Third-party tool integration and method development in OpenMS

[timosachsenberg]

Abstract

OpenMS is a C++ 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) bindings are provided for novel algorithms.

Work plan

Basics:

• We will first get acquainted with the structure of OpenMS, the graphical viewers, and the OpenMS command line tools.
• How OpenMS is far more than a collection of algorithms and tools. It is also service that provides a development infrastructure for the computational MS community
• Then we will give a brief overview of the development process in OpenMS, some background information on the build and test infrastructure and good practices.
• We then briefly show how command line tools are automatically integrated into workflow systems.
• Break for questions and answers like licenses, authorship, etc.

Hands-on:

Rest of the workshop will be in a hands-on fashion where we:

• Show how to write your own tool
• Integrate third-party tools (potential candidates could be: PeptideShaker, novor, direct tag, MS fragger, your favorite tool)
• Show how to build a small benchmarking workflow

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

Contact information

Timo Sachsenberg
University of Tübingen
sachsenb@informatik.uni-tuebingen.de

The OpenMS hackathon is partly supported by the German Network for Bioinformatic Infrastructure (de.NBI):