Sage Bionetworks

Sage Bionetworks is a leading non-profit research organization that uses open science practices to transform biomedical discovery. Based on the belief that high-quality, well-annotated data acts as the foundation of modern biomedical innovation, Sage dreams of a world where people work together across institutional boundaries to address medical research problems.

Today a portion of Sage roughly 120 employees and associates rely on Tower and Nextflow to help improve productivity, simplify collaboration, easily scale computing to the cloud, and manage complex biomedical data securely.

Sage is in the business of building research communities around different datasets. While they do not operate next-generation sequencers in-house, their projects often require them to analyze sequencer output and assemble curated data sets. They use a combination of in-house developed workflows (DAGS) and community pipelines from reputable sources such as nf-core to accomplish this.

Given Sage’s focus on data, compliance and ensuring robust data governance and appropriate use of data is critical. As a publicly funded institution, they also need to operate efficiently, and diligently track various financial grants to show that research dollars are being responsibly managed.

To accomplish these goals, Sage uses Tower alongside several in-house tools regularly used to facilitate collaborative engagements. These tools include their Synapse Platform, Bridge Platform, Challenge Platform, and Mobile Toolbox.

After evaluating several workflow solutions, including CWL on EC2, self-hosted Toil clusters, and integrated bioinformatic analysis platforms, Sage selected Nextflow and Tower from Seqera. Today, Sage runs a mix of in-house developed pipelines (DAGS) and nf-core pipelines, all hosted on GitHub.

“By running our Nextflow pipelines with Tower, we now spend 50% less time compared to running individual workflows on EC2. Also, by leveraging nf-core pipelines and tools, we spend 80% less time developing workflows.”

Sage makes extensive use of Tower Secrets across all of their projects, to facilitate secure connections and data sharing using Synapse, Sage’s platform for research collaboration.