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Tranche Distributed Repository and ProteomeCommons.org

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Data Mining in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 696))

Abstract

Tranche is a distributed repository designed to redundantly store and disseminate data sets for the proteomics community. It has several important features for researchers, including support for large data files, prepublication access controls, licensing options, and ensuring both data provenance and integrity. Tranche tightly integrates with ProteomeCommons.org, an online community resource that offers a variety of useful tools for proteomics researchers, including project management and data annotation. In this chapter, we discuss the development of Tranche and ProteomeCommons.org, paying particular attention to why it is desirable that data be publicly available and unrestricted as well as the challenges facing data archiving and open access. We then provide a technical overview of Tranche and ProteomeCommons.org as well as step-by-step instructions for using these resources, including the graphical user interface (GUI ), command-line tools, and Application Programmer Interface (API). We end with a brief discussion of current and future development efforts and collaborations.

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Acknowledgments

Special thanks to Jayson Falkner, who led the initial development for both Tranche and ProteomeCommons.org. The authors would also like to thank Peter Ulintz, Jared Falkner, Brian Maso, and Panagiotis Papoulias for their contributions. The ProteomeCommons.org and Tranche Repository community resources are primarily sponsored by NCRR grant #P41-RR018627 and the NCI CPTC subcontract #27XS115. We also thank all the users of Tranche who have provided invaluable feedback and suggestions for the Tranche Project and ProteomeCommons.org.

Author information

Authors and Affiliations

  1. Departments of Biological Chemistry, Bioinformatics and Chemistry, University of Michigan, Ann Arbor, MI, USA

    Bryan E. Smith, James A. Hill, Mark A. Gjukich & Philip C. Andrews

Authors
  1. Bryan E. Smith
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  2. James A. Hill
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  3. Mark A. Gjukich
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  4. Philip C. Andrews
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Corresponding author

Correspondence to Bryan E. Smith .

Editor information

Editors and Affiliations

  1. Lead Discovery Center GmbH, Emil-Figge-Straße 76a76a, Dortmund, 44227, Germany

    Michael Hamacher

  2. Medizinisches Proteom-Center, Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, 44801, Germany

    Martin Eisenacher

  3. Medizinisches Proteom-Center, Ruhr-Universität Bochum, Universitätsstraße 150, Bochum, 44801, Germany

    Christian Stephan

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© 2011 Springer Science+Business Media, LLC

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Smith, B.E., Hill, J.A., Gjukich, M.A., Andrews, P.C. (2011). Tranche Distributed Repository and ProteomeCommons.org. In: Hamacher, M., Eisenacher, M., Stephan, C. (eds) Data Mining in Proteomics. Methods in Molecular Biology, vol 696. Humana Press. https://doi.org/10.1007/978-1-60761-987-1_8

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  • DOI: https://doi.org/10.1007/978-1-60761-987-1_8

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-986-4

  • Online ISBN: 978-1-60761-987-1

  • eBook Packages: Springer Protocols

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