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Downloads & Upgrades: Oct 28, 2011

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IO Informatics has launched Knowledge Explorer 3.6, an upgrade of its flagship data-management platform.

The new release offers drag-and-drop ontology management and merging. It also includes an extended application programming interface that allows external developers to write open source or commercial plug-ins for the platform. In addition, it offers performance and search functionality for ontology classes.


IDBS has launched the Omics Workbench, a web-based data-management platform that supports next-generation sequencing and other omics data.

Omics Workbench includes pre-built analytics, visualization, and workflows for all types of omics data including gene expression and copy number variation from sequencing platforms and microarrays.

The platform offers secondary and tertiary analysis of next-gen sequencing data and includes "scientist-oriented" displays to highlight genetic variants between cohort groups, the company said.

Omics Workbench can be deployed on site or hosted in a cloud infrastructure.


The Bioinformatics Research Group at SRI International has released version 15.5 of the BioCyc, EcoCyc, and MetaCyc databases here.

Version 15.5 of BioCyc contains 1,700 pathway/genome databases, including 414 complete bacterial genomes from the Human Microbiome Project.

EcoCyc now includes a functional steady-state metabolic flux model for Escherichia coli produced using flux-balance analysis, while MetaCyc 15.5 contains 1,790 metabolic pathways and 9,600 reactions drawn from 31,000 publications.


The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.