Skip to main content
Premium Trial:

Request an Annual Quote

PLIER, Silicon Graphics Prism, BIOcrawler, ProtoNet, UCSC Proteome Browser, MosaiquesVisuOnline, Reactome


Affymetrix has released PLIER (Probe Logarithmic Error Intensity Estimate), a method that produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error. The software is available under the GNU General Public License at

SGI has released Silicon Graphics Prism, a visualization system built upon Intel Itanium 2 processors and the Linux operating environment with SGI’s graphics technology. The company said that the system is able to address terabyte-sized, highly complex data as a single image, and has a number of applications in drug discovery and biological research.

The National Cancer Institute’s Center for Bioinformatics has released an upgraded version of BIOcrawler at The software is a general-purpose data-querying and -browsing application that provides a keyword search interface to the NCICB caCORE systems.

Hebrew University has released version 4.0 of ProtoNet, an automated classification system for protein sequences based on hierarchical clustering, at The new version classifies all the proteins in Swiss-Prot, supports Trembl entries, and allows users to add their own new proteins to see how they fit into the classification.

The University of California Santa Cruz Genome Bioinformatics Group has released version 1.1 of the UCSC Proteome Browser at The updated version includes direct access to a Proteome Browser gateway via the “Proteome Browser” menu link on the Genome Browser home page, and extended protein coverage that includes all proteins in the Swiss-Prot/Trembl databases, rather than just the human, mouse, and rat protein sets included in the previous version.

Biomosaiques Software, a bioinformatics subsidiary of Mosaiques Diagnostics and Therapeutics, has released MosaiquesVisuOnline, an online software platform for analysis of mass spectrometry data. The software is available at and analyzes time-of flight-MS spectra to yield a list of analytes.

The Reactome database of biological pathways now offers export of human reactions in Systems Biology Markup Language Level 2 format at

Filed under

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.