OpenMS is a programming library and framework for computational mass spectrometry. At times, the large code-base (and C++) might overwhelm novel developers. This project is intended to give a gentle introduction on how to find your way through the OpenMS codebase, how to implement your own tools and algorithms, or how to integrate novel third-party tools to interact in complex workflows. We also show how Python (pyOpenMS) can be used to rapidly prototype novel algorithms.
Work plan
Basics:
First, we get acquainted with the structure of OpenMS, the graphical viewers, the OpenMS command-line tools, and how these can be integrated into workflow systems. Then, we will explore how OpenMS and its development infrastructure assist you in developing new tools for the MS community. We give a brief overview of the development process in OpenMS, some background information on the build and test infrastructure and good practices. Depending on your interest we will show how to make use of pyOpenMS to quickly write simple python scripts to interact with MS data including spectra, identification or quantification results.
Hands-on:
The rest of the workshop will be in a individual hands-on fashion where we:
Support you in writing your own scripts and / or tools
Adapt existing tools with customized functionalities you wish for
Bring your own data and get our support for its analysis using OpenMS
Abstract
OpenMS is a programming library and framework for computational mass spectrometry. At times, the large code-base (and C++) might overwhelm novel developers. This project is intended to give a gentle introduction on how to find your way through the OpenMS codebase, how to implement your own tools and algorithms, or how to integrate novel third-party tools to interact in complex workflows. We also show how Python (pyOpenMS) can be used to rapidly prototype novel algorithms.
Work plan
Basics:
First, we get acquainted with the structure of OpenMS, the graphical viewers, the OpenMS command-line tools, and how these can be integrated into workflow systems. Then, we will explore how OpenMS and its development infrastructure assist you in developing new tools for the MS community. We give a brief overview of the development process in OpenMS, some background information on the build and test infrastructure and good practices. Depending on your interest we will show how to make use of pyOpenMS to quickly write simple python scripts to interact with MS data including spectra, identification or quantification results.
Hands-on:
The rest of the workshop will be in a individual hands-on fashion where we:
Technical details
We encourage participants to build OpenMS from GitHub prior to the workshop. Github: https://github.com/OpenMS/OpenMS Gitter chat: https://gitter.im/OpenMS/OpenMS homepage: www.OpenMS.de
Used programming languages:
C++ (primarily) python possibly R Workflow systems: KNIME or nextflow
Contact information
Timo Sachsenberg Leon Bichmann University of Tübingen sachsenb@informatik.uni-tuebingen.de bichmann@informatik.uni-tuebingne.de
The OpenMS hackathon is partly supported by the German Network for Bioinformatics Infrastructure (de.NBI)