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New Integrated Biology Capabilities Added to Bioinformatics Suite

Jun 14 2012 Read 10953 Times

Agilent Technologies Inc has released GeneSpring 12.0, a major expansion of its popular bioinformatics software designed to enable a new level of medical science breakthroughs. With the new release, GeneSpring users can now analyse next-generation sequencing data and conduct joint analysis at the pathway level across multiple “omics” platforms in a familiar software environment.

These new capabilities expand on existing GeneSpring modules for transcriptomic, genetic, metabolomic and proteomic data analysis.


GeneSpring 12.0 with the new integrated Pathway Architect module is available to all customers for a free evaluation period, now through Aug. 17.

The new release includes an NGS module for next-generation sequencing. The NGS module was designed and tested for use with Agilent’s SureSelect target-enrichment platform as well as un-targeted next-gen sequencing experiments. An integral part of the NGS module is the QC manager, which provides tools for graphical target enrichment, base quality, mapping and alignment QC. DNA-SEQ workflows in the GeneSpring NGS module include tools for identifying and profiling known and novel variants, annotating SNPs, predicting SNP effects, and detecting structural variants. RNA-SEQ workflows support mRNA profiling in absolute and relative space, including detection and differential expression analysis of genes and splice variants. This includes novel gene and exon detection, gene fusion analysis, and sophisticated statistical and pathway analysis tools.

The GeneSpring Pathway Architect module enables scientists to view and analyse curated pathway content. This is accomplished by leveraging WikiPathways, a publicly available resource for building, annotating and querying biological pathways. Mapping of biological identifiers across multiple public and proprietary annotation databases is also supported through integration with BridgeDB, another publicly available resource.

GeneSpring 12.0 customisation capabilities now include enhanced integration of the Jython and R programming languages. Using the embedded scripting editor, bioinformatics scientists can write, execute, and save their own algorithms and workflows in the GeneSpring 12.0 programming framework.

Agilent GeneSpring 12.0 was developed in partnership with Strand Scientific Intelligence, Inc It is powered by Strand’s Avadis platform, which is designed to enable scientists to simplify and solve complex life science challenges.

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