Blog

We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

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

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

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

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

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

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

Custom interactive analysis on all Seven Bridges environments

This week we released Data Cruncher, an interactive analysis tool available on the Seven Bridges Platform, Cancer Genomics Cloud, and Cavatica. By enabling researchers to apply custom scripts in JupyterLab to data stored in the cloud, Data Cruncher supports interactive and collaborative bioinformatic analysis at scale. Bringing custom interactive analysis to the cloud Although some […]

Written by Jessica Lau

Optimizing novoBreak on the Cancer Genomics Cloud

Last week, we released novoBreak—an exciting new bioinformatics software—on the Cancer Genomics Cloud (CGC). The tool, described by Zechen Chong and colleagues in Nature Methods, is a novel approach to detect breakpoints in cancer genomes with high precision and sensitivity. In this post, we explain how Zechen used the Publish your app …

Written by Jessica Lau

Cavatica wins Bio-IT People’s Choice Award

Cavatica is the data sharing platform for pediatric disease Seven Bridges and our partners at The Children’s Brain Tumor Tissue Consortium (CBTTC) and the Pacific Pediatric Neuro-Oncology Consortium (PNOC) were honored with a Bio-IT World People’s Choice award for Cavatica, the collaborative analysis and data sharing platform for pediatric diseases. This award follows Seven Bridges’ previous Best […]

Written by Patrick

We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line. get in touch