Science February 26th, 2018 Circulating Tumor DNA Analysis on the Seven Bridges Platform Next Generation Sequencing (NGS) has brought significant improvements in all areas of biotechnology and healthcare — and cancer screening is no exception. The latest game-changer is liquid biopsy, a novel and challenging NGS application. By directly measuring and analyzing circulating tumor DNA (ctDNA) in blood, liquid biopsy is a promising, … Written by Sanja Mijalkovic, Luka Topalovic, Ognjen Milicevic Science December 18th, 2017 The GA4GH Workflow Execution Challenge: evaluating reproducibility and portability across platforms Large-scale, geographically distributed genomics analysis efforts, such as the PanCancer Analysis of Whole Genomes (PCAWG) project, highlight a trend in our community towards moving compute to where data resides. For PCAWG, this was out of necessity as the genomes for ~2,800 cancer donors were stored across 8 different locations around … Written by Guest Author: Brian O’Connor Cancer Genomics Cloud November 7th, 2017 The Cancer Genomics Cloud: collaborative, reproducible, democratized (and now citable!) Last week we published our paper The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized—A New Paradigm in Large-Scale Computational Research in Cancer Research as part of their special issue on computer resources. Congratulations to everyone who’s worked on the Cancer Genomics Cloud, and many many thanks to the team at … Written by Nick Common Workflow Language September 26th, 2017 Develop, test and scale reproducible bioinformatics workflows with Rabix Rabix: the toolkit for reproducible bioinformatics This summer, our development team announced the public launch of Rabix: the open source toolkit for creating and running reproducible computational workflows. Rabix was founded to overcome the challenges inherent in running reproducible bioinformatics analyses at scale. Here we show how the combination of software containers, workflow language and Rabix gives bioinformaticians the […] Written by Nick Cavatica September 19th, 2017 Big data for big results in childhood cancer Last week Seven Bridges CEO Brandi Davis-Dusenbery joined an expert panel to discuss how data contributes to the fight against childhood cancer. Hosted by The Atlantic, the Children and Cancer forum sought to address the practical realities of pediatric cancer and identify ways to improve outcomes for these patients. You … Written by Nick Genomics August 31st, 2017 A first look at GATK4 on the Seven Bridges Platform One of the big take-away messages from the Bio-It World Conference this year was the Broad Institute’s announcement that they plan to fully open source their GATK4 software. By transitioning to a BSD 3-Clause licence, GATK4 becomes fully open for commercial use without a separate commercial licence, which should particularly … Written by Nick Cancer Genomics Cloud August 23rd, 2017 Reducing bioinformatic analysis costs with AWS Spot instances Although genome sequencing costs have dropped dramatically over the past few years, analyzing large amounts of genomic data remains expensive. As the scale of genomic projects continues to grow, cost-efficient bioinformatic analysis is key to gaining insight from the estimated 100 million to 2 billion human genomes that will be … Written by Jessica Lau Cancer Genomics Cloud August 16th, 2017 CloudNeo: CWL Brings Cancer Genomics to the Cloud A cloud-based workflow for patient-specific tumor neoantigens CloudNeo—a computational workflow for identifying patient-specific tumor neoantigens from Next-Generation Sequencing (NGS) data, was recently published in Bioinformatics. Originating from Jeffrey Chuang’s lab at The Jackson Laboratory, CloudNeo is a neoantigen prioritization workflow designed specifically for the cloud. The authors have made the CloudNeo workflow available on the Seven […] Written by Patrick Science July 18th, 2017 Sequence Bloom Trees, Part I: Motivation and principles Modern bioinformatics involves a lot of searching datasets, like The Cancer Genome Atlas (TCGA), that contain data from many experiments. Wanting to do this efficiently raises not only data management problems but also algorithmic ones. Searching a dataset like TCGA in hopes of figuring out which experiments contain a given … Written by Nate Posts navigation 1 2 3 4 5 6 7 … 12
