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OpenMS 3.0.0 documentation
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OpenMS 3.0.0 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
  • UTILS 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

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?

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.

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TOPPView Hotkeys
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