Experimental Pipeline (Expipe): A Lightweight Data Management Platform to Simplify the Steps From Experiment to Data Analysis

Frontiers in Neuroinformatics

Marianne Fyhn²  Milad Hobbi Mobarhan²  Alessio Paolo Buccino³  Svenn-Arne Dragly⁵  Anders Malthe-Sørenssen⁵  Torkel Hafting⁶  Mikkel Elle Lepperød⁶ 

[1] Center for Integrative Neuroplasticity, University of Oslo, Oslo, Norway;Department of Biosciences, University of Oslo, Oslo, Norway;Department of Biosystems Science and Engineering, ETH, Zurich, Switzerland;Department of Informatics, University of Oslo, Oslo, Norway;Department of Physics, University of Oslo, Oslo, Norway;Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway;

关键词: data management;    Python (programming language);    open source software (OSS);    analysis;    data sharing;    data base (DB);   

DOI  :  10.3389/fninf.2020.00030

来源: DOAJ

【 摘 要 】

As experimental neuroscience is moving toward more integrative approaches, with a variety of acquisition techniques covering multiple spatiotemporal scales, data management is becoming increasingly challenging for neuroscience laboratories. Often, datasets are too large to practically be stored on a laptop or a workstation. The ability to query metadata collections without retrieving complete datasets is therefore critical to efficiently perform new analyses and explore the data. At the same time, new experimental paradigms lead to constantly changing specifications for the metadata to be stored. Despite this, there is currently a serious lack of agile software tools for data management in neuroscience laboratories. To meet this need, we have developed Expipe, a lightweight data management framework that simplifies the steps from experiment to data analysis. Expipe provides the functionality to store and organize experimental data and metadata for easy retrieval in exploration and analysis throughout the experimental pipeline. It is flexible in terms of defining the metadata to store and aims to solve the storage and retrieval challenges of data/metadata due to ever changing experimental pipelines. Due to its simplicity and lightweight design, we envision Expipe as an easy-to-use data management solution for experimental laboratories, that can improve provenance, reproducibility, and sharing of scientific projects.

【 授权许可】

Unknown