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Downloads and Upgrades: Aug 20, 2010

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Agilent Technologies has released OpenLAB Electronic Lab Notebook version 4.1 and has upgraded its ICP-MS MassHunter Workstation software.

Among other features, OpenLAB ELN v4.1 has experimental templates that let scientists create, share, and reuse their custom experiment views and reduce the number of steps between request and result. In addition, v 4.1 has a new module that documents analytical methods, generates sequence files, and captures the results.

According to the company, the updated version of MassHunter software includes a startup scheduler, a batch-and-queue sequence control, and pre-set methods that allow researchers to analyze sample types using pre-defined sets of operating and acquisition conditions to analyze samples. The software also pre-loads analyte lists, selects internal standards and integration times, and defines preferred cell modes.


ADIT 2.0, the newest version of a tool for validating and submitting structures to the Protein Data Bank, is available here.

The new version identifies file format errors, suggests solutions, runs validation checks automatically, and reviews the consistency between sequence and coordinates.


This week, Biomatters announced the beta release of Geneious Pro 5.1

Among other features, the tool lets users assemble to multiple reference sequences, improves memory usage for next-gen sequence data, saves and generates consensus sequences, and provides automatic annotation transfer on alignments.


GenBank 179.0 is available via ftp from the National Center for Biotechnology Information.

The new release grew by about 2 million non-WGS, non-CON sequences and about 400,000 WGS sequences.

Uncompressed, Release 179.0 flatfiles require roughly 451 gigabytes for sequence files only or 484 gigbytes to include the directory, index and text files. The ASN.1 data require approximately 370 gigabytes.


This week, the University of California, Santa Cruz, Bioinformatics Group launched an updated Genome Browser for the latest assembly of the cat genome (Felis catus).

The GTB V17E assembly was produced by the National Human Genome Research Institute’s Genome Technology Branch and National Institutes of Health Intramural Sequencing Center; Agencourt Bioscience; the National Cancer Institute Laboratory of Genomic Diversity; and Hill's Pet Nutrition.

The mitochondrial genome was sequenced by NCI Laboratory of Genomic Diversity.

Detailed sequencing and assembly information is available here

Downloads of the cat sequence data and annotation data are available via the UCSC FTP site or the downloads page.


Sage-N Research said this week that it has integrated a new phosphorylation analysis algorithm,with its Sorcerer Enterprise 4.0 software and Sequest 3G search engine.


Sage-N Research said this week that it has integrated a new phosphorylation analysis algorithm,with its Sorcerer Enterprise 4.0 software and Sequest 3G search engine.

The algorithm, which measures the likelihood of correct phosphorylation site localization, is
based on the Ascore algorithm developed by Steve Gygi of Harvard Medical School.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.