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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.


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Giraffe Species Debate

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