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Executable Simulation Model of the Liver

View ORCID ProfileMatthias König
doi: https://doi.org/10.1101/2020.01.04.894873
Matthias König
1Institute for Theoretical Biology, Institute of Biology, Humboldt-University, Berlin, Germany
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  • For correspondence: koenigmx@hu-berlin.de
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Abstract

To address the issue of reproducibility in computational modeling we developed the concept of an executable simulation model (EXSIMO). An EXSIMO combines model, data and code with the execution environment to run the computational analysis in an automated manner using tools from software engineering. Key components are i) models, data and code for the computational analysis; ii) tests for models, data and code; and iii) an automation layer to run tests and execute the analysis. An EXSIMO combines version control, model, data, units, annotations, analysis, reports, execution environment, testing, continuous integration and release. We applied the concept to perform a replication study of a computational analysis of hepatic glucose metabolism in the liver. The corresponding EXSIMO is available from https://github.com/matthiaskoenig/exsimo.

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  • https://github.com/matthiaskoenig/exsimo

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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 January 06, 2020.
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Executable Simulation Model of the Liver
Matthias König
bioRxiv 2020.01.04.894873; doi: https://doi.org/10.1101/2020.01.04.894873
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Executable Simulation Model of the Liver
Matthias König
bioRxiv 2020.01.04.894873; doi: https://doi.org/10.1101/2020.01.04.894873

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