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Downloads and Upgrades: Jun 17, 2011


Genedata has released Genedata Expressionist 7.0, the latest version of its enterprise solution for managing and analyzing mass spectrometry data.

The new release includes support for multiple reaction monitoring including capabilities for annotation of MRM transitions, novel grid alignment and peak detection activities, and MRM peak exports; improved support of infusion data including adduct detection for 1D and 2D data; and improved handling of multiplex experiments such as TMT and iTRAQ. The software also supports special characters in experiment names or annotations for Asia/Pacific markets.

The company previewed the software at the 59th ASMS Conference last week in Denver and will officially release it in July.

Integromics has released OmicsHub Proteomics 2.0, an upgrade of its data management and analysis tool for mass spectrometry laboratories and core facilities.

Version 2.0 includes protein quantification, protein validation, a pathway viewer, automatic reports, an OMSSA search engine, background importation, and user roles and permissions.

IO Informatics has launched a free version of its semantic data integration software called Knowledge Explorer Personal Edition.

Knowledge Explorer includes a visual interface for integration, visualization, and querying. It also provides a collection of preconfigured resources, including published information about pathways, drugs, diseases, and side effects, as well as integration templates and ontologies.

The Melanoma Molecular Map Project team has released a new application called the Targeted Therapy Analyzer.

The open-access computational tool enables automated analysis of the data collected in the Targeted Therapy Database. It lets users implement the algorithms necessary to summarize the literature data and to match tumor/patient molecular profiles with the available evidence on molecularly targeted melanoma therapies.

Biogazelle has released qbasePLUS 2, the latest version of its real-time PCR data-analysis software.

Among other features, qbasePLUS 2 includes sample grouping ability, new core modules, and alternative normalization methods.

Biogazelle offers premium and basic licenses for its software. An "everlasting" premium license comes with all available analysis features including 12 months of priority support and software upgrade protection while a basic license comes with fewer data-analysis features.

Release 108 of the European Nucleotide Archive/EMBL-Bank is available from the European Bioinformatics Institute's ftp server and several mirror sites.

Full release notes are available here.

CLC Bio has launched Genomics Gateway, a framework for visualizing, combining, and analyzing genome data.

The first version of the tool focuses on comparative filtering of genomic variations using multiple data sources, including external public databases. For example, a user can compare genomic variations like SNPs in cancer samples with somatic or common genomic variants in curated public databases like COSMIC and dbSNP.

Genomics Gateway will be included in CLC Bio's desktop software package, CLC Genomics Workbench, making it available to all existing CLC Genomics Workbench customers who are still eligible for product updates. A public beta of CLC Genomics Workbench including the Genomics Gateway is scheduled for late June.

5AM Solutions has released SNPTips 1.1, a new version of its free analysis software for genotype data generated by consumer genomics services.

The latest version adds support for Firefox version 4 and the upcoming version 5 beta. In addition to working with 23andMe user data, it also adds support for DeCodeMe data.

The release also includes several bug fixes and the security model has been tightened to prevent accidental e-mailing of genotype information from SNPTips-enhanced web pages. SNPTips can now also be used by anyone, whether they are a customer of a personal genomics service or not, providing look-up links for SNP information even when corresponding personal genomic data is not loaded.

SNPTips 1.1 is available here.

The University of California, Santa Cruz, Genome Browser team has released newly re-engineered Online Mendelian Inheritance in Man tracks for both hg18 and hg19.

The OMIM records have been divided into three separate tracks: OMIM allelic variant SNPs, which comprises variants in the database that have associated dbSNP identifiers; OMIM Genes; and OMIM Phenotypes, which contains regions known to be associated with a phenotype, but for which no specific gene is known to be causative as well as known multi-gene syndromes.

This week, IDBS launched the Biomolecular Hub, a data management solution for 'omics data and analysis results.

The software supports translational research, pharmacogenomic studies, biomarker-based diagnostic development, and systems biology projects. It helps users organize their research activities into studies, projects, experiments, analyses; store and manage analysis results that can be queried by their associated metadata and measurements; store and manage 'omics metadata and result files in a way that reflects their relationship with associated research activities; and trace back the origin of selected features, down to CEL, CDF, FASTQ, CSFAST, and SAM/BAM files.

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.