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Downloads and Upgrades: Reactome 40; Partek Software Suite; GeneSpring 12.0; and more


Reactome 40 is available here.

The release includes a new extracellular matrix organization pathway. Topics with new or revised events include the immune system, protein metabolism, signal transduction, and gene expression.

Life Technologies and Partek have made a pact that provides users of Partek's bioinformatics tool suite with access to Life Tech's Taqman assays directly from the software user interface.

Under the terms of the arrangement, users will be able to select the relevant real-time PCR-based assays they need to validate and characterize genes or regions of interest that they identify with Partek Flow, Partek Genomics Suite, and Partek Pathway — a set of tools for analyzing next generation sequencing and microarray data. The assays cover data from RNA-seq, transcriptome, miRNA, single nucleotide polymorphism genotyping, and copy number analysis experiments.

Bio–Rad said this week that a version of its KnowItAll Informatics system software package will be offered for use with Horiba's Raman spectrometers.

This version of the KnowItAll software will provide scientists with an integrated environment for Raman spectroscopy that will include tools for spectral search, analysis, data mining, and Horiba's database of more than 1,700 spectra.

Appistry said this week that its Ayrris/Bio genomic cloud service and on-premise appliance now meets all Heath Insurance Portability and Accountability Act compliance standards.

To meet these standards, Appistry developed and implemented security mechanisms for Ayrris/Bio that provide customers with access to unique user identification, automatic session expiration for its web interface, encryption and decryption of user account details both in transit and at rest, and detailed audit logs.

Agilent Technologies has released GeneSpring 12.0

The release includes a new integrated pathway architect module that enables scientists to view and analyze curated pathway content by leveraging WikiPathways, a publicly available resource for building, annotating, and querying biological pathways. It also lets users map biological identifiers across multiple public and proprietary annotation databases through integration with BridgeDB. Furthermore, primary data from single 'omics experiments can be merged into a multi-omic experiment and used jointly to identify statistically significant pathways involved in biological processes such as signaling events, disease progression, or toxicity.

The release also includes a module for next-generation sequence data analysis that was designed and tested for use with Agilent’s SureSelect target-enrichment platform as well as un-targeted next-gen sequencing experiments. The module includes a quality control manager, which provides tools for graphical target enrichment, base quality, mapping, and alignment quality control.

Workflows in the GeneSpring NGS module include tools for identifying and profiling known and novel variants; annotating and predicting the effects of single nucleotide polymorphisms; and detecting structural variants. It also supports mRNA profiling including detection and differential expression analysis of genes and splice variants.

The National Institute on Aging, part of the National Institutes of Health, has added genetic data from 13,000 consenting participants in the Health and Retirement Study — a 20-year nationwide survey of the health, economic, and social status of older Americans — to the National Center for Biotechnology Information's database of genotypes and phenotypes or dbGAP.

The data comprise approximately 2.5 million genetic markers from each person and are immediately available for analysis by qualified researchers. Data were obtained from saliva samples collected from HRS participants since 2006. NIA expects to add data from a total of 20,000 HRS participants by the end of 2013.

Integromics has launched RealTime StatMiner 4.3, the latest version of its qPCR data-analysis software

The release lets users upload and analyze data from qPCR vendors, such as Life Technologies, Roche, Bio-Rad, Illumina, Qiagen, and Fluidigm.

Its features include automated processing, quality controls, improved interactive visualizations, customized importation capacities, a global normalization method for miRNAs studies, and integration with the Ingenuity Pathway Analysis and the Tibco Spotfire web player.

Amazon Web Services and the National Institutes of Health said this week that data from 1000 Genomes Project is now available on AWS as a publically available data set.

The project currently has about 200 terabytes of genomic data which includes DNA sequenced from more than 1,700 individuals.

The Genomics of Drug Sensitivity in Cancer project has launched a new website to offer access to genomic markers of sensitivity to anti-cancer compounds screened across a cell line resource.

The website provides access to sensitivity data for 130 anti-cancer drugs screened across a large subset of cell lines. Additionally, it offers drug sensitivity data for more than 600 cell lines that have been correlated with genetic data to identify genomic events associated with sensitivity and resistance. Also offered on the website is genetic data from more than 1,000 cancer cell lines that cover common and rare types of adult and childhood cancers of epithelial, mesenchymal, and haematopoietic origin.

The website's data are also linked to the Catalogue of Somatic Mutations in Cancer database in order to connect somatic mutations and other information related to cancer with drug sensitivity information.