Data Mining in Proteomics pp 123-145

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

Tranche Distributed Repository and ProteomeCommons.org

  • Bryan E. Smith
  • James A. Hill
  • Mark A. Gjukich
  • Philip C. Andrews
Protocol

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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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Bryan E. Smith
    • 1
  • James A. Hill
    • 1
  • Mark A. Gjukich
    • 1
  • Philip C. Andrews
    • 1
  1. 1.Departments of Biological Chemistry, Bioinformatics and ChemistryUniversity of MichiganAnn ArborUSA

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