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Downloads and Upgrades: Sep 2, 2011

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The Protein Data Bank has released pdb_extract V3.11 as an online web tool and a downloadable workstation program.

The release includes several bug fixes and new data items among other updates.

Separately, PDB released SF-Tool, a web-based tool for validating structure factor diffraction data files.

The release includes support for neutron and hybrid experiments; incorporates checks from REFMAC1, PHENIX2, and SFCHECK3; and converts multiple data sets into a single mmCIF file.


SBMLToolbox-4.0.1 is available here.

The release includes several bug fixes and new features that create substructures within the MATLAB_SBML structure functions.


SoftGenetics has added a new module to ChimerMarker, the firm's chimerism analysis and monitoring software, which tests samples for maternal cell contamination to ensure that labs interpret results from the fetus alone prior to performing aneuploidy, cystic fibrosis, or other types of molecular genetic testing.


The Galaxy team at Penn State University has launched a new version of its analysis and data integration platform.

This release includes an improved Galaxy Tool Shed for sharing tool definitions; new or updated tool definitions for Trinity, BWA, FASTQ Groomer, Cufflinks, Cuffdiff, and Cuffcompare; enhancements in data visualization capabilities; and improvement to the application programming interfaces for managing histories and datasets and creating histories from library items.

The Galaxy Project also has a new home page and wiki.


BioJava 3.0.2 is available here.

The latest version of the tool adds new modules for calculating the properties of protein sequences and predicting disordered regions in proteins. It also includes improvements to the way protein domains are handled as well as bug fixes.


This week, the European Bioinformatics Institute announced the twentieth release of the BioModels database.

Included in this release are 65 new models as well as various performance improvements.

The public version of the database now contains 366 models in the curated and 398 in the non-curated branch. These 764 models comprise 119,745 species; 135,889 relationships including reactions, rate rules, events, and assignment rules; and 24,666 cross-references.


The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.