Many current physiological techniques require a set of software tools that implement novel techniques ranging from stimulus delivery, data acquisition, real-time or offline analysis and visualisation of data allowing interaction with the experiment. Maintenance of a functional research environment that uses closed-source proprietary solutions may be inefficient and inadequate; it may limit acquisition and analysis and be time-consuming. In consequence laboratories may have restricted access to adequate facilities and could be reluctant to upgrade their current tools. The NeuroDebian project (http://neuro.debian.net) addresses these problems by integrating free software tools which are being continually developed by the scientific community. This project works within the larger Debian project offering universal Linux operating system. NeuroDebian as a result offers a complete desktop environment and tools for various research needs in physiology and beyond. These include: EEG/EMG recording and analysis (e.g., aghermann, OpenMEEG, sigviewer); generic environments for computational research (e.g. IPython, Octave, R); analysis and visualisation of neuroimaging data (e.g. AFNI, FSL), simulation and investigation of magnetic resonance sequences (Odin); delivery of stimuli for psychophysical research (e.g. PsychoPy, Psychtoolbox-3); statistical learning analysis using functional magnetic resonance imaging data (e.g. MDP, PyMVPA). In addition, a number of tools are also being developed for later integration into the NeuroDebian project, that include a specialised patch-clamping solution, patchclamp (http://patchclamp.net). The maturity and reliability of Debian provides a reliable foundation to carry out a wide range of research routines, whilst NeuroDebian tracks and makes available the latest developments of relevant scientific software.For more than eight years the NeuroDebian portal, currently used world-wide, has been providing readily-usable research software packages for Debian-based operating systems; including Ubuntu, making them easily available for all users of these systems. For non-Linux systems NeuroDebian provides a convenient virtual appliance that allows researchers to run these software packages on proprietary systems, such as Windows and Mac OS X. This software-integration project increases the overall quality and accessibility of research software by: helping to fix software bugs; permitting its testing on a wide variety of hardware architectures; and simplifying installation and upgrade procedures.These useful aspects of the NeuroDebian project and benefits from patchclamp integration will be illustrated at the meeting.
Physiology 2014 (London, UK) (2014) Proc Physiol Soc 31, PCA100
Poster Communications: NeuroDebian: an integrated, community-driven, free software platform for physiology
Y. O. Halchenko2, M. Hanke3, V. Alexeenko1
1. Biochemistry and Physiology, University of Surrey, Guildford, United Kingdom. 2. Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire, United States. 3. Department of Experimental Psychology, Otto-von-Guericke University, Magdeburg, Germany.
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Where applicable, experiments conform with Society ethical requirements.