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Downloads and Upgrades: Aug 5, 2011

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The National Center for Integrative Biomedical Informatics at the University of Michigan has released a new version of the MetScape plugin.

In addition to several bug fixes, version 2.2.1 allows users to upload multiple compound, gene, and concept data files; build networks; and save them all within one session. The tool also lets users select columns for fold/log fold change and significance values and set the thresholds for visual features.


The ENCODE Data Coordination Center at the University of California, Santa Cruz, has released several new tracks for the mouse genome browser based on data from the UC, San Diego/Ludwig Institute for Cancer Research, University of Washington, and Stanford/Yale Mouse ENCODE groups.

The new tracks include ChIP-seq based histone modifications and data from genome-wide sensitivity measurements in mouse tissues and cell lines using the Digital DNaseI methodology and DNaseI hypersensitive sites.


Biomax Informatics has released BioXM 4.0, the latest version of its platform for semantic data integration and knowledge management

The release adds the ability to publish browser-based web applications that access the semantic network maintained by the BioXM enterprise server and provides a set of wiki-plugins that let users publish smart folders; query templates and reports; and interactively browse, annotate, add, and modify content in the knowledge environment. It also includes spreadsheet-style formulas that enable on-the-fly calculations within object tables or network graph style definitions.


The Swiss Institute of Bioinformatics and GeneBio have launched NextProt, an online knowledge platform on human proteins.

NextProt builds on human protein-related information contained in the UniProtKB/Swiss-Prot knowledgebase and includes information relative to protein expression and variants. Users can personalize their discoveries of proteins and sets of proteins in context using favorites and tags.

This tool aims to be a comprehensive resource on human proteins, including information such as proteins' function, subcellular location, expression, interactions, and role in diseases, the developers said.


Affymetrix released new versions of several of its tools this week.

Chromosome Analysis Suite Software 1.2 includes support for the analysis of Affymetrix CytoScan HD Arrays, for genotype calling for CytoScan HD Array results and the export of genotyping results, and updates to the segments table among other features.

Version 4.1.1 of the Genotyping Console Software includes improvements to the Genome-Wide Human SNP Array 6.0 LOH segment calling algorithm among other updates.

Fusion Software Developers Kit 1.1.2 provides support for an enhanced version of the CYCHP file format by including C++ and Java source code, file format documentation, example applications, and libraries. Additionally, this release of the SDK updates the primary platform for the binary and library files to 64 bit.

Also released this week is a new version of Affymetrix Data File Formats, which includes updated documentation for the enhanced CYCHP file format.

Affymetrix Power Tools 1.14.3 includes support for the analysis of the new CytoScan HD Array and the updated CYCHP file format as well as bug fixes for the SNP Array 6.0 LOH Calling Algorithm among other updates

Also available is NetAffx Annotation Update 32, which features online search support for the new CytoScan HD Array and Axiom Genome-Wide CHB 1 Array. Furthermore, expression array annotations have also been updated, including SusScr2 genome build support for the IVT GeneChip Porcine Genome Array.


The Scan

Call to Look Again

More than a dozen researchers penned a letter in Science saying a previous investigation into the origin of SARS-CoV-2 did not give theories equal consideration.

Not Always Trusted

In a new poll, slightly more than half of US adults have a great deal or quite a lot of trust in the Centers for Disease Control and Prevention, the Hill reports.

Identified Decades Later

A genetic genealogy approach has identified "Christy Crystal Creek," the New York Times reports.

Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

In Science this week: a novel RNA structural element that acts as a splicing enhancer, and more.