PipeBio

PipeBio is a powerful, cloud-based bioinformatics platform engineered to streamline and accelerate the discovery and development of biologics, including antibodies, T-cell receptors (TCRs), and peptides. Recently acquired by Benchling, a leading R&D cloud platform, PipeBio provides a comprehensive, end-to-end solution for researchers in both academic and commercial settings. It transforms raw sequence data into actionable insights through a suite of sophisticated analysis, visualization, and data management tools.

The platform is built to handle the complexity and scale of modern biologics research, supporting data from various sequencing technologies like Sanger, Next-Generation Sequencing (NGS), and single-cell platforms (e.g., 10x Genomics). It empowers scientists to move beyond manual, error-prone processes, offering standardized and automated workflows that enhance productivity and reproducibility.

How to use PipeBio

Using PipeBio involves a structured workflow designed for efficiency and deep biological insight:

1. Data Upload & Integration: Begin by uploading your sequence data (e.g., FASTA, FASTQ from NGS or Sanger) and associated functional assay data, such as ELISA results or other metadata. The platform can also be integrated with ELN/LIMS systems like Benchling via its REST API.
2. Sequence Analysis & Annotation: Run standardized or custom analysis pipelines with a few clicks. The system automatically annotates sequences, identifying key regions like Framework Regions (FRs) and Complementarity-Determining Regions (CDRs), detects sequence-based liabilities, and performs germline alignments.
3. Clustering & Comparison: Group sequences into clonal families by defining clonotypes. Compare samples across different experiments to analyze enrichment and identify key variants.
4. Interactive Visualization: Explore your data using a rich set of interactive charts and plots. Visualize cluster networks, amino acid frequencies, gene usage, phylogenetic trees, and sequence quality to gain a deeper understanding of your repertoires.
5. Hit Picking & Candidate Selection: Combine sequence data with functional assay results to identify and select the most promising 'hit' candidates for further development. Filter and sort based on multiple parameters to pinpoint leads with optimal properties.
6. Antibody Engineering: Utilize built-in tools to engineer your lead candidates. Edit sequences at the nucleotide or protein level, calculate protein properties, analyze hydrophobicity, and optimize codons for synthesis.
7. Automation & Reporting: Leverage the REST API to build fully automated analysis pipelines, integrating PipeBio into your broader R&D ecosystem. Generate advanced reports to document and share findings.

Core Features of PipeBio

• Advanced Sequence Annotation: Automatically identifies FRs, CDRs, mutations, and liabilities for various antibody formats (IgG, scFv, VHH), TCRs, and custom scaffolds.
• Large-Scale Data Processing: Engineered to efficiently analyze billions of sequences from NGS, Sanger, and PacBio platforms.
• Clonotype Analysis & Clustering: Powerful algorithms to cluster sequences, identify clonal families, and compare sample diversity and enrichment.
• Interactive Data Visualization: A suite of dynamic charts for exploring sequence clusters, amino acid distributions, V(D)J gene usage, and phylogenetic relationships.
• Functional Data Integration: Seamlessly associate sequence data with functional assay results and metadata for comprehensive hit picking and analysis.
• Antibody Engineering Suite: Tools for in-silico sequence editing, property calculation (e.g., hydrophobicity), and codon optimization.
• REST API & Integration: A robust REST API enables programmatic access for integration with LIMS, ELNs, and other internal tools, facilitating full workflow automation.
• Security & Compliance: An ISO27001 compliant platform ensuring the security and confidentiality of proprietary research data.

Use Cases for PipeBio

PipeBio is instrumental across various stages of biologics R&D:

• Therapeutic Antibody Discovery: Analyzing outputs from phage display, yeast display, and other selection technologies to identify high-affinity binders.
• Immune Repertoire Profiling: Characterizing the diversity of B-cell and T-cell repertoires in response to vaccination or disease.
• Antibody Developability Assessment: Predicting and mitigating risks like aggregation by identifying sequence liabilities early in the discovery process.
• Lead Optimization & Engineering: Modifying antibody candidates to improve their efficacy, stability, and manufacturing properties.
• Nanobody and Non-antibody Scaffold Research: Analyzing unique biologic formats like VHH from camelids or synthetic scaffolds like affibodies.
• Single-Cell Analysis: Linking native heavy and light chain pairs from single B-cell sequencing data with functional outcomes.

Advantages of PipeBio

PipeBio offers significant advantages for research organizations:

• Scalability: The cloud-native architecture handles massive datasets with ease, scaling from small academic projects to large-scale enterprise pipelines.
• End-to-End Solution: It consolidates multiple bioinformatics tools into a single, integrated platform, covering the workflow from raw data to engineered lead.
• Collaboration: As a cloud-based service, it enables seamless collaboration among team members, regardless of their physical location.
• Customization: The platform is highly adaptable, allowing users to define custom scaffolds, liability rules, and analysis workflows to fit specific research needs.
• Expert Support: Customers are assigned a scientific success manager to assist with technical needs and workflow optimization.

Pricing and Plans

PipeBio offers a tiered subscription model to cater to different organizational needs. All plans are based on an annual subscription fee and include a free trial for evaluation.

• Academic Plan: Designed for academic institutions (up to 5 users), providing core features for Sanger and NGS analysis, data visualization, and clustering. Discounts may be available.
• Startup Plan: Tailored for growing biotech companies, with special discounts available to accommodate startup budgets.
• Commercial Plan: The full-featured enterprise solution, starting from USD $70,000 per year. It includes all academic features plus advanced tools for antibody engineering, custom workflows, advanced reporting, SSO/SCIM, and full API access.

For detailed quotes, custom development, or to apply for a startup discount, interested parties are encouraged to contact the PipeBio sales team directly.