elab2arc is a web-based Single Page Application (SPA) that bridges eLabFTW (an electronic lab notebook) and PLANTdataHUB (a GitLab-based Annotated Research Context (ARC) repository), enabling seamless synchronization of experimental metadata and raw data into FAIR-compliant ARCs.
🔗 Try it now: nfdi4plants.org/elab2arc/
Modern microbiological and life sciences research generates vast amounts of both metadata and raw datasets. Managing these across different tools — like ELNs for documentation and Git-based platforms for version control — can lead to fragmentation, manual errors, and poor compliance with FAIR (Findable, Accessible, Interoperable, Reusable) principles.
elab2arc automates the transformation of eLabFTW experiments into structured ARCs, ensuring reproducibility, traceability, and long-term data stewardship — all while requiring minimal user input.
- ✅ Web-based & Ready-to-use: No installation needed — just open in your browser.
- 🔗 Seamless Integration: Connects eLabFTW and PLANTdataHUB / DataHUB.
- 📁 Structured Data Conversion: Converts experiments into standardized ARC format.
- 🧾 ISA-Tab Metadata Generation: Produces compliant metadata sheets for traceability.
- 🌐 Dynamic URL Rewriting: Ensures embedded image links work inside the ARC structure.
- 📁 File Handling: Manages binary files (images, FASTQs, etc.) and normalizes paths.
- 📥 Batch Processing: Select and convert multiple experiments at once.
- 💡 Client-Side Git Operations: Uses
isomorphic-gitfor full Git functionality without backend dependencies. - 🖥️ Offline Filesystem Simulation: Uses
memfsfor temporary file handling before committing. - 🔐 DataHUB Token Login: Users can now log in via the NFDI4Plants DataHUB and get an access token directly within the app.
- JavaScript, HTML, CSS
- ARCtrl – for ISA-Tab metadata handling
- isomorphic-git – for client-side Git operations
- memfs – for in-memory filesystem simulation
- turndown – for HTML-to-Markdown conversion
- Open the Tool: Go to nfdi4plants.org/elab2arc/
- Login:
- Enter your eLabFTW API token
- Log in to DataHUB via the app to get your GitLab personal access token
- Select Experiments:
- Browse and select one or more experiments from your eLabFTW instance
- Transform to ARC:
- Let elab2arc automatically structure your metadata and files into a FAIR-compliant ARC
- Commit & Push:
- Review changes and push directly to your GitLab repository
This project is licensed under the GNU General Public License v3.0 – see the LICENSE file for details.
For questions, bug reports, or feature requests, please open an issue on GitHub or reach out via nfdi4plants.org.
- Integration with other ELNs and RDM tools
- LLM-assisted metadata structuring (e.g., ChatGPT, Qwen)
- Support for RO-Crate and .ELN import/export formats
- Enhanced user authentication and error handling
elab2arc empowers researchers to streamline their workflows while adhering to modern data management standards. Start converting your experiments into FAIR-compliant ARCs today using the hosted version at nfdi4plants.org/elab2arc/!