odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments

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

Experimental and numerical investigation of reactive species transport around a small rising bubble

In this article, we present experimental and numerical techniques to investigate the transfer, transport, and reaction of a chemical species in the vicinity of rising bubbles. In the experiment, single oxygen bubbles of diameter d b =0.55…0.85mm are released into a measurement cell filled with tap water. The oxygen dissolves and reacts with sulfite to sulfate. Laser-induced fluorescence is used to visualize the oxygen concentration in the bubble wake from which the global mass transfer coefficient can be calculated. The ruthenium-based fluorescent dye seems to be surface active, such that the rise velocity is reduced by up to 50% compared to the experiment without fluorescent dye and a recirculation zone forms in the bubble wake. To access the local mass transfer at the interface, we perform complementary numerical simulations. Since the fluorescence tracer is essential for the experimental method, the effect of surface contamination is also considered in the simulation. We employ several improvements in the experimental and numerical procedures which allow for a quantitative comparison (locally and globally). Rise velocity and mass transfer coefficient agree within a few percents between experiment, simulation and literature results. Because the fluorescence tracer is frequently used in mass transfer experiments, we discuss its potential surface activity. © 2019 The Author