Literature DB >> 26306864

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

Victoria Hodge1, Mark Jessop2, Martyn Fletcher2, Michael Weeks2, Aaron Turner2, Tom Jackson2, Colin Ingram3, Leslie Smith4, Jim Austin2.   

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.

Keywords:  Collaboration; Execution platform; Interactive publication repository; Interactive publications; Reproducible neuroscience; Scientific workflows; Web portal

Mesh:

Year:  2016        PMID: 26306864     DOI: 10.1007/s12021-015-9276-3

Source DB:  PubMed          Journal:  Neuroinformatics        ISSN: 1539-2791


  27 in total

1.  Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering.

Authors:  R Quian Quiroga; Z Nadasdy; Y Ben-Shaul
Journal:  Neural Comput       Date:  2004-08       Impact factor: 2.026

2.  CARMEN: a practical approach to metadata management.

Authors:  Mark Jessop; Mike Weeks; Jim Austin
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2010-09-13       Impact factor: 4.226

3.  CANDIShare: a resource for pediatric neuroimaging data.

Authors:  David N Kennedy; Christian Haselgrove; Steven M Hodge; Pallavi S Rane; Nikos Makris; Jean A Frazier
Journal:  Neuroinformatics       Date:  2012-07

4.  G-Node: an integrated tool-sharing platform to support cellular and systems neurophysiology in the age of global neuroinformatics.

Authors:  Andreas V M Herz; Ralph Meier; Martin P Nawrot; Willi Schiegel; Tiziano Zito
Journal:  Neural Netw       Date:  2008-06-12

5.  The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

Authors:  Luis Marenco; Giorgio A Ascoli; Maryann E Martone; Gordon M Shepherd; Perry L Miller
Journal:  Neuroinformatics       Date:  2008-10-31

6.  A new spike detection algorithm for extracellular neural recordings.

Authors:  Shahjahan Shahid; Jacqueline Walker; Leslie S Smith
Journal:  IEEE Trans Biomed Eng       Date:  2009-07-17       Impact factor: 4.538

7.  myExperiment: a repository and social network for the sharing of bioinformatics workflows.

Authors:  Carole A Goble; Jiten Bhagat; Sergejs Aleksejevs; Don Cruickshank; Danius Michaelides; David Newman; Mark Borkum; Sean Bechhofer; Marco Roos; Peter Li; David De Roure
Journal:  Nucleic Acids Res       Date:  2010-05-25       Impact factor: 16.971

8.  FigShare.

Authors:  Jatinder Singh
Journal:  J Pharmacol Pharmacother       Date:  2011-04

9.  Biowep: a workflow enactment portal for bioinformatics applications.

Authors:  Paolo Romano; Ezio Bartocci; Guglielmo Bertolini; Flavio De Paoli; Domenico Marra; Giancarlo Mauri; Emanuela Merelli; Luciano Milanesi
Journal:  BMC Bioinformatics       Date:  2007-03-08       Impact factor: 3.169

10.  Mobyle: a new full web bioinformatics framework.

Authors:  Bertrand Néron; Hervé Ménager; Corinne Maufrais; Nicolas Joly; Julien Maupetit; Sébastien Letort; Sébastien Carrere; Pierre Tuffery; Catherine Letondal
Journal:  Bioinformatics       Date:  2009-08-17       Impact factor: 6.937

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