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Downloads and Upgrades: UCSC Genome Browser, KnowItAll, GenBank 191.0, and PerkinElmer


The genome browser team at the University of California, Santa Cruz, has updated its website.

The new website includes a new menu bar as well as changes to the system’s navigation and search mechanisms among other updates.

Separately, the team has also released a new browser for the medium ground finch, Geospiza fortis.

Bio-Rad has released KnowItAll 9.5, the latest version of its spectroscopy software.

The release includes new spectral reference databases that contain more than 1.4 million spectra of pure organic and commercial compounds. It also includes improvements to the software’s spectral search and viewing capabilities as well as its mixture analysis and structure drawing tools among other updates.

The National Center for Biotechnology Information has released GenBank 191.0 via ftp.

Uncompressed 191.0 flatfiles require roughly 561 gigabytes for sequence files only; or 604 gigabytes to include the short directory, index, and text files. The ASN.1 data require approximately 460 gigabytes.

PerkinElmer said this week that it has integrated its electronic laboratory notebook with Elsevier’s Reaxys, a web-based workflow solution for use in drug discovery, chemicals, and academic research.

The integration of the tools provides chemists with access to information on chemical compounds and related physical and pharmacological properties. It also provides researchers with the ability to search and import external data while eliminating transcription errors.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.