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Downloads and Upgrades: KnomeClinic; Cytoscape App Store; CySBML 1.2; and more

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Knome has launched an early access program for KnomeClinic, a software suite that medical researchers and clinicians can use to interpret and annotate human genomes.

KnomeClinic is composed of kGAP, an annotation platform that accepts raw sequence data from major sequencing platforms and generates standardized, annotated data sets; desktop interpretation-support applications for identifying genetic variants, genes, and pathways that underlie disease and tumor growth; a database of curated and harmonized reference data from more than a dozen sources and containing over 100,000 genotype-phenotype associations; and curation applications for genotype-phenotype associations.

Clinics accepted into the early access program will be given installation priority, access to pilot programs, and pre-release prototypes, and they will influence KnomeClinic's feature set upon general release.


This week, the Cytoscape team launched the Cytoscape App Store.

According to the team, researchers will be able to locate Cytoscape apps —formerly called plugins — through this resource either by categories or keywords. Each app has its own page where users can download, rank, and write comments as well as link to external websites, tutorials, and code repositories.


Exiqon has launched an online tool for designing Locked Nucleic Acid-enhanced qPCR assays.

The tool provides access to multiple databases — including Ensembl, RefSeq, and Genbank — and design software so that users can design and select LNA-enhanced qPCR assays without prior knowledge about the annotation applied in the various databases.


CySBML 1.2 is available here.

CySBML is a Cytoscape plugin that lets users import and work with SBML files in Cytoscape. Its features include a Java-based SBML parser; access to SBML models and annotations; and a standard network layout based on the SBML species/reaction model, among other capabilities.


Release 112 of the European Nucleotide Archive/EMBL-Bank database is available from the European Bioinformatics Institute's ftp servers and other verified mirror sites

Full release notes are available here.


The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.