odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments.
Julia Sprenger,Lyuba Zehl,Jana Pick,Michael Sonntag,Jan Grewe,Thomas Wachtler,Sonja Grün,Michael Denker +7 more
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OdMLtables bridges the gap between handling metadata in an intuitive way that integrates well with daily lab routines and commonly used software products on the one hand, and the implementation of a complete, well-defined metadata collection for the experiment in a standardized format on the other hand.Abstract:
An essential aspect of scientific reproducibility is a coherent and complete acquisition of metadata along with the actual data of an experiment. The high degree of complexity and heterogeneity of neuroscience experiments requires a rigorous management of the associated metadata. The odML framework represents a solution to organize and store complex metadata digitally in a hierarchical format that is both human and machine readable. However, this hierarchical representation of metadata is difficult to handle when metadata entries need to be collected and edited manually during the daily routines of a laboratory. With odMLtables, we present an open-source software solution that enables users to collect, manipulate, visualize, and store metadata in tabular representations (in xls or csv format) by providing functionality to convert these tabular collections to the hierarchically structured metadata format odML, and to either extract or merge subsets of a complex metadata collection. With this, odMLtables bridges the gap between handling metadata in an intuitive way that integrates well with daily lab routines and commonly used software products on the one hand, and the implementation of a complete, well-defined metadata collection for the experiment in a standardized format on the other hand. We demonstrate usage scenarios of the odMLtables tools in common lab routines in the context of metadata acquisition and management, and show how the tool can assist in exploring published datasets that provide metadata in the odML format.read more
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The SONATA data format for efficient description of large-scale network models.
Kael Dai,Juan Hernando,Yazan N. Billeh,Sergey L. Gratiy,Judit Planas,Andrew P. Davison,Salvador Dura-Bernal,Salvador Dura-Bernal,Padraig Gleeson,Adrien Devresse,Benjamin Dichter,Benjamin Dichter,Michael Gevaert,James G. King,Werner Van Geit,Arseny V. Povolotsky,Eilif Muller,Jean-Denis Courcol,Anton Arkhipov +18 more
TL;DR: The Scalable Open Network Architecture TemplAte (SONATA) data format is designed for memory and computational efficiency and works across multiple platforms and provides much flexibility for adding new conventions or extensions.
Posted ContentDOI
The SONATA Data Format for Efficient Description of Large-Scale Network Models
Kael Dai,Juan Hernando,Yazan N. Billeh,Sergey L. Gratiy,Judit Planas,Andrew P. Davison,Salvador Dura-Bernal,Salvador Dura-Bernal,Padraig Gleeson,Adrien Devresse,Benjamin Dichter,Benjamin Dichter,Michael Gevaert,James G. King,Werner Van Geit,Arseny V. Povolotsky,Eilif Muller,Jean-Denis Courcol,Anton Arkhipov +18 more
TL;DR: The Scalable Open Network Architecture TemplAte (SONATA) data format is designed for memory and computational efficiency and works across multiple platforms and provides much flexibility for adding new conventions or extensions.
Journal ArticleDOI
Experimental Pipeline (Expipe): A Lightweight Data Management Platform to Simplify the Steps From Experiment to Data Analysis
Mikkel Elle Lepperød,Svenn-Arne Dragly,Alessio Paolo Buccino,Alessio Paolo Buccino,Milad Hobbi Mobarhan,Anders Malthe-Sørenssen,Torkel Hafting,Marianne Fyhn +7 more
TL;DR: Expipe is a lightweight data management framework that simplifies the steps from experiment to data analysis and aims to solve the storage and retrieval challenges of data/metadata due to ever changing experimental pipelines.
Journal ArticleDOI
1024-channel electrophysiological recordings in macaque V1 and V4 during resting state
Xing Chen,Aitor Morales-Gregorio,Julia Sprenger,Alexander Kleinjohann,Shashwat Sridhar,S. V. van Albada,Sonja Grün,Pieter R. Roelfsema +7 more
TL;DR: In this article , the authors carried out electrophysiological recordings from over a thousand chronically implanted electrodes in the visual cortex of non-human primates, yielding a resting state dataset with unprecedentedly high channel counts and spatiotemporal resolution.
Journal ArticleDOI
1024-channel electrophysiological recordings in macaque V1 and V4 during resting state
Xing Chen,Aitor Morales-Gregorio,Julia Sprenger,Alexander Kleinjohann,Shashwat Sridhar,S. V. van Albada,Sonja Grün,Pieter R. Roelfsema +7 more
TL;DR: In this paper , the authors carried out electrophysiological recordings from over a thousand chronically implanted electrodes in the visual cortex of non-human primates, yielding a resting state dataset with unprecedentedly high channel counts and spatiotemporal resolution.
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