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GeneSpring GX 10.0, clusterMaker, Screener 6.0, DrugFinder, Symyx Draw 3.1, Pfam 23.0

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Agilent Technologies announced the launch of GeneSpring GX 10.0, which the company calls the “next generation” of its gene expression bioinformatics platform.
 
GeneSpring GX, which is used for desktop gene expression analysis, now offers tools for systems-level data interpretation and pathway analysis, according to a company release.
 
GeneSpring GX 10.0 adds visualization and analysis tools for applications including alternative splicing, miRNA expression, and real-time PCR.
 
The product now has pathway analysis capabilities and Agilent is providing a database of gene product interactions, allowing scientists to build biological interaction networks from their genes of interest, the company said.  
 
GeneSpring GX 10.0 also provides statistical tools to detect significant changes in miRNA abundance, and integrates TargetScan miRNA gene-target information to determine the biological consequences of detected changes. Additionally, for validation of microarray experiments, GeneSpring GX 10.0 supports analysis of real-time PCR data.
 

 
The Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, has announced the first release of clusterMaker, a Cytoscape plugin for creating and visualizing clusters within Cytoscape networks. 
 
This initial release provides support for hierarchical, k-means, MCL, and FORCE clusters. The hierarchical and k-means clusters are based on the Cluster 3.0 C sources from the Laboratory of DNA Information Analysis at the University of Tokyo and the heat map visualization is based on Alok Saldanha's Java TreeView from Stanford University’s School of Medicine.
 
The hierarchical and k-means clusters may be used for standard expression data on node attributes as well as on epistatic mapping data on edge attributes. The MCL and FORCE implementations are designed to be used primarily with edge-weight protein similarity networks.
 
ClusterMaker requires Cytoscape 2.6.1 and is  available here
 

 
Genedata announced the release of Genedata Screener 6.0, the latest version of its enterprise solution for high-throughput screening and high-content screening analysis.
 
According to the company, Screener 6.0 combines an enterprise-wide assay data management platform with high-performance processing workflows and analysis tools and has a special focus on time series data analysis.  
 
Addressing the complexity of time series data, the latest Screener release includes a feature to address kinetics assay data management challenges, letting users rapidly analyze, integrate, and manage extensive sets of time series data, independent of instrumentation, technology, volume, or location.
 
The application programming interfaces included in this open system can be connected to the many different readers already on the market, as well as implemented to provide custom aggregation functions for specific experiments, the company said.
 

 
The National Foundation for Cancer Research, a Bethesda, Md.-based cancer research organization, and InhibOx, a computational drug discovery company located in Oxford, UK, have launched a virtual screening service called DrugFinder, available here.
 
InhibOx, a University of Oxford spinout, performs the service on its in-house computing facilities. The company has developed computational methods to screen a chemical compound database against a target and return the hit compounds to users via e-mail.
 

 
Symyx Technologies today announced the release of Symyx Draw 3.1, a software package for drawing chemical structures and for searching, registration, and collaboration. Symyx Draw 3.1 replaces ISIS/Draw in the ISIS informatics system and is a component of the Symyx Isentris informatics system that replaces ISIS.
 
Among the new features are the ability to create precise substructure queries, retrieving molecules that contain a common core structure but have different functional groups at specific sites, and the ability to create and edit 3D queries.
 

 
Pfam 23.0 is available from the Wellcome Trust Sanger Institute, Janelia Farm Research Campus, and Stockholm Bioinformatics Centre.
 
This release contains a total of 10,340 families, with 1,063 new families and 52 families removed since the latest release. 73.75 percent of all proteins in Pfamseq contain a match to at least one Pfam domain and 51.22 percent of all residues in the sequence database fall within Pfam domains.
 
Pfam 23.0 is based on UniProt release 12.5, a composite of Swiss-Prot release 54.5 and TrEMBL release 37.5.

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