Overview
ImmunoRaptor is a powerful cloud-based platform designed to streamline immune repertoire analysis for antibody discovery teams. Developed in close collaboration with a leading biotech client, it addresses key challenges such as data management, analysis bottlenecks, and limited computational resources. With an intuitive interface, scalable architecture, and standardized bioinformatics pipelines, ImmunoRaptor enables researchers—regardless of bioinformatics expertise—to efficiently manage, analyze, and track large volumes of BCR and TCR sequencing data. The platform includes advanced bioinformatics visualization tools, sequence tracking, and secure enterprise authentication, ultimately accelerating research timelines and enhancing collaboration across distributed teams. It also supports integration with scientific informatics workflows and scientific application services, enabling smooth data-driven drug discovery approaches.
Our client
A leading antibody discovery company from Europe focused on advanced biomedical research and bioinformatics for immunology.
Client’s challenge
Significant challenges in analyzing their growing volume of adaptive immune receptor repertoire sequencing (AIRR-Seq) data. Their research teams were generating large amounts of ngs data through various protocols including Illumina and 10x Genomics platforms, but struggled with:
- Data management complexity: Researchers had difficulty organizing and tracking hundreds of samples across multiple projects and structured datasets.
- Analysis bottlenecks: Existing tools required specialized bioinformatics applications that most researchers didn’t possess.
- Sequence tracking: The client needed to maintain a comprehensive biomarker database of all processed sequences to track which ones had already been provided to their customers for further analysis.
- Collaboration barriers: Research teams working in different locations couldn’t easily share data and insights.
- Computational resource limitations: Their in-house infrastructure couldn’t efficiently handle the increasing computational demands of immune repertoire analysis and sequence alignment in rna therapeutics.
Client’s goals
The client’s goal was to implement a user-friendly, scalable platform that would streamline their immune repertoire analysis workflow, enable efficient sequence tracking, and accelerate their antibody discovery process without requiring their scientists to become bioinformatics experts. They also aimed to align with fair data principles in pharma and enhance scientific reproducibility across clinical and preclinical trials.
Our approach
Excelra collaborated closely with the client for a year, taking a comprehensive approach to address their challenges:
- Deep understanding of workflow: We collaborated remotely with the client’s research teams to thoroughly understand their specific antibody discovery workflow, scientific informatics requirements, and data assets creation strategies.
- Agile development methodology: We established an agile development process with regular feedback sessions and iterations, allowing us to continuously refine the platform based on real user experiences until the full platform was developed.
- Focus on user experience: We prioritized creating an intuitive interface that would allow researchers without bioinformatics applications experience to easily manage and analyze their data.
- Cloud-First architecture: We designed the platform to leverage cloud enablement, enabling scalable processing of hundreds of samples simultaneously.
- Standardized analysis workflows: We implemented industry-standard bioinformatics workflows for AIRR-seq ngs data processing, ensuring consistent analysis methodologies for BCR and TCR repertoire data across different input formats and sequencing technologies.
- Sequence management: We developed a specialized sequence browser that would allow researchers to track, filter, and manage all processed sequences across samples, integrating with ontology data management where required.
Our solution
The collaboration resulted in ImmunoRaptor, a comprehensive immune repertoire analysis platform that transformed the client’s research capabilities:
Core features
The collaboration resulted in ImmunoRaptor, a comprehensive immune repertoire analysis platform that transformed the client’s research capabilities:
- Streamlined data management: Researchers could easily upload samples and supporting files through a simple interface designed for scientific data management.
- Experiment tracking: The platform provided a centralized dashboard for creating and monitoring experiments, with detailed status updates and notifications.
- Advanced sample browser: We implemented an interactive sample browser that allowed researchers to:
- View all processed samples in a unified interface
- Apply complex filters to find samples of interest
- Generate customized visualizations for selected samples
- Export data in various formats for reporting and sharing
- Comprehensive sequence database: A key innovation was the sequence browser that enabled researchers to:
- View all sequences processed across all samples in a datatable format
- Apply sophisticated filters to identify sequences with specific properties and support biomarker identification
- Track which sequences had already been provided to customers
- Export selected sequences for further bioinformatics analysis
- Interactive visualizations: The platform included multiple advanced analytics workflows and visualization tools:
- CDRH3 overlap diagrams showing shared CDRs between samples
- Clonotype distribution charts
- Amino acid composition analysis
- Phylogenetic trees for lineage analysis
- V-J recombination plots for genomic sequence analysis
- Standardized analysis pipeline: The platform supported all common input data types (BCR/TCR data from Illumina or 10X) and implemented standardized analysis workflows for:
- Assignment of clones/clonotypes/lineages
- Reconstruction of phylogenetic trees
- Analysis of CDR properties
- Analysis of somatic hypermutation rates
- Analysis of gene usage and V-J recombination aligned with bioinformatics solutions and sequence analysis
- Enterprise authentication & access control: We seamlessly integrated with Azure Active Directory, providing:
- Single Sign-On (SSO) capabilities for streamlined user access
- Automatic permission management based on Azure AD groups
- Elimination of separate login credentials
- Enhanced security through enterprise-grade authentication
- Cloud-Based processing: All computational tasks were automatically scaled in the cloud according to demand, eliminating infrastructure limitations and supporting digitalization in drug discovery workflows.
Impact and results
The implementation of ImmunoRaptor delivered significant benefits to the client:
- Accelerated research: Analysis time was reduced significantly due to automated workflows and ai-powered analytics.
- Democratized analysis: Researchers without bioinformatics expertise could now independently perform complex immune repertoire analyses.
- Enhanced collaboration: Teams across different locations could access the same data and results through the centralized platform with enhanced data visualization.
- Improved sequence management: The sequence browser enabled efficient tracking of all processed sequences, eliminating redundant work and improving biomarker testing and reporting.
- Scalable processing: The cloud-based architecture easily accommodated the growing volume of sequencing data and omics data analysis.
- Standardized workflows: All analyses followed consistent, validated protocols, ensuring reliability and scientific reproducibility of results, including rna-sequencing and ngs pipeline tasks.
Conclusion
The success of this collaboration led to the evolution of ImmunoRaptor into Excelra’s broader Online Pipeline Platform (OP²), which now offers a comprehensive suite of bioinformatics pipelines for various next-generation sequencing applications. It aligns with fair data principles, supports scientific application services, and empowers researchers with ai/ml drug discovery, biomarker discovery, and computational biology capabilities—while maintaining the core features that made the original solution so valuable.
