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Cytoscape 2.6.0, miRBase 11.0, Biojava 1.6, MIRA 2.9.25, Simcyp Pediatric Simulator

Cytoscape 2.6.0 is available here.
The latest version of the open-source network-visualization platform includes several improvements, including a web service client manager; access to Pathway Commons, IntAct, and NCBI Entrez Gene; synonym import from BioMart; a network manager that supports multiple network selection; and improved label positioning.

The Wellcome Trust Sanger Institute has released a new version of the miRBase database of published microRNA sequences and associated annotation.
Version 11.0 of miRBase, available here, contains 6,396 entries representing hairpin precursor miRNAs, expressing 6,211 mature miRNA products, in primates, rodents, birds, fish, worms, flies, plants, and viruses.

Biojava 1.6 is available here.
The new release, based on Java 1.5+, includes an improved phylogenetics package, an updated PDB file parser, and other improvements.

Version 2.9.25 of the MIRA 2.9.25 sequence assembler is available here.
MIRA 2.9.25 now includes mapping assemblies of Illumina Genome Analyzer reads, SNP detection with Illumina GA reads, an improved command-line interface, simplified handling of hybrid assemblies that involve Sanger, 454, and Illumina GA reads, and other new features.

Simcyp has released a new version of the Simcyp Pediatric Simulator, a modeling and simulation platform that models pharmacokinetic behavior in “virtual populations” of children to help drugmakers better predict dosing for pediatric medications.

Simcyp Pediatric 2008 is available as a module for the company’s Simcyp Population-based ADME Simulator.

Filed under

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.