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Title: A physiome standards-based model publication paradigm
Authors: Nickerson, D.P. 
Buist, M.L. 
Keywords: Cellml
Mathematical model representation
Model publication
Physiome standards
Issue Date: 28-May-2009
Citation: Nickerson, D.P., Buist, M.L. (2009-05-28). A physiome standards-based model publication paradigm. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 367 (1895) : 1823-1844. ScholarBank@NUS Repository.
Abstract: In this era of widespread broadband Internet penetration and powerful Web browsers on most desktops, a shift in the publication paradigm for physiome-style models is envisaged. No longer will model authors simply submit an essentially textural description of the development and behaviour of their model. Rather, they will submit a complete working implementation of the model encoded and annotated according to the various standards adopted by the physiome project, accompanied by a traditional humanreadable summary of the key scientific goals and outcomes of the work. While the final published, peer-reviewed article will look little different to the reader, in this new paradigm, both reviewers and readers will be able to interact with, use and extend the models in ways that are not currently possible. Here, we review recent developments that are laying the foundations for this new model publication paradigm. Initial developments have focused on the publication of mathematical models of cellular electrophysiology, using technology based on a CellML- or Systems Biology Markup Language (SBML)-encoded implementation of the mathematical models. Here, we review the current state of the art and what needs to be done before such a model publication becomes commonplace. © 2009 the royal society.
Source Title: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
ISSN: 1364503X
DOI: 10.1098/rsta.2008.0296
Appears in Collections:Staff Publications

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