data. The new release includes over 500 new functions and 12 application areas, according to a statement.

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The Scan

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Arizona Bill Before Judge

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Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.