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PubMed Search by Protein Name, Proteome BioKnowledge Library, MATLAB , BioCyc, Pfam 11.0, Bioconductor 1.3, CellDesigner 1.1

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Ariadne Genomics has released a free web service — PubMed Search by Protein Name — at http://www.ariadnegenomics.com/products . The text-mining service is designed to retrieve abstracts containing all aliases for proteins of interest, while avoiding casual keyword matches, according to the company. The underlying technology for the service is Ariadne’s MedScan text-mining tool.

Incyte is offering free access to Alzheimer disease-related data in its Proteome BioKnowledge Library during November as part of its monthly Disease Spotlight program. The Alzheimer Disease Spotlight provides 25 protein reports related to Alzheimer disease with curated annotations based on relevant publications. The data is available at www.incyte.com/diseaseview

The MathWorks has released a Bioinformatics Toolbox for MATLAB — an addition to the data analysis and algorithm development environment that provides access to standard genomic file formats, Web-based databases such as GenBank and PIR, and online data sources. The toolbox also offers specialized routines for visualizing microarray data. The Bioinformatics Toolbox is available immediately for Windows, UNIX/Linux, and Macintosh systems. Pricing starts at $1,000.

Version 7.6 of BioCyc is now available at http://biocyc.org/. Highlights include two new pathway/genome databases: E. coli O157:H7 and Shigella flexneri 2457T. In addition, the HumanCyc database is now available as an open database for downloading as a set of flat files at http://biocyc.org/download.shtml.

Pfam 11.0 is now available from the Pfam consortium at http://www.sanger.ac.uk/Software/Pfam and other sites. The collection of protein domain family alignments constructed using profile hidden Markov models now contains 7,255 families.

Bioconductor 1.3, which is intended to be operated with R version 1.8.X, is available at http://www.bioconductor.org/. New features include several improvements to the Affy package, improved graph/network handling, and an interface to the curated SNPper data resource maintained at Children’s Hospital Boston.

CellDesigner 1.1, a modeling tool for biochemical networks with a graphical user interface, is available from the Systems Biology Institute at http://www.systems-biology.org/002/001.html. Features include read/write models in SBML Level 1 format, drawing state transition diagrams of proteins, and simulations using the Systems Biology Workbench simulator modules.

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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.