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DrugMatrix, Koadarray V2.6, ACD/Web Librarian, dbSNP Mouse Build 126, UCSC Genome Browser, Athena Bio-Bundle, BioHealthbase, VBI Microbial Database, RiceTFDB

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Iconix Pharmaceuticals has added new data to its DrugMatrix toxicogenomic database from the Affymetrix GeneChip RG-230 2.0 Array. The expanded version of DrugMatrix includes data for hundreds of compound treatments in liver, kidney, heart, and cultured primary rat hepatocytes.


Koada Technology has released Koadarray V2.6, a software package for automated microarray image analysis and quantification that includes improved spot-finding algorithms. The new version can also output data in a GenePix-compatible format. A free download of a 30-day evaluation version of Koadarray is available at http://www.koadarray.com/.


Advanced Chemistry Development has released an upgrade of ACD/Web Librarian, a browser-based software product for sharing and viewing spectral, chromatographic, and chemical data. ACD/Web Librarian enables users to view more than 130 file and database types. New features include the display of hyphenated datasets, which allow users to scroll through and view individual scans. The new version also allows users to add images to records, and export raw spectral data to ACD/Labs desktop processing tools for re-processing and review.


The National Center for Biotechnology Information has released dbSNP Mouse Build 126 ftp.ncbi.nih.gov/snp/. The database includes 1,641,446 new submissions and 3,194,110 validated RefSNP clusters.


The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the Purple Sea Urchin genome (Strongylocentrotus purpuratus) in the UCSC Genome Browser. This assembly, UCSC version strPur1, was produced by the Baylor College of Medicine Human Genome Sequencing Center. The assembly includes around 7 million reads, representing about 800 Mb of sequence and about 6X coverage of the genome.


Electronic Business Solutions has released the Athena Bio-Bundle, a suite of open source bioinformatics software that is pre-installed on its Athena series of high-performance workstations. EBS said that it has optimized the applications to take advantage of the Athena's 64-bit AMD processors, multi-processing capabilities, and Solaris 10 operating system. Applications include Blast, the CCP4 crystallography suite, and EMBOSS. EBS said that it also supports other programs that require separate licensing, including the crystallography program O, the molecular dynamics package Amber, and the GCG sequence-analysis package.


Northrop Grumman, the University of Texas Southwestern Medical Center, Vecna Technologies, and Amar International have released BioHealthbase, a public website for organismal bioinformatics funded by the NIAID Bioinformatics Resource Center program, at http://www.biohealthbase.org/GSearch/. The database focuses on Francisella tularensis, Giardia lamblia, Microsporidia, Ricinus communis, multi-drug resistant Mycobacterium tuberculosis, and the influenza virus.


The Virginia Bioinformatics Institute has launched the VBI Microbial Database, which contains genome sequence and annotation data for the plant pathogens Phytophthora sojae and Phytophthora ramorum, at http://phytophthora.vbi.vt.edu. The database will be expanded in 2006 to include genome sequences for the fungal pathogen Alternaria brassicicola and the oomycete pathogen Hyaloperonospora parasitica.


CLC Bio said this week that all of its software products now support Apple's Intel-based computers, including its CLC Free Workbench, CLC Protein Workbench, CLC Gene Workbench, and CLC Combined Workbench.


Version 2 of the Rice Transcription Factor Database (RiceTFDB) is available from the University of Potsdam at http://ricetfdb.bio.uni-potsdam.de/v2.0. The database is an effort to identify and catalog all rice genes involved in transcriptional control and is based on the latest version (Release 4) of the TIGR Rice Pseudomolecules from the Oryza sativa genome. This database currently contains 2,856 gene models coded from 2,305 loci and arranged in 53 gene families.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.