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MIC-BAN, GeneNets, EMBOSS 2.8.0, MSDbar 0.5, MartShell, EnsMart, TOPS

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Hippron Physiomics’ Dynamic Signaling Maps collection of web tools for cell signaling research (http://www.hippron.com/hippron/index.html) now offers biological signaling pathways in DSML, PDF, and PPT formats, as well MIC-BAN, a molecular interaction cluster tool for searching the BIND database, and GeneNets, a tool for extracting gene interaction networks from time-series expression profiles.


EMBOSS 2.8.0 is available for download from http://www.uk.embnet.org/Software/EMBOSS and ftp://ftp.uk.embnet.org/pub/EMBOSS. New functions include ajRegPre, which returns the original string before a regular expression match; ajStrArrayDel, which deletes a string array; and ajListstrToArrayApp, which appends strings in a list to the end of a string array.


MSDbar 0.5, a Netscape/Mozilla toolbar application to search the MSD, PDB, and PDB Japan databases, is available from the MSD group at the European Bioinformatics Institute at http://www.ebi.ac.uk/msd-srv/docs/msdbar.html. The latest version of the toolbar allows users to search using MSD, RCSB, PDBj, or OCA search systems, as well as by author, keyword, ligand, source, and other search parameters.


MartShell, a java command-line interactive shell environment for Ensembl’s EnsMart data-mining application is available at ftp://ftp.ebi.ac.uk/pub/software/ensembl/ensmart. It comes with specifications for the Homo sapiens and Mus musculus Ensembl data sets, as well as the VEGA and SNP datasets.


A new version of the TOPS topology-based protein structure comparison server is available from the Bioinformatics Research Center at the University of Glasgow at http://balabio.dcs.gla.ac.uk/tops/compare.html.

 

Filed under

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.