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xml2jupyter: Mapping parameters between XML and Jupyter widgets

View ORCID ProfileRandy Heiland, View ORCID ProfileDaniel Mishler, View ORCID ProfileTyler Zhang, View ORCID ProfileEric Bower, View ORCID ProfilePaul Macklin
doi: https://doi.org/10.1101/601211
Randy Heiland
1Intelligent Systems Engineering, Indiana University
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Daniel Mishler
1Intelligent Systems Engineering, Indiana University
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Tyler Zhang
1Intelligent Systems Engineering, Indiana University
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Eric Bower
1Intelligent Systems Engineering, Indiana University
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Paul Macklin
1Intelligent Systems Engineering, Indiana University
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  • For correspondence: Paul.Macklin@MathCancer.org
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Abstract

Jupyter Notebooks [4, 6] provide executable documents (in a variety of programming languages) that can be run in a web browser. When a notebook contains graphical widgets, it becomes an easy-to-use graphical user interface (GUI). Many scientific simulation packages use text-based configuration files to provide parameter values and run at the command line without a graphical interface. Manually editing these files to explore how different values affect a simulation can be burdensome for technical users, and impossible to use for those with other scientific backgrounds. xml2jupyter is a Python package that addresses these scientific bottlenecks. It provides a mapping between configuration files, formatted in the Extensible Markup Language (XML), and Jupyter widgets. Widgets are automatically generated from the XML file and these can, optionally, be incorporated into a larger GUI for a simulation package, and optionally hosted on cloud resources. Users modify parameter values via the widgets, and the values are written to the XML configuration file which is input to the simulation’s command-line interface. xml2jupyter has been tested using PhysiCell [1], an open source, agent-based simulator for biology, and it is being used by students for classroom and research projects. In addition, we use xml2jupyter to help create Jupyter GUIs for PhysiCell-related applications running on nanoHUB [5].

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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. It is made available under a CC-BY 4.0 International license.
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Posted April 07, 2019.
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xml2jupyter: Mapping parameters between XML and Jupyter widgets
Randy Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, Paul Macklin
bioRxiv 601211; doi: https://doi.org/10.1101/601211
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xml2jupyter: Mapping parameters between XML and Jupyter widgets
Randy Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, Paul Macklin
bioRxiv 601211; doi: https://doi.org/10.1101/601211

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