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Downloads and Upgrades Feb 4, 2011


This week, CLC Bio released version 4.5 of the CLC Genomics Workbench.

The latest version of the software includes tools to handle paired-end data for RNA-seq analysis, a batching functionality that lets users analyze multiple datasets in one go, redesigned multiplexing and Blast tools, as well as a new algorithm for mapping SOLiD reads, among other features.

The European Bioinformatics Institute has released a search service that enables scientists to browse its publicly available biological data and related information.

Driven by Lucene and Distributed Annotation Service technologies, the search engine provides access to information stored in EBI’s databases from a single query and summarizes the results in a logical structure that can be exported or printed.

Users can explore genes, protein sequences, gene expression, molecular structures, and the scientific literature. In addition, a species selector allows researchers to compare key information for human, mouse, fly, and other species.

DNAStar has launched version 3 of SeQMan NGen, the firm’s sequence assembly software.

According to the company, the software can assemble a human genome at a normal depth of coverage on a desktop computer in less than a day and bacterial genomes in less than a minute. The product includes a graphical user interface that leads scientists through experimental set-up for a wide variety of sequence assembly and analysis workflows and accepts data from all next-generation sequencing technologies.

SeqMan NGen 3 will be marketed with the SeqMan Pro analysis software, which supports Bayesian SNP identification and scanning of genomic data in BAM format.

Freeslate has released Library Studio version 8.3, a tool for designing and executing high-throughput experiments, which is part of the firm’s Laboratory Execution and Analysis software suite.

The updated version supports new software interactions including the Windows 7 operating system and provides integrated multi-instrument automation and experiment control with real-time data collection and data processing through a single application.

The tool also allows scientists to design experiments for a variety of applications, including polymer formulation, catalyst synthesis, pharmaceutical API salt selection and crystallization, and material synthesis.

This week, IDBS launched ScienceLink, a platform that provides scientific content from a range of third parties, through the firm’s E-WorkBook Suite.

ScienceLink enables customers to access external resources and find information on chemistry, metabolites, and biological pathways to support their experiments. Using a free plug-in to E-WorkBook, researchers can select their preferred internal and licensed data sources and store the data in the notebook to provide added context to conclusions, methods, or hypotheses.

IDBS also announced that Elsevier’s Reaxys is now interoperable with the IDBS E-WorkBook Suite.

Reaxys provides information on chemical compounds, related physical and pharmacological properties, and synthesis information. Scientists using E-WorkBook can now integrate experimentally validated data from Reaxys into their workflows.

GenomeQuest has integrated disease information from National Center for Biotechnology Information's GeneTests into its sequence data management and analysis platform to enable clinical practitioners to produce and query patient reports for disease diagnosis.

The data covers more than 2,000 inherited diseases, including Alzheimer's, multiple sclerosis, Huntington's disease, and hereditary breast cancer, from a single whole-genome or exome sequence, and can work on a single sample or on a database of samples from patient groups.

The report includes susceptibility and diagnostic guidelines for found variations including: history and prevalence, genetic pathogenesis, prognosis and traits, differential diagnosis, prevention, recommended testing and evaluations, treatments, carrier testing, testing of relatives, prenatal testing, and reference materials.

The new functionality will be available on Feb. 15.

SoftGenetics has added a new module to Version 2.1 of its NextGENe software that enables it to process sequence output from Ion Torrent’s Personal Genome Machine.

The new module converts sequencing output into a standard format readable by NextGENe, allowing Ion Torrent data to be used in applications supported by the software, including SNP and indel discovery, capture techniques, RNA-seq, and others.

Complete Genomics said this week that will provide public access to 60 complete, high-coverage human genome sequences.

The genomes were selected from the National Institute of General Medical Sciences' Human Genetic Repository and the National Human Genome Research Institute's Sample Repository for Human Genetic Research. The genomes have on average more than 55x mapped read coverage and provide more than 12.2 terabases of data.

Complete Genomics is also posting its variant reports for each sample, which include SNPs, indels, copy number variations, and structural variations, together with the read alignments supporting those calls, coverage information, and quality scores.

Currently 40 genomes can be downloaded from Complete Genomics' website. The remaining 20 genomes will be released by the end of March.

The genomes will also be available on a mirror site that is part of the Bionimbus Cloud — a cloud-based system for managing, analyzing and sharing genomic data — making it possible for researchers in the Bionimbus community to analyze the data without moving it. In addition, scientists with access to research networks such as Internet2 or the National LambdaRail can download and analyze the data.

Labcyte launched the Access Laboratory Workstation this week.

According to the developers, the tool uses a suite of software applications and automation control combined with the firm’s Echo liquid handler tool to help researchers improve assay results by easily creating automation routines, managing sample inventory, and customizing reports.

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.