Usage

Starting the application

Run the Flask development server:

flask --app biosimdb_interface run --debug -p 5002

Then visit http://127.0.0.1:5002/ in a browser.

Workflow

  1. Upload files — provide a topology file and one or more trajectory files.

  2. Extract metadata — click Extract Metadata from Files to populate the form automatically using MDAnalysis and biosim-extractor.

  3. Review and edit — inspect the extracted fields and fill in any missing information.

  4. Save or submit:

    • Save Metadata downloads the metadata as a simulation_metadata.json file.

    • Submit to BioSimDB validates the metadata against the BioSim schema and uploads it to BioSimDB, redirecting you to the created record.

Authentication

Submitting to BioSimDB requires OAuth login. If you are not logged in, you will be redirected to the BioSimDB login page, asked to verify the biosimdb-interface application and returned to the form after a draft record has been submitted to BioSimDB.