A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience
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.
KeywordsInteractive publications Collaboration Reproducible neuroscience Interactive publication repository Execution platform Web portal Scientific workflows
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).
- Brase, J. (2009). Datacite-a global registration agency for research data. In 4th International Conference on Cooperation and Promotion of Information Resources in Science and Technology, (pp. 257–261). IEEE.Google Scholar
- Collage Authoring Environment, (2013). https://collage.elsevier.com/Accessed 28th November 2013.
- DataCite Metadata Working Group, (2011). DataCite metadata schema for the publication and citation of research data.Google Scholar
- DataDryad, (2013) http://datadryad.org/ Accessed 28th Nov 2013.
- Davidson, SB., & Freire, J. (2008). Provenance and scientific workflows: challenges and opportunities. In Procs ACM SIGMOD International Conference on Management of Data (pp. 1345–1350).Google Scholar
- de Kamps, M. & Baier, V. (2007). Multiple Interacting Instantiations of Neuronal Dynamics (MIIND): a Library for Rapid Prototyping of Models in Cognitive Neuroscience. Procs International Joint Conference on Neural Networks (IJCNN’2007), FloridaGoogle Scholar
- Digital Object Identifier (DOI). (2013). http://dx.doi.org/ Accessed 28th Nov 2013.
- Eckerson, W. (1995). Three Tier Client/Server Architecture:Achieving Scalability, Performance, and Efficiency in Client Server Applications. Open Information Systems, 10.Google Scholar
- Fielding, RT. (2000). Architectural styles and the design of network-based software architectures, Doctoral dissertation. University of California, Irvine.Google Scholar
- Gibson F., Overton PG., Smulders TV. et al. (2009). Minimum Information about a Neuroscience Investigation (MINI): Electrophysiology. Nature Precedings. http://hdl.handle.net/10101/npre.2009.1720.2.
- Google Web Toolkit, (2013). http://code.google.com/webtoolkit/ Accessed 28th Nov 2013.
- Gray, J., Szalay, A. S., Thakar, A. R., et al. (2002). Online scientific data curation, publication and archiving (Technical Report MSR-TR-2002-74). Redmond: Microsoft Research.Google Scholar
- HDF Group. (2000). Hierarchical data format version 5. Software package, http://www.hdfgroup.org/HDF5 Accessed 28th Nov 2013.
- Hodge, V., Turner, A., Fletcher, M. et al. (2012). Enhancing YouShare: the online collaboration research environment for sharing data and services. Digital Research 2012, Oxford, UK.Google Scholar
- Ingram, C., Jessop, M., Weeks, M. et al. (2012). Development of a workflow system for the CARMEN Neuroscience Portal. 5th INCF Neuroinformatics Congress, Munich, Germany.Google Scholar
- International Neuroinformatics Coordinating Facility (INCF) Dataspace, (2013). http://www.incf.org/resources/data-space/data-space Accessed 28th Nov 2013.
- Lakhani, KR., Jeppesen, LB., Lohse, PA. et al. (2007). The Value of Openness in Scientific Problem Solving. Division of Research, Harvard Business School. Google Scholar
- Liang, B., Fletcher, M. & Austin, J. (2010). The design and implementation of a Neurophysiology Data translation Format (NDF), 9th UK e-Science All Hands Meeting (AHM 2010), Cardiff, UK.Google Scholar
- McCandless, M., Hatcher, E., & Gospodnetic, O. (2010). Lucene in action, second edition: Covers apache lucene 3.0. Greenwich: Manning Publications Co.Google Scholar
- Michener, W., Vieglais, D., Vision, T., et al. (2011). DataONE: data observation network for earth-preserving data and enabling innovation in the biological and environmental sciences. D-Lib Magazine, 17(1), 3.Google Scholar
- Mittelbach, F., Goossens, M., Braams, J. et al. (2010). The LaTeX Companion. Addison-Wesley. Google Scholar
- MySQL, (2013). http://www.mysql.com/ Accessed 28th Nov 2013.
- Neurophysiology Data Translation Format (NDF) Specification – V1.2.1. (2013) http://www.carmen.org.uk/standards/CarmenDataSpecs.pdf Accessed 28th Nov 2013.
- ResearcherID, (2013). http://www.researcherid.com/ Accessed 28th Nov 2013.
- Run My Code. (2013). www.runmycode.org/ Accessed 28th Nov 2013.
- Sernagor, E. (2011). CARMEN for the storage and analysis of rich datasets obtained from 60 and 4,096 channels MEA recordings of retinal activity. CARMEN Consortium Meeting, Newcastle University, UK.Google Scholar
- Simonotto, J., Eglen, S., Kaiser, M. et al. (2009). Analysis of spontaneous activity patterns in the developing retina: extracting and analyzing dynamical networks. Society for Neuroscience (SfN) Meeting, Chicago, USA. Google Scholar
- Simonotto, J., Kaiser, M., Sernagor, E. et al. (2011). Network Extraction and Analysis in CARMEN. CARMEN Consortium Meeting, Newcastle University, UK.Google Scholar
- Sivagnanam, S., Majumdar, A., Yoshimoto, K. et al. (2013). Introducing The Neuroscience Gateway. Proceedings of the 5th International Workshop on Science Gateways, Zurich, Switzerland.Google Scholar
- Springer (2014). http://www.springeropen.com/about/supportingdata Accessed 28th April 2014
- Süptitz, T., Weis, SJJ. & Eymann, T. (2013). Was müssen Virtual Research Environments leisten?-Ein Literaturreview zu den funktionalen und nichtfunktionalen Anforderungen. In Wirtschaftsinformatik (p. 21).Google Scholar
- Weeks, M., Jessop, M., Fletcher, M. et al. (2013). The CARMEN software as a service infrastructure. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 371(1983).Google Scholar
- White Rose Grid. (2013). http://www.wrgrid.org.uk/ Accessed 28th Nov 2013.
- Woodman, S., Hiden, H., Watson, P., et al. (2009). Workflows and applications in e-science central. Oxford: All Hands Meeting.Google Scholar