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Downloads and Upgrades: Sep 2, 2011


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

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.