Science May 28th, 2018 Accurate Analysis of Differential Methylation Data With few exceptions, every human cell is composed of an identical DNA sequence. However, there are around 200 different cell types in our bodies. What is the underlying reason? Each different cell type represents a specific gene expression pattern. One of the main mechanisms that enables this is epigenetics. Epigenetics … Written by Milos Nikolic, Tamara Stankovic, Milan Domazet, Sanja Mijalkovic Science May 28th, 2018 Optimized Workflow for Bisulfite Sequencing Data Analysis Epigenetics is an extra layer of information that is not encoded in the primary sequence of an organism’s DNA. While several mechanisms of epigenetic regulation exist, DNA methylation is one of the most commonly studied ones. Typically, the presence of methylated cytosines within a promoter region represses gene expression. The … Written by Vesna Pajic, Tamara Jovanovic, Ana Damljanovic Science May 15th, 2018 3-hour Whole Genome Analysis with GATK4 In the pursuit of accelerating next generation sequencing data processing for clinical applications, Seven Bridges has developed a configurable GATK4 workflow 3.0 times faster than previous iterations. Following up on our initial push of the GATK4 workflow in 2017, and our recent update with the Broad’s Best Practices, we’ve worked … Written by Vladimir Kovacevic, Teodora Aleksic, Jack DiGiovanna, Stefan Risteski Common Workflow Language May 11th, 2018 Enabling portable, reproducible, and scalable biomedical data analysis using Rabix Composer and CWL v1.0 We are excited to announce the release of version 1.0 of Rabix Composer, our integrated development environment for creating bioinformatics tools and workflows, and of support for Common Workflow Language (CWL) v1.0 on the Seven Bridges Platform! For an introduction to Rabix Composer and CWL, we encourage you to read … Written by Adrian Sharma & Liz Williams Science May 7th, 2018 Spatial Transcriptomics on the Seven Bridges Platform As our understanding of biology deepens, many researchers are moving away from bulk gene expression analyses to single-cell analyses. However, current RNA-Seq methods that assay pooled RNA from tissue samples, or even from single cells, fail to conserve the spatial distribution of gene expression within the original tissue. In addition, … Written by Michele Mattioni 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 Posts navigation 1 2 3 4 5 6 7 8 9 10 … 16
