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Downloads and Upgrades: BioCyc Database, DiscoveryQuant 3.0, RefSeq 68, Cytoscape 3.2, and more

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SRI International has updated its BioCyc database collection to include a mobile application for remote access, as well as additional repositories that support researchers studying genomes and metabolic pathways. With these additions, version 18.5 of the resource adds access to 5,500 genomes and information about connections between sequences and biological function. It also links the sequences of microbial genomes to curated metabolic pathways among other updates.


AB Sciex has released DiscoveryQuant 3.0 software, a new version of its ADME solution for high-throughput drug discovery. The release speeds up the method development process using existing database information, automates on-column optimization, and easily analyzed and processes multiple samples at the same time among other capabilities


Cytoscape 3.2 is available here.

New features include faster startup, session loading, and drawing of large networks; the ability to display a node as a chart; and safer internal data handling of multi-threaded apps among others.


RefSeq 68 is now available from the National Center for Biotechnology Information via ftp.

The release has over 66 million records describing 46,968,574 proteins, 9,069,704 RNAs, and sequences from 49,312 distinct NCBI TaxIDs.


BioGazelle has released version 3.0 of its qbase+ qPCR data-analysis software. Features in this release include a data analysis wizard that simplifies the process of analyzing qPCR data. It provides step-by-step directions for importing data, annotating runs, doing data quality control, validating reference gene stability, performing normalization, and more.


MacVector has released MacVector 13.5, the latest version of its sequence analysis software. This release makes comparing large sequences faster and improves handling of NGS data. Specifically, it has a new interface and includes enhancements to the Align to Reference and Align to Folder functions among other updates.


Affymetrix has added a new feature to version 3 .0 of its Chromosome Analysis Suite software, a tool that enables researchers analyze and visualize the functional impact of copy number changes on gene expression in cancer samples. The company's newly added concurrent molecular analysis profiling capability lets cancer researchers combine whole-genome copy number data with gene expression profiles and explore the functional impact of copy number alterations.


The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.