Open-source data lifecycle management for research teams and core facilities.
Bioloop at PEARC '26
"SciLINC: an instrument to archival data management platform based on Bioloop" will be presented on Tuesday, July 28, 2026, from 12:00–12:15 PM in Auditorium Room 1 at PEARC '26.
Bioloop connects instrument output and existing filesystem data to project-based, auditable workflows for ingestion, archival, staging, and secure delivery. Rather than replacing an institution's storage and computing infrastructure, Bioloop provides an orchestration and governance layer that connects those services through a web portal, API, and extensible workers.
Bioloop was created for research environments that generate large, complex datasets and need to move them reliably from instruments to researchers while preserving access controls, provenance, and long-term retrievability.
- Project-based organization and access: Group datasets and collaborators within projects, with role- and membership-based authorization.
- Flexible data ingestion: Support automated instrument ingestion, browser-based uploads, and allowlisted filesystem imports.
- Tiered storage workflows: Coordinate active disk and long-term archival storage while retaining the context needed to retrieve and reuse data.
- Provenance and auditability: Track raw datasets, derived data products, lineage, workflow state, and access history.
- Secure data delivery: Stage archived data and provide token-scoped downloads to authorized researchers.
- Extensible processing: Compose and scale custom data workflows with Celery and Rhythm.
- Operational visibility: Keep users informed through notifications, workflow histories, and status tracking.
- Portable deployment: Run the service components in Docker containers on institutional infrastructure or in public cloud environments.
Bioloop separates its web interface, API, authentication, secure-download service, workflow engine, workers, and storage integrations into independently deployable services.
The PEARC '26 paper describes SciLINC, Indiana University's managed instrument-to-archive service built on Bioloop:
Daniel Havert, Charles Brandt, Deepak Duggirala, and Le Mai Weakley. 2026. SciLINC: an instrument to archival data management platform based on Bioloop. In Proceedings of the Practice and Experience in Advanced Research Computing 2026: Resilient Roots + Empowered Communities. https://doi.org/10.1145/3785462.3815868
To cite the Bioloop software itself, use the metadata in
CITATION.cff or the
Bioloop v1.0.0 Zenodo record.
Bioloop integrates with several other open-source projects:
- Signet provides OAuth-based authentication.
- Rhythm API exposes workflow orchestration services.
- Rhythm provides reusable Celery workflow patterns.
Bioloop is licensed under the Educational Community License, Version 2.0.