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EMBL-EBI, NCBI, CLC bio, Michael Smith Genome Sciences Center, NCI, Cold Spring Harbor Laboratory, New York University, Nature Publishing Group, SRI International, Wellcome Trust Sanger Institute, Equinox Pharma

ArrayExpress, the publicly available database of transcriptomics data at the European Molecular Biology Laboratory’s European Bioinformatics Institute, doubled in size in 2007, reaching the 100,000-hybridization mark, EBI said this week.
The database now holds gene expression snapshots for more than 180 species under thousands of experimental conditions.

EBI said that the acceleration in growth reflects not only the increased numbers of direct submissions, but also the mass importation of data from the Gene Expression Omnibus, which is produced by the National Institute of Biotechnology Information.

GEO data entering ArrayExpress are curated and scored for compliance to MIAME, the microarray community’s minimum information standard.
The imported GEO data, like all the data in ArrayExpress, have also been integrated with other EBI resources. 

ArrayExpress is freely available here.


CLC bio this week released version 2.0 of CLC RNA Workbench. The new release includes user-friendly versions of partition function calculation for RNA secondary structure and minimum energy free scanning — functions that were previously only available through highly advanced scripting, the company said.
CLC bio is offering a free 30-day trial of CLC RNA Workbench here.

The Michael Smith Genome Sciences Center has released SSAKE (Short Sequence Assembly by K-mer search and 3' read Extension) v3.0, an application for assembling millions of short nucleotide sequences by progressively searching for perfect 3’-most k-mers using a DNA prefix tree.
The new version of SSAKE now supports paired-end read data to build scaffolds. SSAKE is written in Perl and runs on Linux. It cycles through short sequence reads stored in a hash table and searches through prefix trees for overlapping sequences.
SSAKE is available here.

The National Cancer Institute Center for Bioinformatics has released caBIO version 4.0.
The release features annotations for various microarray platforms. It supports expression arrays, including Affy’s U133 Plus 2.0 Array and Exon 1.0 ST, and Agilent’s 44K Array; SNP/genome arrays including Affy’s 500K and 100K arrays and Illumina’s 550K array; and Agilent’s human genome CGH 244K.
The new release also features “Freestyle Lexical Mine Search,” a text-based search engine that offers a Google-like mechanism to search caBIO objects. FreestyleLM is built upon the Hibernate search engine, which implements a Lucene search, the company said.
caBIO 4.0 is freely available here.

Version 23 of the Reactome Knowledgebase is available here.
Reactome is a curated knowledgebase developed and maintained by the Reactome Knowledgebase team, which includes Lincoln Stein's group at Cold Spring Harbor Laboratory, Ewan Birney's group at the EBI, and Peter D’Eustachio’s group at New York University.
dditions to curated content include a new pathway, Signaling in BMP, and new modules within existing pathways: Apoptotic Execution Phase, Cell Surface Interactions, and TRKA Signaling. The release also includes a new pathway-visualization tool.
In addition, access to 703 Reactome-curated pathways and a primer for using Reactome data are available from the Pathway Interaction Database, a collaborative project between the National Cancer Institute and the Nature Publishing Group.

SRI International has released BioCyc version 11.6 here
Version 11.6 is considered a minor release in which the web site and downloadable files
were updated, but not the downloadable software/database bundle.
Enhancements include two new pathways to EcoCyc: 2-ketoglutarate dehydrogenase complex and fructose degradation, SRI said.

In addition, a number of pathways were re-organized into superpathways with
shorter component pathways, SRI said.

In addition, 79 new pathways, including one superpathway, were added to MetaCyc since the last release. In addition, 30 pathways were “significantly” revised by adding
commentary and updated enzyme and gene information, for a total of 109 new
and updated pathways.


The Wellcome Trust Sanger Institute and European Bioinformatics Institute have released version 48 of Ensembl with additional and upgraded features and enhancements.


The 48 release fixes a problem with the SNP distribution in chromosomes 5 and 6, and there are also additional updates to the human, mouse, and rat variation database.
Ensembl 48 includes new species such as the american pika and mouse lemur cDNA,
updated gene name projections, and minor changes to the mosquito karyotype.

Equinox Pharma has launched of, a new web portal that enables researchers worldwide to access Equinox proprietary bioinformatics software on a ‘pay as you go’ basis.
The first product available will be Equinox’s Phyre homology modelling and fold-recognition software, the company said.

Filed under

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.