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Downloads and Upgrades: Ensembl REST API, Reactome 42, Bio-Formats 4.4.4, OMERO 4.4.4


The European Bioinformatics Institute has released a beta version of its programming-language-agnostic REST API for data from Ensembl 68.

The initial release, available here, provides access to sequences, the Variant Effect Predictor, homologies, gene trees, and assembly and coordinate mapping.

Reactome 42 is available here.

Topics with new or revised information include immune system, disease, cell cycle, metabolism, membrane trafficking, and gene expression. New pathway illustrations include signal transduction, signaling by hippo, signaling by SCF-KIT, and mitochondrial protein import.

The OME Consortium has released Bio-Formats 4.4.4 and OMERO 4.4.4.

The latest version of Bio-Formats includes bug fixes, support for Zeiss AxioVision TIFF datasets and Leica SCN datasets, and API support for large image "pyramids."

OMERO 4.4.4 is primarily a bug-fix release.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.