openms / streamlit-template

OpenMS streamlit template

This repository contains a template app for OpenMS workflows in a web application using the streamlit framework. It serves as a foundation for apps ranging from simple workflows with pyOpenMS to complex workflows utilizing OpenMS TOPP tools with parallel execution. It includes solutions for handling user data and parameters in workspaces as well as deployment with docker-compose.

Features

• Workspaces for user data with unique shareable IDs
• Persistent parameters and input files within a workspace
• local and online mode
• Captcha control
• Packaged executables for Windows
• framework for workflows with OpenMS TOPP tools
• Deployment with docker-compose

Documentation

Documentation for users and developers is included as pages in this template app, indicated by the 📖 icon.

References

• Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7

• Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Jan;14(1):74-7. https://doi.org/10.1002/pmic.201300246. PMID: 24420968.