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Downloads and Upgrades: Feb 11, 2011

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The Rosetta Commons group has released Rosetta 3.2.

Included in this release are tools to build structural models of proteins using one or more known structures as templates for modeling; create high-resolution models of complexes between flexible peptides and globular proteins; predict the structure of symmetric homo-oligomeric protein assemblies starting from the structure of a single subunit; search through a protein backbone to find positions where a binding site for a desired small molecule target can be introduced; solve molecular replacement problems; and perform specificity prediction and library design.

Academic users can download the software here.


Release 8 of Ensembl Genomes is available here.

The new version includes software migration to Ensembl 61 and a new Pan Compara database comprised of a selection of vertebrate genomes from Ensembl 61.

Also included are three new oomycete genomes in the protists database, including Phytopthora infestans and P. ramorum, and five new genomes in the metazoan database, including Strongylocentrotus purpuratus, Apis mellifera, and Nematostella vectensis.


Crossbow Version 1.1.1 is now available from the Center for Bioinformatics and Computational Biology at Johns Hopkins University.

The latest version includes added support for the .sra file format, used by the Sequence Read Archive. Examples that included defunct SRA FASTQ files have been updated to point to new .sra files instead.

Myrna Version 1.1.1 is also available here.

The release includes added support for the .sra file format and improvements to the Ensembl.pl/Ensembl.R scripts, among other features.


RemedyMD has launched ComprehensiveBMT, a software tool that lets hematopoietic stem cell transplant researchers aggregate, link, harmonize, and analyze data from patients and donors and then report data as necessary to the Center for International Blood and Marrow Transplant Research.

According to the developers, the software includes a complete HSCT Registry that links data from disparate sources such as electronic health records, research databases and spreadsheets, gene arrays, imaging data, patient and donor self-reported data, and many others to help researchers recognize patterns or identify trends that were not previously visible.


The Scan

Follow-Up Data Requests to Biobank Participants Ineffective, Study Finds

An effort to recontact biobank enrollees for additional information reports low participation in a new BMJ Open study.

Study Finds Widespread Transmission of Resistant Bacteria in Vietnam Hospitals

A sequencing study in The Lancet Microbe finds widespread transmission of drug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two Vietnam ICUs.

Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

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.