Helmholtz: a customizable framework for neurophysiology data management
The benefits of capturing the output of neurophysiology laboratories in structured databases are potentially very large, both in improved data management within a laboratory and in easier and more effective sharing of data, whether with close collaborators or in public databases. However, at present the task of systematically annotating every experiment with sufficient metadata to enable the data to be correctly analysed and interpreted is typically an arduous one. Then, once the effort to create a laboratory database has been made, considerable further effort is needed, due to lack of software tool support, to make use of the database in the day-to-day life of the laboratory, and so realise the potential benefits.
To improve this poor cost-benefit ratio requires that both entering data/metadata into a database system and making use of it later in analyses, visualization etc. be made much easier. This in turn will require software tools that can either integrate with or replace the existing software for data acquisition and analysis used in the laboratory, and that provide a smooth and intuitive workflow to minimize the time required for the potentially tedious process of data annotation. Meeting these requirements in the highly heterogeneous fields of neurophysiology and systems neuroscience can be very difficult, since there is very little standardization of data formats, equipment, software platforms or experimental protocols between different labs.
In this presentation we review some general principles that we think should be followed in trying to address these difficulties, and present a specific solution we have developed: Helmholtz, an open-source framework for developing databases that are customized to the needs of an individual neurophysiology lab.
The Helmholtz framework is built on top of the Django web framework (http://www.djangoproject.com/; following the tradition in the web development community of naming Django-based projects after famous jazz musicians, we named our project after a famous physiologist.) Using Django as a basis brings several advantages: (i) it can be used both for a local database, using the simple, built-in webserver and for a centralized repository; (ii) an abstraction layer on top of the underlying relational database allows any of the widely-used database systems to be used interchangeably (e.g. MySQL, PostgreSQL, Oracle, or the built-in, configuration-free SQLite); (iii) the same abstraction layer makes it easier for non-programmers to extend and customize the database: no knowledge of SQL is required; (4) it is easy to build multiple interfaces to the same database, for example interfaces to acquisition or analysis software, using web technologies.
Helmholtz provides core components which handle elements that are common to all or many domains of neurophysiology. For example, information about data acquisition: metadata for experimental setups (equipment, etc.), subjects (species, weight, anaesthesia, surgery, etc.), stimulation and recording protocols, for electrophysiology (in vivo and in vitro), optical imaging and morphological reconstructions. Another component supports databasing of analysis results, linked to the original data on which they are based, and with descriptions of the analysis methods used. Extension components to support the specific needs of individual labs are straightforward to write, requiring minimal programming experience.
Helmholtz supports multiple interaction methods: via a web interface (with support for tablet computers); batch data import from spreadsheets; programmatic interaction via a web-services API. The API generates and accepts multiple data formats: XML, JSON, YAML and odML; RDF support is planned in the near future.
Acknowledgements
This work was supported by European Union projects FP7-269921 (BrainScaleS) and FP6-015879 (FACETS).
Keywords:
database,
web-services,
data management,
Electrophysiology,
metadata,
ease-of-use,
provenance,
customization
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
General neuroinformatics
Citation:
Davison
AP,
Brizzi
T,
Guarino
D,
Manette
OF,
Monier
C,
Sadoc
G and
Frégnac
Y
(2013). Helmholtz: a customizable framework for neurophysiology data management.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00025
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Received:
08 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Andrew P Davison, CNRS, UNIC, Gif sur Yvette, 91198, France, andrew.davison@cnrs.fr