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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

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Viral Integration Study Critiqued

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Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.