Last month, I announced our Golden Helix Gives Back Campaign. During times like this, when funding is tight, we wanted to make a statement to our community. We at Golden Helix are committed to empower researchers and practitioners in the life science field. For those hard working people it is nice to catch a break from time to time.
After our announcement, we were surprised at the volume of inquiries, numbering into the hundreds. While we wish we could help everyone, our team of reviewers had a difficult job to select the three researchers that we felt were most deserving. Continue reading
The major interest in genomic prediction is best understood by looking at the growth of the human population. Over the last few hundred years we have experienced an increase in population due to medical advances and massive increase in agricultural productivity. The planet’s population continues to explode: from 1 billion in 1820 to 2 billion in 1930, 3 billion in 1960, 4 billion in 1974, 5 billion in 1987, 6 billion in 1999, and 7 billion in 2012. Just between 1990 and 2010 the world population grew by 30% (see Fig 1). In short, people live longer due to advances in science and medical care. This growth compels us to develop a better food supply. Continue reading
As Andreas Scherer mentioned in his post last Tuesday, we will kick off our 2nd annual Abstract Challenge Monday, December the 15th. Here are the details.
All academic, government, and commercial organizations world-wide working with genetic data (regardless of species) are invited to apply. Your project should be using DNA-Seq, RNA-Seq, SNP, or CNV methodology, as well as testing gene panels or searching for rare variants. Continue reading
As Dr. Andreas Scherer mentioned in a blog post earlier this year, Golden Helix is committed to supporting the education of the next generation of genetic researchers. And as such, over the course of 2014, we at Golden Helix are working with education programs across the US and Canada to make teaching and learning bioinformatics easier.
This fall semester at the University of Illinois, Urbana-Champaign, Dr. Jeffrey Moore introduced his students to VarSeq. Dr. Moore, who was recently named a Howard Hughes Medical Institute Professor seeks to integrate genetics into organic chemistry education to investigate the underlying causes of conditions explored in many facets of science. Continue reading
If you’ve seen the recent webinars given by Gabe Rudy and Bryce Christensen, you’ve no doubt been impressed by the capabilities of VarSeq when it comes to annotation and filtering. However, we sometimes forget that the power that enables all this complex analysis can also be used in more mundane tasks like VCF subsetting. And although these day-to-day tasks don’t make for an impressive demo, they are central to the work of anyone who deals with genetic data.
Some might scoff at the idea of using a full featured application for basic bioinformatic tasks, when excellent open source tools can get the job done. I completely agree and am the first to defend, support, and contribute back to the open source community.
Last year, as part of our ongoing commitment to empower genetic research, we hosted our first research competition. The competition was very successful and now we will make the competition an annual event.
Here at Golden Helix, we are dedicated to creating powerful software that enables researchers to complete complex analysis. This competition allows us to enable discovery by awarding software to those making an impact in the field.
This year’s competition will be much like last year’s – we will award a new laptop, software licenses, and the chance to present your work to the community in a live webcast. The one big difference is that this year, winners have the option to choose between two great software tools – SNP & Variation Suite (SVS) which is an integrated collection of powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic dataor our new offering, VarSeq which streamlines the process of annotating and filtering variants obtained from next generation sequencing pipelines in order to find variants of interest in a very efficient and straightforward manner.
The contest will open on Monday, December 15th. Please look for more information from us in the coming days.
It’s come to my attention in recent weeks, through various customer interactions, that many are not aware of the fantastic functionalities that exist in SNP and Variation Suite (SVS) for large-n DNASeq workflows; this includes large cohort analyses with case/control variables.
The data you’ll see below is the publically available 1kG Phase 1 v3 Exome sequences from 1,092 individuals with a simulated case/control phenotype. In this dataset there are 167 cases and 925 controls. I’ve filtered this dataset down to the rare variants based on exons from RefSeq Genes version 105; NHLBI ESP6500SI-V2 Exomes Variant Frequencies 0.019 (using MAF threshold of 0.01) and removed all variants defined as common by dbSNP version 137 provided within SVS. And finally the dataset was filtered only to non-synonymous coding variants by using the Coding Variant Classification function, which left a dataset of 204,818 markers. Continue reading
The Golden Helix team enjoys following our customers’ success. And we would like to share some recent client work to demonstrate what is possible with our software, as well as to inspire researchers to continue questioning current scientific norms. Continue reading
To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement.
Basically, there were two types of talks at ASHG. Those that proceeded the official ExAC release talk and referred to it, and those that followed the talk and referred to it.
Why is this a big deal? Well, since they have generously published their data not only in a great online browser but also in a downloadable VCF file, let’s take a look at the data and see for ourselves. Continue reading
Over the last several years, NIH funding and academic budgets have been taking drastic cuts. This means for many of our clients, that they have to submit more grants than ever. We want to give the community a bit of break. Continue reading