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qPortal – A science gateway for biomedical applications

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1 Applied Bioinformatics, Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
2 University of Tübingen, Quantitative Biology Center (QBiC), Tübingen, Germany
3 Max Planck Institute for Developmental Biology, Tübingen, Germany
DOI
10.7287/peerj.preprints.2839v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Data Science, Databases, Distributed and Parallel Computing
Keywords
portlet, high-throughput, portal, next-generation sequencing, workflows, science gateway, multi-omics, experimental design, quality control, high-performance computing
Copyright
© 2017 Mohr 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
Mohr C, Friedrich A, Wojnar D, Kenar E, Polatkan AC, Codrea MC, Czemmel S, Kohlbacher O, Nahnsen S. 2017. qPortal – A science gateway for biomedical applications. PeerJ Preprints 5:e2839v1

Abstract

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. Nowadays, it is common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for large amounts of storage, data management, and easily accessible means of analysis. We present qPortal, a web-based science gateway providing users with an intuitive way to manage and analyze quantitative biological data. Pre-programmed analysis pipelines, quality control workflows, and visualization tools are offered to the user. Through intensive user interactions, appropriate data models have been developed. These models build the biological data management system and provide possibilities to annotate data, query existing metadata for statistics and future re-analysis on a high-performance computing system via a coupling to gUSE, a workflow management system.

Author Comment

The abstract was presented during the IWSG 2016 workshop, 8-10 June 2016, Rome, Italy.

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Christopher Mohr analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Andreas Friedrich analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

David Wojnar contributed reagents/materials/analysis tools, performed the computation work, reviewed drafts of the paper.

Erhan Kenar performed the computation work, reviewed drafts of the paper.

Aydin Can Polatkan prepared figures and/or tables, reviewed drafts of the paper.

Marius Cosmin Codrea contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Stefan Czemmel contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Oliver Kohlbacher reviewed drafts of the paper.

Sven Nahnsen wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

qbicsoftware - https://github.com/qbicsoftware

Funding

M.C.C., S.C., D.W., O.K. and S.N. acknowledge funding from Deutsche Forschungsgemeinschaft (core facilities initiative, KO-2313/6-1 and KO-2313-2, Institutional Strategy of the University of Tübingen, ZUK 63). All authors acknowledge funding from Deutsche Forschungsgemeinschaft (Institutional Strategy of the University of Tübingen, ZUK 63). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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