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Related Experiment Videos

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

Benjamin C Hitz1, Laurence D Rowe1, Nikhil R Podduturi1

  • 1Stanford University School of Medicine, Department of Genetics, Stanford, California, United States of America.

Plos One
|April 14, 2017
PubMed
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The Encyclopedia of DNA elements (ENCODE) project catalogs functional genomic elements. SnoVault, an open-source system, manages ENCODE

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The Encyclopedia of DNA elements (ENCODE) project aims to identify all functional elements in the human genome.
  • Data management for large-scale genomics projects like ENCODE presents significant challenges.
  • The ENCODE Data Coordination Center (DCC) is responsible for data validation, storage, and distribution.

Purpose of the Study:

  • To describe the SnoVault software system developed by the ENCODE DCC.
  • To highlight SnoVault's role in managing metadata and experimental data for the ENCODE project.
  • To announce the release of SnoVault as an open-source Python package.

Main Methods:

  • Development of a general-purpose software system (SnoVault) for metadata and file submission.

Related Experiment Videos

  • Implementation of a database for metadata storage and web interfaces for data display.
  • Creation of a robust API for querying metadata.
  • Release of SnoVault as an open-source Python package.

    • Main Results:

    • SnoVault successfully supports metadata and file submission for over 6500 experiments.
    • The system provides a unified platform for managing complex genomic data.
    • The open-source release facilitates broader adoption and use in bioinformatics.

    Conclusions:

    • SnoVault is a crucial tool for managing the vast and intricate data generated by the ENCODE project.
    • The open-source nature of SnoVault promotes reproducibility and collaboration in genomic research.
    • The SnoVault system offers a scalable solution for bioinformatics data management.