New biotechnology companies juggle multiple challenges on the road to commercializing a breakthrough technology from discovery to large-scale deployment. By using the Seven Bridges Platform, BD Cellular Research found that delivering complex bioinformatic tools to customers was the easiest part of its new product development.

Overview

Biotechnology companies that work with genomic data can reduce their risk, and dramatically speed their time to market, by eliminating bioinformatics processes from their business processes.

Rather than spending nine-to-twelve months standing up their own department, cluster, software processes, and storage, new companies are increasingly choosing Seven Bridges — meaning their bioinformatics solution is up and running faster than they can prepare their first sequencing library.

Molecular Tagging

The scientists at BD Cellular Research set out to remove one of the biggest pain points in modern RNA sequencing: understanding not just which transcripts are expressed, but accurately counting how many are expressed in a given cell.

While traditional RNA-Seq is often used for transcript quantification, the BD Cellular Research Molecular IndexingTM kit deploys a novel molecular tagging solution. This allows researchers to uniquely label each individual RNA molecule before amplification and sequencing, thus leading to highly accurate quantification results. The tags allow for deduplication after sequencing, meaning a biologist can accurately reconstruct the exact quantity of transcripts present in the original sample.

For BD Cellular Research, however, a novel chemistry was just a start. They also needed custom, accurate, easy-to-use bioinformatic software to interpret the meaning behind the tags.

Developing, Delivering, Updating, and Supporting Bioinformatic Tools

At first, BD Cellular Research delivered their custom tools via downloadable binaries. However, they discovered it was difficult to support and created a less-than-compelling customer experience.

People had trouble installing the tools. Running them on local machines was often a slow process.

Getting customers on the latest versions, which provided critical bug fixes, proved difficult. And supporting installations on a potpourri of systems around the world was expensive.

After a comprehensive survey of the market, BD Cellular Research decided that the best way to serve their customers was to partner with Seven Bridges to deliver their bioinformatic tools at scale, via the cloud.

A Custom Cloud-Based Portal for BD Cellular Research Users

A team of more than 20 of Seven Bridges’ bioinformaticians worked with BD Cellular Research to determine how to best deliver their custom tools.  Together, the teams determined that a custom portal for BD Cellular Research’s users would be optimal.  Placing these pipelines on the Seven Bridges Platform meant BD Cellular Research could focus on quality improvements, instantly update everyone to the latest version of their tools, and entirely remove their software support burden.

The Seven Bridges team started by working with BD Cellular Research’s existing tools. First, in the process of understanding how the tools operated, the team discovered not only their current function, but also made suggestions for how to improve their performance.

Next, the team became an internal customer for our mature Software Development Kit (SDK) — based on the open-source Common Workflow Language — which allows anyone to easily port their tools and pipelines onto the Seven Bridges Platform.

Then, they handed the project off to our front- and back-end engineering team. The front-end team prepared a customized portal for BD Cellular Research users.

This portal, available at www.sbgenomics.com/cellular-research/, allows biologists to easily register for the Seven Bridges Platform, and load their data directly into a project populated with best-practice workflows. The back-end engineering team then took this workflow, and optimized it for the Seven Bridges Platform.

Delivering the BD Cellular Research Product and Ongoing Support

With the portal in place, the tools prepared, and documentation directing users of the Molecular IndexingTM kit to Seven Bridges for their bioinformatics, BD Cellular Research created, for the first time, a product that could scale infinitely.

Despite bioinformatics being a core piece of their solution, BD Cellular Research’s sales were limited only by how many kits they could produce.

Our work with BD Cellular Research did not end at the product launch. As they refined their computational tools, the Seven Bridges SDK team organized training sessions for their developers. After quickly learning the well-documented Seven Bridges SDK, BD Cellular Research benefited from delivering their tools via the Seven Bridges cloud-based Platform and by the ability to deliver updates on their own time line.

All without buying a single server, or distributing a binary.