Data management routines for reproducible research using the G-Node Python Client library

Sobolev, Andrey; Stoewer, Adrian; Pereira, Michael; Kellner, Christian J.; Garbers, Christian; Rautenberg, Philipp L. und Wachtler, Thomas (2014): Data management routines for reproducible research using the G-Node Python Client library. In: Frontiers in Neuroinformatics, Bd. 8, 15

Abstract

Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology. The G-Node Python Library exposes these services to the Python environment, enabling researchers to organize and access their experimental data using their familiar tools while gaining the advantages that a centralized storage entails. The library provides powerful query features, including data slicing and selection by metadata, as well as fine-grained permission control for collaboration and data sharing. Here we demonstrate key actions in working with experimental neuroscience data, such as building a metadata structure, organizing recorded data in datasets, annotating data, or selecting data regions of interest, that can be automated to large degree using the library. Compliant with existing de-facto standards, the G-Node Python Library is compatible with many Python tools in the field of neurophysiology and thus enables seamless integration of data organization into the scientific data workflow.

• Dokumententyp: Zeitschriftenartikel
• Fakultät: Biologie > Department Biologie II > Neurobiologie
• Themengebiete: 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften; Biologie
• ISSN: 1662-5196
• Sprache: Englisch