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Downloads and Upgrades: May 27, 2011

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This week, Ingenuity Systems and the Center for Translational Oncology at the Medical University of Mainz announced the availability of an early version of a Galaxy plugin for Ingenuity Pathway Analysis software.

The plugin, which is still under development, will enable researchers to take RNA-seq and resequencing processed datasets directly from Galaxy into IPA for upstream analysis.

Once in IPA, researchers can leverage the biological context of Ingenuity’s curated content and analytics to understand which key pathways and biological processes those genes are involved in.


Cufflinks 1.0.2 is now available here.

The release includes several bug fixes and has a few enhancements, for example, cuffcompare now creates .tmap and .refmap in the directory of the input files, and cuffdiff and cufflinks now accept new options that control whether all hits are counted towards the FPKM denominator, or only those compatible with some transcript in the reference annotation.


Crossbow version 1.1.2 and Myrna version 1.1.2 are now available from the Center for Bioinformatics and Computational Biology at Johns Hopkins University.

The latest version of Crossbow includes several bug fixes among other changes.

The new Myrna release includes updated jar files that use Ensembl v61, several bug fixes, and other updates.


Cresset has released command-line interfaces and free workflow components for its Field-based molecular design tools.

The company has released new command-line interfaces and workflow components for FieldStere, FieldAlign, and FieldView as well as a number of core tools based on its XED force field including XedeX, a Field-based conformation hunter, and XedMin, a ligand minimizer.


Optibrium has released a range of quantitative structure activity relationship models of key toxicity endpoints, based on data made available by the US Environmental Protection Agency as part of its Toxicity Evaluation Software Toolkit.

The models were built with the Auto-Modeller module of the company's newly launched StarDrop 5 drug discovery software and are available to all StarDrop users free of charge.

StarDrop helps scientists make decisions on the design and selection of compounds. Its probabilistic scoring algorithm allows users to create predictive models of toxicity while taking into consideration the uncertainty in each prediction. The "glowing molecule" feature within the tool lets users visualize regions of a compound that have a significant influence on a predicted property.


The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.