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Downloads and Upgrades: Oct 1, 2010


As part of an international collaboration to collect and disseminate structural variation data, the National Center for Biotechnology Information has launched the Database of Genomic Structural Variation, or dbVar, and the European Bioinformatics Institute has launched the Database of Genomic Variants archive, or DGVa.

Both databases will catalog of genomic insertions, deletions, duplications, and rearrangements from multiple individuals within species.

In addition to dbVar and DGVa, the collaboration includes the Database of Genomic Variants, or DGV, in Toronto. The databases will exchange data on a regular basis "so that each can provide complete data with their own user interfaces, data analysis tools, and suites of integrated resources," NCBI said.

NextBio has launched three new scientific search applications that are built on the Elsevier SciVerse platform to help users search for content stored in databases and repositories.

The Matching Sentences application lets users search for matching sentences or paragraphs, and then create a custom clipboard document with references to the articles and sentences, which can be then printed or emailed.

The Methods Search application lets users search for documents that have all the search terms mentioned in the methods section of the document.

The Prolific Authors application uses Elsevier's Scopus API to show the most prolific authors for a particular search term.

Thermo Fisher Scientific has released updates for five proteomics software products.

ProteinCenter is a web-based tool that lets users integrate, interpret, and share their proteomics data. The software links peptide information with protein data from repositories such as UniProt and the NCBI databases. The tool now contains more than 13 million protein sequences and updates publicly available protein information biweekly.

Proteome Discoverer, which offers users a wide array of software tools and customizable workflows for proteomics experiments, now supports a wide range of stable isotope labeling with amino acids in cell culture experiments and offers capabilities for relative quantitation using isobaric mass tags and provides statistical analysis of results.

SIEVE lets users perform differential expression analysis of proteins, peptides, and metabolites. It includes a machine-learning algorithm to compute false discovery rates and a statistical analysis tool that lets users distinguish between disease and normal protein classes and identify relevant biomarker candidates, among other features.

Pinpoint lets researchers use previously acquired discovery data to develop quantitative assays, perform retention time modeling to simplify reproducibility assessments, and minimize run-to-run variability.

ProSightPC lets users identify and characterize peptides and intact proteins. The tool lets users process MS/MS data, including proteins with known sequence variants and post-translational modifications, among other features.

Accelrys has released Isentris 3.3, a new version of its decision-support software.

According to the company, the latest version of the tool lets users visualize, manipulate, and compare spectral, chromatographic, and XY graphical data. The tool also lets users explore, compare, and report on scientific information captured in its Lab Execution and Analysis software suite, in electronic lab notebooks, in laboratory information management systems, and in other in-house and online information management systems.

DNAStar has released ArrayStar 4, which is fully integrated with its Q-Seq application, as an updated microarray and next-gen sequencing technology software suite. According to the company, in addition to its RNA-seq capabilities, the combined software can also be used to perform ChIP-seq data alignment and analysis and miRNA analysis and to visualize the data.

Version 2.7 of the Cytoscape plugin NetworkAnalyzer is available here.

The latest release lets users plot node attributes, compute topological parameters for a subset of nodes, perform batch analysis of multiple networks, and visualize correlations between two complex parameters, among other features.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.