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iHOP, CellML API, ProteinCenter 1.1, dbGaP, MIRA 2.6

Memorial Sloan Kettering Cancer Center has released an updated version of the iHOP service, which provides summary information on more than 80,000 biological molecules by automatically extracting key sentences from millions of PubMed documents when a search is requested. The new release offers daily updates and processes about 2,000 new publications per day.

Version 1.0 of the CellML API is available here. Improvements include interface changes, performance improvements, bug fixes, and three new optional supplementary services: CellML Context, which allows user-interface programs to manage the list of models that are loaded into memory; CellML Code Generation Service, which allows C code to be generated for a model; and CellML Integration Service, which allows users to run CellML models that are systems of ordinary differential equations.

Proxeon has released ProteinCenter 1.1. The software allows users to mine proteomics data, remove redundancy, compare data sets, and get an overview of large data sets. ProteinCenter integrates sequence information and annotation from all major publicly available protein databases including GenBank, RefSeq, EMBL, UniProt, Swiss-Prot, Trembl, PIR, IPI, and Ensembl. It contains more than 7 million proteins.

The National Center for Biotechnology Information has released dbGaP (the database of Genotype and Phenotype), a new database designed to archive and distribute data from genome-wide association studies. The database provides a central location for study documentation and summaries of measured variables. It also provides pre-computed analyses of the level of statistical association between genes and selected phenotypes. The initial release contains data on two studies: the Age-Related Eye Diseases Study, a 600-subject prospective study of the clinical course of age-related macular degeneration and age-related cataracts supported by the National Eye Institute; and the National Institute of Neurological Disorders and Stroke’s Parkinsonism Study, which gathered DNA, cell line samples, and detailed phenotypic data on 2,573 subjects.

MIRA 2.6, a sequence assembly system for genome and EST sequences, is available here. The release includes new parameter switches for predefined tasks, quick switches for selecting parameters, reduced memory footprint, and increased speed.

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The Scan

Two J&J Doses

Johnson & Johnson says two doses of its SARS-CoV-2 vaccine provides increased protection against symptomatic COVID-19, CNN reports.

Pfizer-BioNTech Vaccine Response in Kids

The Pfizer-BioNTech SARS-CoV-2 vaccine in a lower-dose format appears to generate an immune response among children, according to the Washington Post.

Chicken Changes to Prevent Disease

The Guardian writes that researchers are looking at gene editing chickens to help prevent future pandemics.

PNAS Papers on Siberian Dog Ancestry, Insect Reproduction, Hippocampal Neurogenesis

In PNAS this week: ancestry and admixture among Siberian dogs, hormone role in fruit fly reproduction, and more.