Containerization and wrapping of a mass spectra prediction workflow
1
Applied Bioinformatics, University of Tübingen, Tübingen, Germany
2
Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
3
Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Published
- Accepted
- Subject Areas
- Bioinformatics, Scientific Computing and Simulation
- Keywords
- workflow, mass spectra prediction, Docker, UNICORE, quantum chemistry
- Copyright
- © 2016 Krüger et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Containerization and wrapping of a mass spectra prediction workflow. PeerJ Preprints 4:e2528v1 https://doi.org/10.7287/peerj.preprints.2528v1
Abstract
Practical experiences are reported about implementing a workflow for the prediction of mass spectra. QCEIMS is used to simulate the fragmentation trajectories consequently leading to predicted mass spectra for small molecules, such as metabolites. The individual calculations are embedded into UNICORE workflow nodes using Docker containerization for the applications themselves. Challenges, caveats, but also advantages are discussed, providing guidance for the deployment of a scientific protocol on high performance computing resources.
Author Comment
This is a short paper presented at the 8th International Workshop on Science Gateways (IWSG 2016), 8-10 June 2016, Rome, Italy.