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Downloads and Upgrades: Nov 19, 2010


Agilent Technologies has released GeneSpring GX 11.5, an expansion of the bioinformatics software package that now enables the interpretation of exon microarray, proteomics, and metabolomics experiments in a single interface.

These new analysis capabilities join existing GeneSpring GX applications for gene expression analysis, genomic copy number analysis, genome-wide association analysis, and transcriptomics data analysis.

GeneSpring GX 11.5 was developed in conjunction with Strand Scientific Intelligence under a partnership that was announced in October (BI 10/8/2010).

Agilent said that GeneSpring GX 11.5's splicing analysis capability has been "greatly extended and enhanced" to support the company's SurePrint G3 Exon Microarrays and that the new metabolomics and proteomics analysis capabilities are a result of the integration of Agilent's Mass Profiler Professional into the software.

GeneSpring GX 11.5 is also integrated with GeneGo’s MetaCore pathway analysis tool, which gives users the ability to combine statistical analysis in GeneSpring with MetaCore’s pathway analysis capabilities.

Biomatters' Geneious Pro 5.3 Beta is now available for download here.

The beta release is compatible with the company's Geneious Server and lets users fine-tune imported reference assemblies. Other features include reduced memory usage when importing large contigs and alignments; separate raw paired 454 data by linker sequence; separate multiplex sequences by barcode; multi-threaded Blast for faster sequence searching; GFF 3.0 import and handling; FramePlot functionality for GC prediction; and chromatogram trace resizing.

Microsoft has released the National Center for Biotechnology Information’s Blast on the Windows Azure cloud.

Through a web interface, NCBI Blast on Windows Azure provides access to cloud computing for very large Blast computations on hundreds of compute nodes, as well as smaller-scale operations. The application allows scientists to use and collaborate with their private data collections, as well as with data hosted on Windows Azure, including NCBI’s public protein data collections.

NCBI’s Blast on Windows Azure is available here at no cost.

The University of Wisconsin-Madison's Laboratory for Optical and Computational Instrumentation and Glencoe Software have released Bio-Formats version 4.2.1.

The updated version of the software supports seven new formats including CellWorX .pnl, ECAT7, varian FDF, perkin elmer densitometer, FEI TIFF, compix/simplePCI TIFF, and Nikon Elements TIFF. Also included in the release is updated Zeiss LSM metadata parsing and enhanced file stitching functionality

Softberry has released MolQuest version 2.3, which the company describes as the cross-platform version of its desktop biomedical data analysis package.

According to the developers, MolQuest brings together more than a hundred proprietary and publicly available programs and includes parameters for about 50 different genomes, as well as basic versions of the firm’s pipelines used to annotate eukaryotic and bacterial genomes.

Also included are tools for primer design, internet database searches, promoter identification, regulatory element mapping, pattern discovery, protein sequence and structure analysis, ligand docking, multiple sequence alignment, phylogenetic reconstruction, and statistical data analysis tools among other features.

Pacific Biosciences has updated its DevNet informatics resource.

Updates include an E. coli resequencing pipeline and dataset; the SMRT (single-molecule real-time) Pipe software, which includes the BLASR program for mapping SMRT sequences to a reference genome and the EviCons tool for producing a consensus sequence; and updated documentation.

Shimadzu Scientific Instruments has released LabSolutions 5.3, a software suite for operating liquid and gas chromatography systems.

According to the company, the software lets users control LC and GC systems on a common platform and automate system operations including auto-startup, system check, auto-purge, baseline check, action with SST or QC results, and auto-shutdown.

The tool also lets users browse data in a single window; utilize calculation schemas required for various regulations; customize screen icons and layouts according to preferences and workflows; and create reports.

Researchers from the Universidad Politécnica de Madrid's Biomedical Informatics Group have created a tool called PubDNA Finder, which they claim is the first search engine for linking biomedical articles to nucleic acid sequences.

PubDNA Finder is an online repository that uses natural language processing, text mining, and knowledge engineering to retrieve genetic sequences. According to the developers, the tool enables researchers to search for documents that cite one or more specific nucleic acid sequences and retrieve the genetic sequences appearing in different articles.

Elsevier has launched SciVerse Applications beta, a new module within the SciVerse platform that lets users develop and share customized solutions.

The launch includes content application programming interfaces from SciVerse, ScienceDirect, SciVerse Scopus, and SciVerse Hub beta, as well as framework APIs that allow applications to be integrated directly into SciVerse. The tool supports applications like Ontology Driven Semantic Search, which lets users locate biomedical resources in databases like DrugBank and NCBI’s Online Mendelian Inheritance in Man.

The module also features a gallery where applications can be displayed and shared and users can post feedback on individual applications.

Amazon Web Services has launched Amazon Cluster GPU Instances — a new instance type that’s designed to deliver the power of graphics processing units in the cloud.

According to the company, the new instance provides 22 GB of memory, 33.5 EC2 compute units, and utilizes the Amazon EC2 cluster network. Furthermore, each GPU instance features two Nvidia Tesla M2050 GPUs that deliver more than one trillion double-precision floating point operations per second.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.