Andreas Scherer

SVS 8.2 – New Capabilities and Features

Earlier this year we completed the marriage of SVS and GenomeBrowse. When we released Version 8 of SVS we completed a major engineering task. A lot of things under the hood of both products had been changed to create a seamless experience for our users. The new and improved SVS platform is based on a technology stack that allows us to accelerate method development and even helps us to launch new product faster. More about the latter in another blog post.

Now, the new SVS 8.2 comes with a number of new methods and features:
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Posted in Big picture, News, events, & announcements, Personal genomics, Plant & animal | 1 Comment
Bryce Christensen

Have you ever had a bad experience with a VCF file?

“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of difficulty with the format’s complexity or practical limitations. Among other responsibilities at Golden Helix, I give frequent demonstrations of our SVS software and train people to use it. In this capacity I have observed many of the challenges people encounter with VCF files, and I’d like to discuss some of those issues here. Continue reading

Posted in Best practices in genetic analysis, Bioinformatic support, Customer Questions | Tagged , , , | 4 Comments
Chelsey Clayton

And the winners are…

Drumroll, please! Voting has come to a close for the 2014 Golden Helix T-shirt contest, and there were some clear favorites among the finalists.

We are very excited at the wealth of creativity that came forward with this contest, and are happy to announce that our final decisions have been made. Continue reading

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Guest Post: Population Structure & Genetic Improvement in Livestock by Dr. Heather Huson

Dr. Heather Huson of Cornell University

Genetic improvement in livestock, particularly dairy cattle, has been a priority for both industry and researchers for nearly a century.  While the animal itself is the foundation for improvement, our research and the implementation of improvement has progressed with developing technologies and priorities.  In terms of genetics, we have evolved from basic measures of heritability to identifying specific mutations and their biological role affecting a trait.  My research focuses on population structure and trait association in domestic animals using high-density genome-wide single-nucleotide polymorphism (SNP) array data and fine-mapping sequence data.  My end goal is to conduct research that will assist in the genetic improvement of domestic animals through an increased understanding of the genetic mechanisms controlling biological pathways and the development of genomic tools for implementation. Continue reading

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Greta Linse Peterson

New MM-KBAC Method Explained

Last month, June 2014, we announced a new method that Golden Helix developed–the soon to be available MM-KBAC. MM-KBAC, or Mixed Model Kernel Based Adaptive Clustering combines the KBAC method developed by Lui and Leal (2010) with a random effects matrix to adjust for relationships between samples. The KBAC algorithm takes a binary dependent variable and transformations are used to convert the logistic regression model to a linear model so that EMMAX (Efficient Mixed Model Association eXpedited) can be used to solve the equations.

We are also very excited that we have been accepted to present this material at ASHG this October  (we’ll be in booth 422)! More importantly, we will be making this method available to our customers with the next release of SVS due out in August. Continue reading

Posted in Assessment of new methods | Tagged , , , | 3 Comments
Chelsey Clayton

It’s time to vote for your favorite Golden Helix t-shirt!

With the t-shirt submission deadline behind us, it’s time for the exciting part of the contest – picking the winners! We received a ton of fantastic designs and had a hard time narrowing them down. But, the Golden Helix team has picked seven designs that truly embody the Golden Helix spirit.
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Andreas Scherer

The added value of GenomeBrowse

GenomeBrowser users worldwide

This map indicates countries that have GenomeBrowse users

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data.

GenomeBrowse allows a user to sift through vast amounts of genomic data, and make it easy to focus on a single part or the whole. GenomeBrowse has reached global adoption; as of July 2014 thousands of users worldwide have begun to use this product.

Do you want to review a few hundred genomes on your desktop computer? No problem. We want to make this process as simple and intuitive as possible. Here are some key aspects of GenomeBrowse:

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Cheryl Rogers

Introducing Dr. Heather J. Huson

Dr. Heather Huson

Dr. Heather Huson

It is with great excitement that we introduce our next webcast: Population Structure & Genetic Improvement in Livestock, presented by Dr. Heather J. Huson of Cornell University. Huson was one of the first place winners in this year’s research abstract competition. As part of the competition Huson has the opportunity to present her research in a webcast on Tuesday July 22nd.

Heather received a Bachelor’s in Animal Science from Cornell University in 1997 and went on to complete her Ph.D. in Molecular Genetics at the University of Alaska Fairbanks in 2011.

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Ashley Hintz

The Differences Between EMMA and EMMAX

I recently gave a webcast on GWAS in a model organism: Arabidopsis thaliana; a question was brought up about the differences between EMMA and EMMAX and why the results with each would differ. Continue reading

Posted in Bioinformatic support, Customer Questions | Tagged , , , | 1 Comment
Alyssa Burzynski

Join us for a GWAS in Arabidopsis Thaliana

Join us tomorrow, July 9th at 12PM EDT, for Ashley Hintz’s webcast on GWAS in a Model Organism: Arabidopsis Thaliana.

Joining the Golden Helix team as a Field Application Scientist in April of 2014, Hintz is the perfect candidate to present on Arabidopsis Thaliana given her background in zoology and phylogenetics of planigales. Continue reading

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