TraceBase

TraceBase is a data repository and analysis tool for mass-spectrometry data from isotope tracing studies used to quantify metabolism in vivo. Lab members submit peak data exported from El-Maven and processed for natural abundance correction by AccuCor, IsoCor, or Iso-AutoCor along with details about their experiment. TraceBase computes useful metrics such as enrichment, normalized labeling, and estimated FCirc (rate of appearance/disappearance), making it simple to browse, collate, compare, and download the data.

Directory Structure

• DataRepo - Django App Folder for the TraceBase Database Interface: This is the main application package.
• TraceBase - Django Project Folder: Contains core configuration files.
• docs - Documentation by user type.
• requirements - Python dependencies by deployment type.
• static - Media and JavaScript files.
• .github - GitHub settings.

Installation

See INSTALL.md.

Testing

In brief, the main test package can be run using:

python manage.py test

For detailed and comprehensive testing instructions and verification, see:

• The Verification section of INSTALL.md.
• The Testing section of CONTRIBUTING.md.

Usage

• Using the site.
  • See our online user guide.
  • Mirrored in /docs/user/.
• Loading Study data.
  • See docs/curator/Loading.md.

Contributing

See CONTRIBUTING.md. Helpful tips can be found in docs/contributor/Development_Notes.md.

License

See LICENSE.md.

Support

• GitHub Repository
• Feature & Bug Request
• Feedback

Technology

• Python
  • See requirements/* for dependencies.
• Django
• Postgres
• JavaScript

Authors & Acknowledgments

See The TraceBase Team.

Citing

Citation coming soon.