Golden Helix Newsletter

 
Is Free Software Really Free?
Examining the hidden costs of open-source bioinformatic software tools
Is Free Software Really Free


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 allow new methodologies to be created and expanded. They tie a community of researchers together across countries, universities, and subject matter. They create the opportunity for genomic research to expand exponentially as there is unlimited access to analysis tools. However, many researchers never stop to consider the hidden costs of open-source software. Continue reading »

Guest Post: Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS
by Guest Author, Dr. Stephen Turner, Bioinformatics Core Director at University of Virginia

Dr. Stephen Turner
I'm a huge supporter of the Free and Open Source Software movement. Every now and then, however, something comes along that just might be worth paying for. As a director of a bioinformatics core with a very small staff, I spend a lot of time balancing costs like software licensing versus personnel/development time, so that I can continue to provide a fiscally sustainable high-quality service. But recently we had a client who wanted to run a fairly standard case-control analysis on a dataset from dbGaP. Since this isn't the focus of my core's service, I didn't want to invest the personnel time in deploying a GWAS analysis pipeline, downloading and compiling all the tools I would normally use if I were doing this routinely. Continue reading »

Nature or Nurture: What Insight Can Science Provide?
by Dr. Jared Bowden, Field Application Scientist

Bee
I recently transitioned jobs from researching early diagnostics for Type II Diabetes using several omics technologies such as proteomics, metabolomics, and lipidomics to working with genomics data at Golden Helix. As scientists, one of the questions we face in examining these many areas of data is differentiating between what Nature has provided us (in our genetic code) and what is the result of Nurture (environmentally-induced variations in the expression RNA, proteins, and metabolic signatures). Continue reading »
 
   Featured Webcast
Learning From Our GWAS Mistakes: From experimental design to scientific method
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   Featured Resource
How SVS Treats Gender in Calculating Genotype Statistics
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   Featured Case Study
Dr. Julia Pinsonneault Uses SVS for Pharmacogenetic Associations for 10 Years
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   SNP-ITS
SVS Now Part of the PacBio Partner Program
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Golden Helix Partners with Complete Genomics
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Illumina's BaseSpace Apps to Include Golden Helix
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PLoS ONE
Cholesteryl Ester Transfer Protein (CETP) Polymorphisms Affect mRNA Splicing, HDL Levels, and Sex-Dependent Cardiovascular Risk
Papp, A et al.
Ohio State University
Read the article »

PLoS Genetics
Variation in MSRA Modifies Risk of Neonatal Intestinal Obstruction in Cystic Fibrosis
Henderson, L et al.
Johns Hopkins University, Maryland
Read the article »

PLoS ONE
DCLK1 Variants Are Associated across Schizophrenia and Attention Deficit/Hyperactivity Disorder
Havik, B et al.
University of Bergen, Norway
Read the article »

Obesity
Association of Type 2 Diabetes Susceptibility Loci With One-Year Weight Loss in the Look AHEAD Clinical Trial
Peter, I et al.
Genetics Subgroup of the Look AHEAD Study
Read the article »

PLoS ONE
Amplified Genes May Be Overexpressed, Unchanged, or Downregulated in Cervical Cancer Cell Lines
Vazquez-Mena, O et al.
Facultad de Medicina Universidad Nacional Autonoma de Mexico
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About Golden Helix
Founded in 1998, Golden Helix is known for helping genetic research groups working with large-scale DNA-sequencing or microarray data overcome the frustration and challenges of bioinformatic roadblocks: delayed projects, lack of quality findings, and low productivity. By empowering researchers with highly effective software tools, world-class support, and an array of complementary analytic services, we refute the notion that analysis has to be difficult or time consuming. Golden Helix's flagship software product, SNP & Variation Suite (SVS), is an integrated collection of powerful data management, quality assurance, visualization, and tertiary analysis tools for genetic data. SVS is delivered in a user-friendly, scalable platform and is supported by a team of highly trained bioinformaticians, statistical geneticists, and computer scientists that together make advanced statistical and bioinformatic methods accessible to scientists of all levels.

 

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