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gene2xml, Open Access, Discovery, GARBAN, PhenoBank


The National Center for Biotechnology Information has released gene2xml, a tool for converting Entrez Gene binary ASN.1 files to XML, at

Thermo Electron has released the Open Access and Discovery software applications for its Xcalibur 1.4 SR1 mass spectrometry data system. The applications can be used with any Finnigan ion trap or quadrupole mass spectrometer, as well as with liquid chromatography systems released for Xcalibur 1.4 SR1. The software enables “seamless operation of multiple instruments on one open access system,” according to the company.

Researchers at Navarre University have released GARBAN (Genomic Analysis for Rapid Biological Annotation), a software package that classifies all known genes and proteins according to their molecular function, molecular composition, and biological process, at

The Max Planck Institute for Molecular Cell Biology and Genetics and Cenix BioScience have released PhenoBank, a database of information from the company’s genome-wide RNAi screen for cell division genes in C. elegans. The company released the dataset concurrently with the publication of a study in Nature last week in which it screened nearly all 19,500 genes of the worm genome. The database provides access to around 40,000 time-lapse recordings, still micrographs, and text annotations from more than 300,000 microinjection experiments, and is available at


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The Scan

Follow-Up Data Requests to Biobank Participants Ineffective, Study Finds

An effort to recontact biobank enrollees for additional information reports low participation in a new BMJ Open study.

Study Finds Widespread Transmission of Resistant Bacteria in Vietnam Hospitals

A sequencing study in The Lancet Microbe finds widespread transmission of drug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two Vietnam ICUs.

Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.