Golden Helix Blog

I Want a GPU for Computational Analysis! Which One Should I Get?

Apr 14, 2011

A GPU can produce an enormous boost in performance for many scientific computing applications. Since we announced the availability of SNP & Variation Suite’s incorporation of GPUs to dramatically speed up copy number segmentation, we’ve received numerous inquiries on recommendations for what GPU to purchase. Unfortunately the technical terminology and…

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Recent Publications on Polycystic Ovary Syndrome, Bovine Calving Ease, Systemic Lupus Erythematosus, and much more

Mar 29, 2011

We’ve had another busy few weeks for Golden Helix customers who have been hard at work publishing in all sorts of journals on all sorts of topics. (All abstracts below.) First off, from the Cedars-Sinai Medical Center in LA, “Replication of association of a novel insulin receptor gene polymorphism with…

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Updates to CNAM Make SVS the Fastest and Most Accurate Copy Number Tool for Common and Rare CNVs

Mar 16, 2011

A recent email from a user of SVS: “Your CNAM Optimal Segmentation algorithm is by far the best I ever used and believe me, I’ve tried many. Great use of the GPU for segmentation – it is 3x faster than using my 8 CPUs alone and 25x faster compared to…

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Getting Your Research Questions Answered Quickly with the Various Golden Helix Support Mediums

Mar 9, 2011

From the Customer Support Desk… At Golden Helix, we place a strong emphasis on customer support and helping our customers use the software to the best of their abilities to answer any research questions they have. Due to such a strong emphasis on customer and technical support, there are numerous…

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Recent Publications on Asthma, Schizophrenia, Peripheral Neuropathy, Rheumatoid Arthritis, Alzheimer Disease, and Esophageal Cancer

Feb 17, 2011

As you may have guessed from the title of this post, we’ve had a lot of customers publishing in the first six weeks of 2011. We are always excited to hear about about our customers’ findings and how they were able to use SNP & Variation Suite to accelerate their…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 3

Jan 19, 2011

The advances in DNA sequencing are another magnificent technological revolution that we’re all excited to be a part of. Similar to how the technology of microprocessors enabled the personalization of computers, or how the new paradigms of web 2.0 redefined how we use the internet, high-throughput sequencing machines are defining…

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Recent Publications on Schizophrenia, Cocaine Abuse, Childhood IgA Nephropathy, CNV Regions, and Genetic Variants in Metabolic Traits

Jan 5, 2011

Happy New Year! Golden Helix customers published 92 papers in 2010 unveiling new associations and novel findings using SNP and Variation Suite – a great feat for all! We anticipate an even more “significant” 2011. Wrapping up last year, congrats to Subba Rao Indugula, Guangyun Sun, and Ranjan Deka over…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 2

Dec 9, 2010

When you think about the cost of doing genetic research, it’s no secret that the complexity of bioinformatics has been making data analysis a larger and larger portion of the total cost of a given project or study. With next-gen sequencing data, this reality is rapidly setting in. In fact,…

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Recent Publications on Type 2 Diabetic Retinopathy, Grapevine Flavor, Pulminary Function, and Pharmacogenetics Testing

Nov 30, 2010

Let’s kick off this month’s recognition with Audrey Papp and Wolfgang Sadee at Ohio State University for their work on “Flavopiridol Pharmacogenetics: Clinical and Functional Evidence for the Role of SLCO1B1/OATP1B1 in Flavopiridol Disposition” just published in PLoS ONE. (All abstracts below.) Also in pharmacogenetics (albeit in mice) this month…

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CNV Analysis Tips for Illumina Data

Nov 24, 2010

Please see our updated tutorials for CNV Analysis by visiting: https://www.goldenhelix.com/resources/SNP_Variation/tutorials/index.html The following statement is representative of a common question that is posed to the Golden Helix support team: “I followed all of the steps in the SVS7 CNV analysis tutorial, but my results seem kinda funny. The segment means…

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A Hitchhiker’s Guide to Next Generation Sequencing – Part 1

Nov 15, 2010

If you have had any experience with Golden Helix, you know we are not a company to shy away from a challenge. We helped pioneer the uncharted territory of copy number analysis with our optimal segmenting algorithm, and we recently handcrafted a version that runs on graphical processing units that…

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Recent Publications on Bladder Cancer, Schizophrenia, Childhood IgA Nephropathy, and Ancestry Markers

Nov 5, 2010

Recognition this month begins with Eric Londin at Coriell Institute for Medical Research for his publication in PLoS ONE: “CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins.” (Abstract below). Also recently published in PLoS ONE is Chiara Magri with Brescia University School of Medicine on her…

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Conference Report: International Genetic Epidemiology Society and Genetic Analysis Workshop

Oct 27, 2010

The week of October 10-16th was a busy time in our industry.  Hundreds of biostatisticians, genetic epidemiologists, and statistical geneticists gathered in Cambridge, MA for the annual conference of the International Genetic Epidemiology Society (IGES) on October 10-12, followed by the biennial Genetic Analysis Workshop (GAW) on October 13-16.  I…

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Video Graphics and Genomics: A Real Game Changer?

Oct 20, 2010

Why should a genetic researcher care about the latest in video gaming technology? The answer is video graphics cards or Graphics Processing Units (GPUs). For certain computational tasks, a single GPU can perform as well as an entire cluster of CPUs for only a fraction of the cost. And because…

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Four New Add-on Scripts Available for Strand Flipping, Histogram Means, and Chi-Squared Calculation

Oct 14, 2010

The scripting environment in SVS 7 allows for cross-communication between the powerful Python scripting language and the tools used in data analysis. Scripting is often the most effective way to make new features available to customers prior to new software releases. We often write scripts based on a specific customer’s…

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Best Practices for Incorporating Public Genotype Data in Your Study

Oct 12, 2010

The Golden Helix sales team recently came to me for recommendations regarding best practices for incorporating public controls in SNP GWAS.  It seems that there has been a surge of questions regarding this practice over the past few weeks from our customers.  Initially, I laughed at the irony of being…

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Recent Publications on Ankylosing Spondylitis, Asthma, Heroin Dependence, and Lupus

Oct 6, 2010

It’s been a busy month for the genetics community, and Golden Helix customers are no exception. First in the line up, congrats to Marta Artieda with Progenika Biopharma in Spain for her work on “Association of the Intergenic Single-Nucleotide Polymorphism rs10865331 (2p15) with Ankylosing Spondylitis in a Spanish Population” in…

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Stop Ignoring Experimental Design (or my head will explode)

Sep 29, 2010

Over the past 3 years, Golden Helix has analyzed dozens of public and customer whole-genome datasets and candidate gene datasets for a host of studies.  Though genetic research certainly has a number of complexities and challenges, the number one problem we encounter, which also has the greatest repercussions, is born…

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Report from Capita Selecta in Complex Disease Analysis Conference in Belgium

Sep 14, 2010

How much fun is a person allowed to have when going to a conference? That kind of sums up my personal experience going to the first ever Capita Selecta in Complex Disease Analysis (bi-annual) conference in Leuven, Belgium. Not only was it fun, but the conference program was packed with…

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Recent Publications on Late-Onset Sporadic Parkinson’s and Renal Cell Carcinoma

Sep 1, 2010

We’re inspired by significance. Every tool we develop and every service we deliver is designed to help our customers achieve significance in their research. Not only statistical, but scientific and personal significance as well. The icing on the cake is being able to share what our customers do and discover…

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