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OpenMS 3.1.0dev documentation
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OpenMS 3.1.0dev documentation

Introduction

  • What is OpenMS?
  • Background
  • Entry Points to OpenMS

OpenMS Applications and Tools

  • Installation
    • GNU/Linux
    • macOS
    • Windows
  • OpenMS Graphical User Interfaces
  • TOPP Tools
    • Introduction to TOPP
    • Types of TOPP Tools
  • Command Line Interface
  • TOPPView: Visualize with OpenMS
    • Views in TOPPView
    • Display Modes and View Options in TOPPView
    • Data Analysis in TOPPView
    • Data Editing in TOPPView
    • TOPPView Hotkeys

Run Workflows with OpenMS Tools

  • Recommended Workflow Systems
  • OpenMS in KNIME
    • Installation of KNIME and its OpenMS plugin
    • Ready-made OpenMS KNIME workflows
    • OpenMS KNIME User Tutorial
  • OpenMS in Nextflow
    • Installation of nextflow and nf-core
    • Ready-made OpenMS nextflow workflows
    • Tutorial
  • OpenMS on Galaxy
  • OpenMS on TOPPAS

Tutorials and Quick Start Guides

  • User Quickstart Guide
  • OpenMS User Tutorial
  • Worked Examples: Different OpenMS Methods to Achieve the Same Outcome

Develop with OpenMS

  • OpenMS C++ Core Library
  • OpenMS API Reference
  • pyOpenMS
  • Build From Source
  • External Code using OpenMS
  • Developer Tutorial

Contribute to OpenMS

  • Contributor’s Quick Start Guide
  • OpenMS Git Workflow
  • Write and Label GitHub Issues
  • Adding New Tool to The TOPP suite
  • Pull Request Checklist
  • Reporting Bugs and Issues
  • Advanced
    • Developer Guidelines For Adding New Dependent Libraries
    • Custom Compilation of OpenMS
    • Build Custom KNIME Plugin

Downloads

  • OpenMS Installers
  • Workflows
  • OpenMS Releases
  • Other Resources

Quick Reference

  • Contributor FAQ
  • Developer FAQ
  • Contact Us
  • OpenMS Glossary
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Recommended Workflow Systems#

Which workflow environment to choose for running OpenMS tools?

You can run OpenMS TOPP tools from the command line using your custom scripts, or use powerful workflow systems designed to make workflow creation and maintenance more fun:

KNIME

Free, open source, desktop app. An analytics platform with workflow editor and a nice drag-and-drop user interface. Very interactive and has built-in nodes for related tasks like working with chemical structures, databases, machine learning, scripting. Distributed computing is best achieved with a KNIME server (License required) which also allows user management and a web interface to interact with workflows. In KNIME you can easily construct your own workflows or just download our ready-made creations for the most common analysis tasks.

KNIME

Free, open source, desktop app. An analytics platform with workflow editor and a nice drag-and-drop user interface. Very interactive and has built-in nodes for related tasks like working with chemical structures, databases, machine learning, scripting. Distributed computing is best achieved with a KNIME server (License required) which also allows user management and a web interface to interact with workflows. In KNIME you can easily construct your own workflows or just download our ready-made creations for the most common analysis tasks.

Nextflow

Script/DSL-based workflow language, executor and utilities (such as the browser based launcher and supervisor nf-tower). Automatically runs on various different cloud (AWS, Google, …) and HPC environments (SLURM, LFS, Kubernetes, …). It is recommended to use our ready-made nf-core compatible workflows for ease of use via the browser-based configuration and launcher.

Nextflow

Script/DSL-based workflow language, executor and utilities (such as the browser based launcher and supervisor nf-tower). Automatically runs on various different cloud (AWS, Google, …) and HPC environments (SLURM, LFS, Kubernetes, …). It is recommended to use our ready-made nf-core compatible workflows for ease of use via the browser-based configuration and launcher.

Galaxy

Server and browser-based interactive workflow editor and runner. A public server instance can be used for testing and smaller experiments. Provides nice guided tutorials.

Galaxy

Server and browser-based interactive workflow editor and runner. A public server instance can be used for testing and smaller experiments. Provides nice guided tutorials.

TOPPAS

OpenMS’ build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.

TOPPAS

OpenMS’ build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.

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OpenMS in KNIME
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TOPPView Hotkeys
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