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BioLab Data Server Platform, BRENDA, ClearForest, Grid-Blast, Ensembl Release 18, UCSC Genome Browser, caCORE 2.0, caBIO, MINT, Build 118


BioLab Software of Seattle, Wash., has launched the BioLab Data Server Platform, open source data management software that enables collaboration between researchers via local area networks or the web.

Biobase of Wolfenbuttel, Germany, has begun marketing BRENDA (the Braunschweiger Enzyme Database), developed and maintained by researchers at the University of Cologne. BRENDA contains information on 80,000 enzymes, which have been largely extracted by hand from scientific publications.

ClearForest has released version 5 of the ClearForest text extraction and analysis software suite. New features include plug-in modules for several vertical domain areas — including life sciences, which guide the automatic tagging and discovery of relevant textual elements for each specific domain or industry.

The National Center for Supercomputing Applications, along with the W.M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign, has released Grid-Blast, a web portal that enables Blast to be run on NCSA’s Platinum and Titan Linux clusters, at

Ensembl Release 18 is available at The release contains the Ensembl gene build on NCBI human assembly 34. It has 22,184 genes comprising 27,941 coding transcripts and 1,853 pseudogenes. The release also contains 22,159 rat genes.

The University of California Santa Cruz genome bioinformatics group has added the Drosophila melanogaster assembly to the UCSC Genome Browser at

caCORE 2.0 is now available from the National Cancer Institute Center for Bioinformatics at The release includes an expansion of caBIO (, as well as a full API to other caCORE components. CaBIO’s object model has been extended to cover model organism systems (caMOD). An implementation of the MAGE object model API provides access to the NCI’s gene expression data portal microarray database.

Version 2.0 of the MINT molecular interaction database is available at The relational structure of the database has been redesigned to meet Protein Standard Initiative (PSI) recommendations.

Build 118 of dbSNP is available from the National Center for Biomedical Information at


Filed under

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.