Agilent Technologies Adds New Integrated Biology Capabilities to Bioinformatics Suite
28 Mar 2012

Agilent Technologies Inc. today 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 analyze 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.

“With the release of GeneSpring 12.0, Agilent is continuing to deliver on its strong commitment to help researches realize the promise of systems biology by providing advanced instrumentation and powerful software tools,” said Gustavo Salem, Agilent vice president and general manager, Biological Systems Division. “The GeneSpring bioinformatics software suite enables a new breed of integrated biology research with sophisticated analytical, visualization and data-management software.”

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.

Agilent’s new bioinformatics software makes it easy for biologists with little experience in next-generation sequencing bioinformatics to manage and analyze their data by guiding them through wizard-driven workflows. It provides a convenient way to group, classify and explore data processed by a bioinformatics facility. GeneSpring 12.0 is also integrated with Agilent’s free eArray portal, enabling users to custom-design experiments through an easy-to-use interface.

Integrating data from heterogeneous ’omics technologies is a key component of systems biology research, which involves measuring the abundance of various biological entities in the same or closely related biological samples. The GeneSpring Pathway Architect module is designed to enable researchers to conduct joint pathway-level analysis of virtually any biological entity. This includes transcripts and splice variants, affected gene panels from variant analysis, metabolites and proteins.

The GeneSpring Pathway Architect module enables scientists to view and analyze 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. Primary data from any of the single-omic experiments can be merged into a multi-omic experiment and used jointly to identify statistically significant pathways involved in many biological processes, such as signaling events, disease progression or toxicity.

GeneSpring 12.0 customization 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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