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Downloads and Upgrades Oct 30, 2009


The Bioconductor development team has released Bioconductor 2.5. The release includes 34 new software packages, for a total of 352. There are also changes to several existing packages.

Bioconductor 2.5 is compatible with the recently released R 2.10.0.

The National Center for Biomedical Ontology at Stanford University has released BioPortal 2.2, a resource for accessing and sharing biomedical ontologies.

New features include Ontology Views, which are subsets of ontologies in the repository that users can share with colleagues; the NCBO Resource Index, which is an automated indexing of the contents of public databases using ontology terms; and new REST (representational state transfer) web services.

GeneGo has made free pathway content available through its website for human, mouse, and rat signaling and metabolism.

The site includes 37 cystic fibrosis-specific disease maps, which are the result of a collaborative development project with the Cystic Fibrosis Foundation.

Symyx Technologies has released an out-of-the-box integration of Symyx Notebook and Thermo Fisher Scientific's Watson LIMS that enables scientists to easily transfer study information, sample lists, experimental results, and reports between the electronic laboratory notebook and the LIMS, Symyx said.

The integration also allows users to design studies in Watson LIMS and publish them in Symyx Notebook, annotate Watson LIMS worklists in Symyx Notebook, and transfer completed Watson LIMS reports back to Symyx Notebook.

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.