Dataset Information

Handling Metadata in a Neurophysiology Laboratory.

ABSTRACT: To date, non-reproducibility of neurophysiological research is a matter of intense discussion in the scientific community. A crucial component to enhance reproducibility is to comprehensively collect and store metadata, that is, all information about the experiment, the data, and the applied preprocessing steps on the data, such that they can be accessed and shared in a consistent and simple manner. However, the complexity of experiments, the highly specialized analysis workflows and a lack of knowledge on how to make use of supporting software tools often overburden researchers to perform such a detailed documentation. For this reason, the collected metadata are often incomplete, incomprehensible for outsiders or ambiguous. Based on our research experience in dealing with diverse datasets, we here provide conceptual and technical guidance to overcome the challenges associated with the collection, organization, and storage of metadata in a neurophysiology laboratory. Through the concrete example of managing the metadata of a complex experiment that yields multi-channel recordings from monkeys performing a behavioral motor task, we practically demonstrate the implementation of these approaches and solutions with the intention that they may be generalized to other projects. Moreover, we detail five use cases that demonstrate the resulting benefits of constructing a well-organized metadata collection when processing or analyzing the recorded data, in particular when these are shared between laboratories in a modern scientific collaboration. Finally, we suggest an adaptable workflow to accumulate, structure and store metadata from different sources using, by way of example, the odML metadata framework.

SUBMITTER: Zehl L

PROVIDER: S-EPMC4949266 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Handling Metadata in a Neurophysiology Laboratory.

Zehl Lyuba L Jaillet Florent F Stoewer Adrian A Grewe Jan J Sobolev Andrey A Wachtler Thomas T Brochier Thomas G TG Riehle Alexa A Denker Michael M Grün Sonja S

Frontiers in neuroinformatics 20160719

To date, non-reproducibility of neurophysiological research is a matter of intense discussion in the scientific community. A crucial component to enhance reproducibility is to comprehensively collect and store metadata, that is, all information about the experiment, the data, and the applied preprocessing steps on the data, such that they can be accessed and shared in a consistent and simple manner. However, the complexity of experiments, the highly specialized analysis workflows and a lack of k ...[more]

PMID: 27486397

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Project description:Handling of laboratory mice is essential for experiments and husbandry, but handling can increase anxiety in mice, compromising their welfare and potentially reducing replicability between studies. The use of non-aversive handling (e.g., tunnel handling or cupping), rather than the standard method of picking mice up by the tail, has been shown to enhance interaction with a handler, reduce anxiety-like behaviours, and increase exploration and performance in standard behavioural tests. Despite this, some labs continue to use tail handling for routine husbandry, and the extent to which non-aversive methods are being used is currently unknown. Here we conducted an international online survey targeting individuals that work with and/or conduct research using laboratory mice. The survey aimed to identify the handling methods currently being used, and to determine common obstacles that may be preventing the wider uptake of non-aversive handling. We also surveyed opinions concerning the current data in support of non-aversive handling for mouse welfare and scientific outcomes. 390 complete responses were received and analysed quantitatively and thematically. We found that 35% report using tail handling only, and 43% use a combination of tail and non-aversive methods. 18% of respondents reported exclusively using non-aversive methods. The vast majority of participants were convinced that non-aversive handling improves animal welfare and scientific outcomes. However, the survey indicated that researchers were significantly less likely to have heard of non-aversive handling and more likely to use tail handling compared with animal care staff. Thematic analysis revealed there were concerns regarding the time required for non-aversive methods compared with tail handling, and that there was a perceived incompatibility of tunnel handling with restraint, health checks and other routine procedures. Respondents also highlighted a need for additional research into the impact of handling method that is representative of experimental protocols and physiological indicators used in the biomedical fields. This survey highlights where targeted research, outreach, training and funding may have the greatest impact on increasing uptake of non-aversive handling methods for laboratory mice.

Dataset Information

Handling Metadata in a Neurophysiology Laboratory.

Publications

Handling Metadata in a Neurophysiology Laboratory.

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