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A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

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Abstract

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

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Acknowledgments

The CARMEN VL was developed under funding provided by the UK Engineering and Physical Sciences Research Council (grant number EP/E002331/1) and development of the VL is now supported by the UK Biotechnology and Biological Sciences Research Council (grant number BB/I000984/1).

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Authors and Affiliations

  1. Department of Computer Science, University of York, Deramore Lane, York, YO10 5GH, UK

    Victoria Hodge, Mark Jessop, Martyn Fletcher, Michael Weeks, Aaron Turner, Tom Jackson & Jim Austin

  2. Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK

    Colin Ingram

  3. Department of Computing Science and Mathematics, University of Stirling, Stirling, UK

    Leslie Smith

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  1. Victoria Hodge
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  2. Mark Jessop
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  3. Martyn Fletcher
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  4. Michael Weeks
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  5. Aaron Turner
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  7. Colin Ingram
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  8. Leslie Smith
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  9. Jim Austin
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Correspondence to Victoria Hodge.

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Dedication

We dedicate this paper to the memory of our dear friend and colleague Professor Colin Ingram who passed away on December 15th 2013. Colin was the lead investigator on the CARMEN project and co-author of this paper.

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Hodge, V., Jessop, M., Fletcher, M. et al. A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience. Neuroinform 14, 23–40 (2016). https://doi.org/10.1007/s12021-015-9276-3

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