The Golden Helix Blog

Is Free Software Really Free?

May 23, 2012

The prevalence of open-source bioinformatic tools in the genetic research space is enormous. According to The North Shore LIJ Research Institute, there are over 500 genetic analysis software packages – the great majority of which are free – as of August 2010. Open-source tools are incredibly important in genetics. They…

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Guest Post: Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS

May 16, 2012

I’m a huge supporter of the Free and Open Source Software movement. I’ve written more about R than anything else on my blog, all the code I post on my blog is free and open-source, and a while back I invited you to steal my blog under a cc-by-sa license. Every now and then,…

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Researcher Uses SVS for Pharmacogenetic Associations for 10 Years

Apr 11, 2012

Dr. Julia Pinsonneault is a Research Scientist at The Ohio State University where she works to find biomarkers that guide effective treatment. Published recently in Neuropsychopharmacology, Julia has found success using SVS to find novel associations that move her research forward. Usually managing 3-5 research projects at a time from…

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Analyzing PacBio Data with SNP & Variation Suite

Mar 21, 2012

As most in the Golden Helix community are aware, SNP & Variation Suite (SVS) can handle all sorts of data including files from Affymetrix, Illumina, Agilent, and Complete Genomics with its powerful data management capabilities. Announced in February, SVS is now part of the Pacific Biosciences Partner Program and has…

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New Features in SVS: Accounting for Sex Chromosomes and Filter Columns by Variant Type

Feb 29, 2012

In the last couple of weeks, the SVS Script Repository has seen a handful of new additions. This blog post highlights three new scripts, but as always, we welcome you to check out our repository regularly to enjoy the new and exciting functionality made possible by our Python integration in…

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Admixture and Blaine Bettinger

Jan 25, 2012

Allow me to introduce you to Blaine Bettinger. Blaine is a patent attorney who holds a PhD in Biochemistry with a concentration in genetics. He is also a family history enthusiast who writes the Genetic Genealogist blog, where he gives commentary on applications of genomic science for advancing personal and…

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Leaky Sprinklers and “The Future of NGS Market Study 2011”

Nov 23, 2011

Have you ever chosen to do something yourself instead of paying money for the alternative, when, in the long run, the alternative is not really that expensive? We all have, as we all have limited budgets. One particular example comes to mind in my own life. My boyfriend, Ben, and…

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Is NGS the Answer?

Nov 9, 2011

While there is a lot of excitement in the industry about Next-Generation Sequencing, questions remain as to whether it will be “the answer” to the ails of the genetic research industry. I recently had the opportunity to sit down with three of Golden Helix’s thought leaders and ask a few…

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Sequence Analysis Methods Not Just for Sequence Data

Oct 12, 2011

Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve in the past. Whenever I make a breakthrough in one…

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Influencing the Global Dialog on Healthcare

Sep 28, 2011

On September 16-17th, I attended the Asia-Pacific Economic Cooperative (APEC) Health Systems Innovation Policy Dialog in San Francisco. It was a stimulating opportunity to look at global healthcare concerns from the perspective of developing and developed economies. There was much opportunity to dialog and frame the issues around transforming healthcare…

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Wondering what SVS can do for a PhD student? Just ask Sander.

Sep 14, 2011

Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s…

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Marker Map Manipulation Improvements in SVS 7.5

Aug 31, 2011

Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5. Have you ever wanted to view annotation data next to marker map data? Or expand the current marker map with spreadsheet data to create a custom map? SVS 7.5 features two new functions…

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SVS 7.5 Now Available!

Jul 28, 2011

More powerful rare variant analysis and visualization techniques We are proud to unveil SNP & Variation Suite (SVS) 7.5! The fifth installment of SVS delivers the most powerful rare variant analysis tools with the latest advances in tertiary or “sense making” methods for DNA next-gen sequencing. This release also adds…

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Please Help Me Get My Regression Model Set Up!

Jul 6, 2011

Golden Helix’ SNP & Variation Suite (SVS) has a Regression Module to enable researchers with varying degrees of statistical knowledge to interrogate their data using regression models to account for potential confounding effects of covariates and interaction terms. While these tools are labeled “basic”, they can be difficult to use…

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Going Coast to Coast for the Latest NGS News

Jun 23, 2011

Last week I was able to attend two very interesting conferences about the latest developments in the analysis of sequence data. I started the week in San Diego at the Illumina iDEA Conference and finished it in Philadelphia at Children’s Hospital of Philadelphia’s (CHOP) Third Annual Next-Generation Sequencing Symposium. The…

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SVS 7.5 Feature Sneak Peek: Grouping and Filtering in the Genome Browser

Jun 8, 2011

Ever since the release of SNP & Variation Suite (SVS) 7.4 back in January, our software engineers have been hard at work developing new functionality for the next version, to enable researchers to have even more control over their data. (Okay, well really, they started working on it before 7.4…

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NGS Tools and Formats for Secondary Analysis: A Primer

Apr 20, 2011

In a series of previous blog posts, I gave an overview of Next Generation Sequencing trends and technologies. In Part Two of the three part series, the range of steps and programs used in the bioinfomatics of NGS analysis was defined as primary, secondary and tertiary analysis. In Part Three…

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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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