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Epithelial Modelling Platform: A Tool for Model Discovery and Assembly with the Physiome Model Repository

View ORCID ProfileDewan M. Sarwar, View ORCID ProfileYuda Munarko, View ORCID ProfileDavid P. Nickerson
doi: https://doi.org/10.1101/631465
Dewan M. Sarwar
Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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  • For correspondence: dsar941@aucklanduni.ac.nz
Yuda Munarko
Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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David P. Nickerson
Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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ABSTRACT

In this paper we present a web-based platform enabling scientists to construct a novel epithelial transport model to investigate their hypotheses, aided by building on existing models discovered in the Physiome Model Repository (PMR). We have comprehensively annotated a cohort of epithelial transport models deposited in the PMR as a seeding collection of building blocks that are freely available for reuse. On the platform, users are able to semantically display models for visualization, graphical editing, and model assembly. In addition, we leverage web services from the European Bioinformatics Institute (EBI) to help rank similar models based on the suggestions provided by the platform. In addition to potential use in biomedical and clinical research, novice modellers could use our platform as a learning tool. The source code and links to a live demonstration of the platform are available at https://github.com/dewancse/ epithelial-modelling-platform.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 08, 2019.
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Epithelial Modelling Platform: A Tool for Model Discovery and Assembly with the Physiome Model Repository
Dewan M. Sarwar, Yuda Munarko, David P. Nickerson
bioRxiv 631465; doi: https://doi.org/10.1101/631465
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Epithelial Modelling Platform: A Tool for Model Discovery and Assembly with the Physiome Model Repository
Dewan M. Sarwar, Yuda Munarko, David P. Nickerson
bioRxiv 631465; doi: https://doi.org/10.1101/631465

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