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Single Cell Data Visualization in Multinational Biopharma Org’s Fight Against Disease

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Industry

Healthcare & Life Sciences

Summary

  • By providing scientists the capability to analyze single cell experiments from their laptops, a leading multinational biopharmaceutical company and Plotly have eliminated a barrier in discovering new targets for drug design.
  • Exploring the gene expression in single cells will enable scientists to more deeply understand cancer and other diseases to create better medicines. A typical experiment contains tens to hundreds of thousands of cells, each expressing more than 10,000 genes.
  • By developing a single cell RNA sequencing visualizer application, the biopharma company saves hours of app development time and provides real-time research data access to hundreds of biologists and chemists across the org.
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Introduction

A multinational biopharma organization is well known for being a global leader in pharmaceutical development. Its research and development efforts unite scientific expertise on the immune system and human genetics with technologies like artificial intelligence and machine learning. 

With dozens of vaccines and medicines currently in active development, the company is leveraging cutting-edge technologies to accelerate innovation in therapies for infectious diseases, HIV, cancer, and immune system disorders.

"By helping our team to create tools that can visualize millions of rows of data in seconds, Plotly Dash Enterprise has enabled us to deliver powerful capabilities into the hands of our researchers. These tools are flexible, reproducible, and integrate well with our larger systems, accelerating our research and development."

Head of advanced analytics, Multinational biopharmaceutical company

Challenge

The organization’s advanced analytics team required a single cell RNA-sequencing analysis tool that would enable scientists to analyze these complex data sets, apply custom parameters, and share analyses in an interactive way. The app would be a resource for hundreds of researchers in R&D and clinical departments across the company’s global presence.

The app would need to address several challenges:

Real-time large data: A performant app would have to ingest and visualize, in real time, large datasets of up to a couple million rows, displaying up to 27,000 different gene expressions across thousands to hundreds of thousands of cells while distinguishing between cell types.

Variable skillsets and tooling: While computational biologists could code data apps using R, there was no centralized, standardized tooling for R&D scientists to visualize and share single cell data analyses prior to Dash. The lack of appropriate tooling presented pain points including delays for several weeks for a scientist to view the single cell analysis data from their own experiments, and the inability of scientists to interact with their data in real time.

Regulatory compliance: Pharmaceutical development is a highly regulated industry, and biopharmaceutical companies have stringent internal requirements for documenting internal tools and workflows. The app would have to meet strict standards for code development.

System integration: The single cell RNA sequencing app would need to integrate smoothly with the company’s existing gene data virtualization platform, research study databases, and greater omics visualization platform.

Solution

With a Dash Enterprise license, the company’s advanced analytics team leveraged the expertise of Plotly's Professional Services team to actualize their vision of the single cell RNA sequencing visualizer app and fully capitalize on Dash Enterprise capabilities, benefitting from:

In-depth knowledge of Dash libraries and application components. To address the single cell data use case, the app uses powerful Vaex analytics to rapidly process and visualize large data sets.

Custom component development to deliver specialized data filtering based on scientists specific user inputs and parameters. 

Development best practices guidance on back-end Python processes like caching and background scheduling. Plotly Professional Services ensured the app’s internal dependencies connected with the company’s cloud data storage system.

UI/UX consulting on the styling and branding capabilities available with Dash Enterprise resulted in a beautiful application interface and ensured the app’s seamless alignment with the company’s internal branding standards.

Results

The single cell RNA sequencing visualizer app is centrally managed in Dash Enterprise and embedded within the biopharma company’s larger omics platform. The app supports single sign-on with users’ existing credentials.

  • By leveraging Dash Enterprise and Plotly’s Professional Services, the company saved multiple hours of application development and integration time.
  • The single cell RNA sequencing visualizer app grants hundreds of biologists/chemists/collaborators real-time access to data from 200 research studies. 
  • Millions of rows of data can be rendered in just a few seconds as rich, interactive visualizations. 
  • Custom-filtered analyses can be shared through a simple URL link, accelerating time to insight from days to minutes.
  • Dash Enterprise grants greater visibility into app usage data, enabling better optimization of resources and identification of user trends for informed decision-making

About Plotly

Plotly is a software company whose mission is to enable every company, around the world, to build data apps. Our product, Dash Enterprise, is a platform of best-in-class development tools to quickly and easily visualize data in Python from virtually any data source. With customers across the Fortune 500, Plotly is a category-defining leader in enabling data-driven decisions from advanced analytics, machine learning, and artificial intelligence.

About Plotly

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