Leveraging the power of computational biology to advance scientific discovery
Situation
The research team at a leading biopharmaceutical company was struggling with a cumbersome and time-consuming variant calling analysis workflow.
Their current process involved manual manipulation of data files, complex command-line tools, and fragmented data visualization.
This inefficiency hampered their ability to analyze next-generation sequencing (NGS) data efficiently and identify relevant variants for further investigation.
They lacked the specific in-house resources to develop a solution in-house, so they turned to Bridge Informatics (BI) for help.
Strategy & Process
BI collaborated with the research team to understand their specific requirements and design an app roadmap for the custom bioinformatic application (app).
Leveraging R and Shiny, BI’s engineers developed the app in a secure and controlled staging environment, ensuring code quality and functionality.
This interactive web app streamlined the entire variant calling analysis process, providing a user-friendly interface for:
Data Upload: Users can easily upload raw NGS data files in standard formats directly into the app.
Streamlined Workflow: The app integrates various bioinformatic tools for pre-processing, alignment, variant calling, and filtering steps. Users can select specific tools and parameters through intuitive drop-down menus and sliders, eliminating the need for complex command-line syntax.
Interactive Visualization: The app generates real-time visualizations of the analysis results, including variant calls, quality scores, and coverage depth. Users can explore these visualizations interactively, filter variants based on specific criteria, and download results for further analysis.
Collaboration: The app allows multiple users to access and analyze data simultaneously, fostering collaboration within the research team.
After implementing robust security measures and establishing a monitoring system to ensure application stability and performance, the app was deployed to our Client’s preferred cloud platform.
Results
The custom R-Shiny application developed by BI transformed the research team’s variant calling analysis workflow in the following ways:
Increased Efficiency: The R-Shiny app significantly reduced the time required for variant calling analysis, allowing researchers to analyze data faster and focus on biological interpretation.
Improved Accuracy: By automating repetitive tasks and integrating robust bioinformatic tools, the app minimized the risk of errors associated with manual data manipulation.
Enhanced User Experience: The user-friendly interface simplified data analysis for researchers with varying levels of bioinformatic expertise. Interactive visualizations provided clear insights into the data, facilitating informed decision-making.
Scalability and Collaboration: The R-Shiny app can be easily scaled to accommodate larger datasets and support collaboration among multiple research teams.
BI continues to provide ongoing maintenance to address any bugs or issues and support the research team with any future application enhancements.
Bridging Bioinformatics and Discovery
With the custom R-Shiny app, our Client’s research team transformed their variant calling analysis into a streamlined, scalable, and user-friendly process. This case study highlights the power of tailored bioinformatics solutions to accelerate scientific breakthroughs.
Contact us today to explore how Bridge Informatics can revolutionize your workflows.
Jessica Corrado, Head of Business Development & Commercial Operations, Bridge Informatics
As the Head of Business Development & Commercial Operations, Jessica is responsible for driving strategic growth initiatives and overseeing the company’s commercial activities. She has both a keen understanding of the life sciences industry and a strong track record in building successful partnerships.
Prior to joining Bridge, Jessica held a number of leadership roles across sales, marketing, and communications. Outside of work, Jessica is responsible for the majority of marketing and event planning for Shore Saves, a non-profit animal rescue. She enjoys reading and is often reading at least two books of various genres at a time. If you’re interested in reaching out, please email [email protected].
