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 »
I can’t believe it’s that time again! Next week we are heading off to Montreal, Canada for the week of October 11-15 for the 2011 American Society of Human Genetics annual meeting, this year in conjunction with the 12th International Congress of Human Genetics. We are excited as ever to hear what everyone has been up to, how your studies… Read more »
httpv://www.youtube.com/watch?v=_5CUPMD0Agk 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 systems to meet pressing problems such as aging populations,… 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 »
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 some cool and productive features to our popular Genome Browser…. Read more »
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 and results hard to interpret for those who have only… Read more »
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 Illumina conference was an opportunity to learn about the latest… Read more »
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 even came out.) While the full details of 7.5 are… Read more »
The common disease-common variant hypothesis has established the foundation of SNP-basis genome-wide association studies for the last several years. However, with few strong associations found, researchers are beginning to consider the effects of rare variants through the burgeoning availability of DNA sequencing. Qianqian Zhu and Dongliang Ge, of the Center for Human Genome Variation at Duke University, and others recently… Read more »
Academic Software, Productivity, and Reproducible Research httpv://www.youtube.com/watch?v=pGMLCxKPMSE&NR=1 Do you ever feel like Dr. McCoy on Star Trek, where your job and expertise is to do x, but to achieve your goals you also have to do y and z, which you either don’t want to do or don’t have the skills to do? Genetic researchers are faced with this every… Read more »
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 data was defined as primary, secondary and tertiary analysis. In Part Three I went into more details on the needs and workflows… Read more »
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 choices can be a bit confusing. In this article I… Read more »
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 polycystic ovary syndrome” was recently in Fertility and Sterility with… Read more »
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 1 CPU.” SNP & Variation Suite (SVS) version 7.4 introduced… Read more »
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 sources of help available. These include the low tech option… Read more »
Our recent blog post about the release of SNP & Variation Suite v7.4 gave you a sneak peek into what can be achieved with the revamped SVS/Python integration, which includes the incorporation of NumPy and SciPy libraries and new graphical layout capabilities. A Python package (such as SciPy) is similar to an R package, which you may be more familiar… Read more »
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 research. (All abstracts below.) First, in the pharma world, congrats… Read more »
Almost every statistic that is used for significance testing in scientific research comes with a set of assumptions. If the test is applied to data that does not meet those assumptions, then the results of the test may not be valid. The statistics commonly used in genome-wide association studies (GWAS), such as the Fisher’s Exact Test or the Chi-Square Test,… Read more »
