As a senior studying statistics at Montana State University, I was fortunate to be granted the opportunity to intern with the development team at a local software company. I was even more fortunate when this internship turned into full-time employment after I graduated. Working on a team with extremely talented individuals, I realized the significant impact our company makes through… Read more »
Happy new year! We hope all of our readers, clients, and users had a great holiday season filled with friends and family! While Golden Helix did take a break from blogging in December, we’ve still been pretty busy bringing you new and exciting things. We’re pleased to announce the addition of genome maps and annotation tracks for two new plant… Read more »
In preparation for a webcast I’ll be giving on Wednesday on my own exome, I’ve been spending more time with variant callers and the myriad of false-positives one has to wade through to get to interesting, or potentially significant, variants. So recently, I was happy to see a message in my inbox from the 23andMe exome team saying they had… Read more »
Recently, I have been spending some time analyzing real patient data. I’m preparing for a webcast I’ll be giving in which I will walk through the process of replicating the findings of Dr. Gholson Lyon‘s study on the novel disease diagnosis he named Ogden Syndrome. Being so close to data that comes directly from clinical settings got me thinking about… Read more »
Since Dr. Ken Kaufman gave his webcast on Identifying Candidate Functional Polymorphisms in SVS, we’ve been working with Dr. Kaufman to simplify and automate many of the steps in his workflow. I touched on this in my last blog post, and I’m excited to report that with Ken’s help, we’ve been able to simplify the workflow even more. In particular… Read more »
It has now been about a year since Illumina and Affymetrix announced their respective exome genotyping arrays. Both products were launched with ambitious visions of how they would enable researchers to learn significantly more about the cause of human diseases. Sales of the Illumina chip exceeded expectations, and the company said that it sold enough exome chips through the first… Read more »
As first announced in October 2011 and previewed in a blog post last month, Golden Helix has been hard at work for the last year developing a free genome browser called GenomeBrowseTM. We are now beyond excited to announce that GenomeBrowse will be available to the public on September 12th on our website. (Did we mention it’s free?) GenomeBrowse raises… Read more »
I recently curated the latest population frequency catalog from the 1000 Genomes Project onto our annotation servers, and I had very high hopes for this track. First of all, I applaud 1000 Genomes for the amount of effort they have put in to providing the community with the largest set of high-quality whole genome controls available. My high hopes are… Read more »
Last month I was inspired to create a new way to keep our customers apprised of the latest information on Golden Helix software without cluttering inboxes and overwhelming our blog. I happened to receive a link to an article for one of Illumina’s bulletins and realized that was exactly what we needed at Golden Helix as well! On Wednesday, we… Read more »
There is nothing cooler than having something arrive that you have been excitedly waiting for: last week I got an email notification that my 23andMe exome results were ready. Actually, I got 3 emails that my exome results were ready. You see, I lucked out. It all began two years ago on DNA day when Hacker News reported that 23andMe… Read more »
Recently I gave a presentation on bioinformatic filtering: the process of using quality scores, annotation databases, and functional prediction scores to intelligently and quickly reduce your variant search space. View the recording here» In this webcast, I mention that filtering is something we have been doing for a long time, and that there are some great examples that use exome… Read more »
As Product Quality Manager, I have been spending quite a bit of time lately thinking about the best way to communicate with our Golden Helix customers with regards to product quality and customer support issues. Most of our customers at this point have already seen several emails from me this year! Email is certainly one way to get an announcement… Read more »
My work in the GHI analytical services department gives me the opportunity to handle data from a variety of sources. I have learned over time that every genotyping platform has its own personality. Every time we get data from a new chip, I tend to learn something new about the quirks of genotyping technology. I usually discover these quirks the… Read more »
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, however, something comes along that just might be worth paying… Read more »
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 the ability to analyze PacBio files.
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 questions about NGS – Gabe Rudy, Vice President of Product… Read more »
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 project, I find I want to abandon the current project… Read more »
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 always too much to do. And he finds command-line tools… Read more »
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 that can accomplish these tasks. Adding Annotation Data to a… Read more »
As I’ve mentioned in previous blog posts, one of the great aspects of our scientific community is the sharing of public data. With a mission of providing powerful and accurate tools to researchers, we at at Golden Helix especially appreciate the value of having rich and extensive public data to test and calibrate those tools. Public data allow us to… Read more »
