EuroPython 2016

PyMICE - a library for analysis of IntelliCage™ data

Speaker(s) Jakub Kowalski

Life sciences are suffering badly from a “research reproducibility crisis”. One of possible countermeasures is automation of data acquisition and analysis.

Automated data acquisition systems facilitate standardization of conditions and measurements by minimization of human disturbance. One of such systems is IntelliCage™, dedicated for long-term behavioural experiments on cohorts of mice in social context.

The robustness of data analysis may be improved with automated data analysis workflows (ADAWs): computer programs analysing the data in batch mode. Also, the source code of such program is an unequivocal, formal specification of the performed analysis. The only drawback of such approach is a significant effort and technical knowledge necessary to define an ADAW.

Our goal was to simplify development of ADAWs and to shift the developer’s focus from technical details (like data format) to the analysis itself. To meet the goal, we developed the PyMICE library (resource identifier: RRID:nlx_158570). The library provides an user-friendly and intuitive API to access IntelliCage data, encouraging development of ADAWs according to object-oriented and functional programming paradigms.

Acknowledgements Project sponsored by Symfonia NCN grant: UMO-2013/08/W/NZ4/00691

in on Wednesday 20 July at 10:30 See schedule

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