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Downloads and Upgrades: Enzyme Portal; CIRO+ Data Center; BioCyc 16.0; and more


The European Bioinformatics Institute has launched the Enzyme Portal, a free resource for researchers studying the biology of enzymes and proteins with enzymatic activity.

The tool mines and displays data about proteins with enzymatic activity from public repositories and includes biochemical reactions, biological pathways, small-molecule chemistry, disease information, 3D protein structures, and relevant scientific literature. It includes information from UniProt; the Protein Data Bank; Rhea, a database of enzyme-catalysed reactions; Reactome; and IntEnz, a resource with enzyme nomenclature information.

Biomax and CIRO+ have released the CIRO+ Data Center, an integrated patient-centric knowledge management system for patient stratification and targeted therapy in chronic obstructive pulmonary disease.

The tool is expected to help users to better predict patient outcomes and optimize therapies for chronic lung disease.

BioCyc 16.0 is available here.

The release includes the addition of new metabolic pathways to the EcoCyc and MetaCyc databases, downloadable data files, and a downloadable Pathway Tools software/database bundle.

The Cancer Commons has published a molecular disease model for lung cancer.

The model classifies the disease into subtypes based on a tumor's histology and its molecular profile. Each subtype is then linked to published clinical treatment guidelines and other proposed therapy options, including investigational agents available through clinical tests. This information can help physicians understand therapy options for individual patients based on their tumor's molecular subtype.

Linguamatics has launched a natural language processing-based text mining service called I2E Managed Services that runs on the cloud.

This release is based on I2E OnDemand, the software-as-a-service version of Linguamatics’ I2E text mining software. The service includes a dedicated, secure I2E server with full-time operational support; the Medline document set, updated and indexed regularly; and access to features to enable the creation and tailoring of proprietary indexes.

The Protein Data Bank in Europe has launched a new browser based on the Gene Ontology system.

The tool can be used to explore 3D structures for proteins with a given function, role or localization.

Ensembl 66 is available here.

The release includes updates to the human genome assembly and the Ciona intestinalis assembly. It also includes a new Coelacanth species, Latimeria chalumnae.

Prognosys Biosciences has launched an updated version of Voila!, its cloud-based data analysis service, that includes a study-level analysis workflow for RNA-seq analysis.

The module guides users through study design, selects appropriate statistical methods, performs differential expression and splicing analysis, and integrates significant associations with Gene Ontology terms.

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.