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Downloads and Upgrades: CLC Cancer Research Workbench, GenePool Reference, SureCall 2.0, and more

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Qiagen said this week that it plans to launch the CLC Cancer Research Workbench, a customizable bioinformatics solution that will offer flexible, cancer-specific analysis workflows in April 2014.

The solution would provide scientists and clinicians with tools to identify prognostic markers and subclonal somatic mutations, detect inherited traits, find biomarkers for drug response, and determine new oncogenes.

CLC Genomics Workbench 7 is also available. It includes new features and improvements, such as multi-sample RNA-seq visualization capabilities, new statistical tools for analyzing differential expression, and a redesigned graphical user interface among other updates.


Station X has launched GenePool Reference, a new product in the GenePool portfolio that gives scientists free access to a growing reference library of important public genomic datasets, including public gene expression data from the Cancer Genome Atlas.


Agilent Technologies has released SureCall 2.0, a new version of its software for its target enrichment portfolio.

The updated software features enhanced exome analysis for both SureSelect and HaloPlex. It has customizable algorithms that help users identify copy number changes and somatic mutations in tumors when comparing them to normal sample analyses and de novo mutations with trio analysis. It is available online and free-of-charge to HaloPlex and SureSelect users.


Human genome annotation release 106 is now available from the National Center for Biotechnology Information. The data is available in the nucleotide, protein and gene databases, is searchable using Blast, and can be downloaded Bowtie 2 is available here.

Version 2.2.0 offers improved index querying efficiency, added support for large and small indexes, bug fixes, and other updates.


F1000Research has published the BioJS collection, 14 open-access articles that detail the functionality, design, implementation, and potential applications of a suite of open-source, JavaScript software components contributed by the BioJS community — initiated at EMBL-EBI and coordinated by The Genome Analysis Center — which are intend to help researchers visualize biological data better.


SoftGenetics has released a new version of its GeneMarker software, which now includes automated quality control evaluation in its Multiplex Ligation-dependent Probe Amplification (MLPA) analysis module. MLPA is a technique used to detect deletions and insertions and is used in clinical research on a various genetics diseases and cancers. This new feature detects and flags samples that do not meet the criteria of MLPA kits to make data analysis more efficient and improve the research workflow.


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