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Downloads & Upgrades: Mar 12, 2010


Genedata has released Genedata Analyst, a software platform for statistical analysis and data visualization. The company said that the software allows non-expert users to benefit from statistical tools for data integration, mining, and interpretation through the use of "context-sensitive help, guided workflows, and carefully chosen default settings."

In addition, the client-server architecture supports the analysis of more than a billion data points "with no limit on the number of observables, experiments, or covariates." Visualization tools include histograms, bar charts, box plots, heat maps, scatter plots, trees, maps, and parallel coordinate plots. Statistical tools include ANOVA, linear models, principal components and partial least square analysis, self-organizing maps and clustering methods, and machine-learning algorithms such as support vector machines, k-nearest neighbor, and linear discriminant analysis.

Tibco has launched Tibco Spotfire 3.1, the latest version of its predictive analytics platform. The new version includes a statistics services layer, which enables central deployment and execution of both S+ and R-based models, which can then be run from a Spotfire client.

Spotfire 3.1 also allows users to analyze data from a number of enterprise data sources, including SAP NetWeaver BI, SAP ERP,, Siebel eBusiness Applications, and the Oracle E-Business Suite.

GenomeQuest said that it has opened an application programming interface for its GenomeQuest Sequence Data Management platform. With the new API, bioinformatics developers and computational biologists can customize the platform to support all their research and clinical workflows; cloud-enable the platform across all users, instruments, tools, databases, projects, and organizations; and scale the platform to large-scale workflows, "including broad-based support of next-generation sequencing and secure, cloud-level sharing of sequence data and results," the company said.

Ensembl 57 is available here.

The release includes a complete genebuild for turkey, which is a new species for Ensembl; new assemblies and genebuilds for gorilla, rabbit, and elephant; and an online tool called SNP Effect Predictor, which can calculate the consequences of different types of SNPs.

SoftGenetics has released an update of its Mutation Surveyor software that includes a new quality control report that provides color-coded confidence scoring of all found variant calls. The new release also allows users to customize views of particular patients or samples, the company said.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.