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SRS Gateway for Oracle, SilicoCyte, GeneSifter.Net., BioBrew, eGOn


Lion Bioscience has released the SRS Gateway for Oracle, which allows users to access the SRS engine and associated databases from Oracle using SQL or from any Oracle application. The gateway permits the integration of flat file and relational databases, and is available immediately for SRS 7.1. It supports Oracle 9i Database Release 2 and subsequent versions, including Oracle 10g.

CytoGenomics has launched version 1.3 of SilicoCyte, a gene expression analysis platform. New features include principal component analysis, self-organizing maps, and Venn analysis. The commercial rate for the software is $5,000, and the academic rate is $999. A trial version is available for evaluation at

VizX Labs has released version 2004.1 of GeneSifter.Net. The new version includes several Affymetrix-related upgrades, such as the robust multi-array average (RMA) probe-level analysis method and improved methods for CEL file uploads. In addition, the release includes a GO report using z-score statistics to find particular families of genes, MIAME-compliant protocols, and statistical analysis techniques.

Version 1.0 of BioBrew, an open source Linux cluster package based on the NPACI Rocks cluster distribution and enhanced for bioinformatics, is available for the x86 architecture at BioBrew includes the NCBI toolkit, Blast, mpiBlast, Hmmer, ClustalW, Gromacs, Phylip, Wise, Fasta, and EMBOSS.

Version 1.0 of eGOn (explore Gene Ontology), a tool that uses GO to analyze genes selected from high-throughput analysis, is available from the Norwegian Institute of Science and Technology at The software enables users to visualize gene annotations in an editable GO hierarchical structure.

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The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.