Dear GeneSpring User,

We are excited to bring you the new GeneSpring newsletter, which will keep you informed of current development efforts, news, and research trends within the GeneSpring community. We will provide an option for future editions if you don’t wish to receive communications from us. However, for this first edition, we’re excited to share information about the upcoming release of GeneSpring (version 12), which includes a great number of enhancements as well as the brand-new GeneSpring NGS module. We hope that you will like the newest member of the GeneSpring family of products!

Inside this edition:
- GeneSpring 12 is coming!
- Introducing GeneSpring NGS
- GeneSpring gets social

Integrated Biology at Agilent. Coming in GeneSpring 12.

After almost a year of constant development efforts, we are extremely excited to announce the upcoming release of GeneSpring 12! Known as the “IB” release (for “Integrated Biology”), GeneSpring 12 also includes a complete overhaul to the pathway capabilities in GeneSpring, updated annotations and content, and GeneSpring NGS.

Integrated biology is a large emerging trend in life science research. Multi-omics research themes are emerging as priorities at NIH and top research institutions.

GeneSpring is uniquely positioned to address these efforts with cross-omics analysis workflows, supporting emerging application spaces that span the entire life sciences. Analytically, combinations of heterogeneous data reduces cross-omics noise and yields the most information at the level of biological annotation – through networks and pathways. GeneSpring is a unique bioanalytical tool which combines data management, visualization, and statistical pathway analysis for multiple datatypes together in one easy-to-use package.

What’s inside GeneSpring 12:

- Next-generation sequencing analysis for SureSelect target enrichment (DNA and RNA)
- Multi-Omic Analysis for Integrated Biology
- Joint network and pathway analysis for Integrated Genomics
- New Pathway Analysis and Visualizations
- Updated biological annotations and content
- New Statistical Algorithms
- Enhanced Visualizations
- Extensibility Improvements

Upgraded / enhanced analytical modules within GeneSpring 12:

- GeneSpring GX: qPCR and microarray-based RNA and DNA analysis
- GeneSpring NGS: DNAseq, RNAseq, and SureSelect Target Enrichment Analysis
- GeneSpring MPP: Mass-Spec-based protein and metabolite analysis
- GeneSpring PA: Fully integrated Pathway Analysis for any of the modules listed

Introducing the newest member of the GeneSpring Family. Optimized for SureSelect Target Enrichment.

GeneSpring NGS will be available as a stand-alone module or as a fully integrated component with other GeneSpring modules (such as GX, MPP, and PA) in GeneSpring 12.0. It supports the SureSelect portfolio with a special emphasis on quality analysis for SureSelect target enrichment.

What’s inside GeneSpring NGS:

- DNA-Seq: WGS and SureSelect kits
- Pre-packaged complete genomic annotations
- Extensive, actionable quality analysis including QA report generation (PDF)
- SNP, MNP, and InDel detection
- Large structural variant identification
- Novel and known variant classification, comparison with known SNPs, effects on coding region reporting
- Multi-sample variant reporting
- Machine learning and pathway analysis (affected gene panels)
- RNA-Seq: WGS and SureSelect kits
- Pre-packaged complete genomic annotations
- Extensive, actionable quality analysis including QA report generation (PDF)
- Comparative gene expression, alternative splicing and novel exon / gene detection
- Gene fusion identification

How to get GeneSpring NGS:

- Available as a stand-alone program for SureSelect NGS analysis
- Can be purchased as add-on for any other module of GeneSpring

We’ve begun posting tutorials using GeneSpring NGS online! Learn more here:

Introduction to GeneSpring NGS Data Analysis Software siteurl=agilenteseminar&theAction=poprecord&path=pop_program_info&recordID=3894382

Introduction to DNA-Seq in GeneSpring NGS Software siteurl=agilenteseminar&theAction=poprecord&path=pop_program_info&recordID=3992297

Introduction to RNA-Seq in GeneSpring NGS Software siteurl=agilenteseminar&theAction=poprecord&path=pop_program_info&recordID=3983892

GeneSpring Gets Social

Building a community of GeneSpring users

GeneSpring supports thousands of users world-wide, enabling cutting-edge scientific research and receiving over 12,000 citations (that’s 100 citations per month for10 years!). With such a vibrant and active research community, we are excited to announce new ways for GeneSpring users to connect, share information, find collaboration opportunities, and get the very latest research news from GeneSpring. We’ve recently introduced @GeneSpring on Twitter as well as a FaceBook page ( If you have something you’d like posted, just let us know!

We’ve also been collecting hundreds of publications that use GeneSpring and organized them according to subject and interest areas. We’ve started a CiteULike library for all of these GeneSpring articles as a useful online tool for GeneSpring users. We’ll be unwrapping that new resource soon, and we’re not stopping there – we will continue to work on new ways for GeneSpring users to connect together. Stay tuned!

Lastly, before we forget, (a belated) Happy 2012 from the entire GeneSpring Team!