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des-ist: A Simulation Framework to Streamline Event-Based In Silico Trials

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Computational Science – ICCS 2021 (ICCS 2021)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12744))

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Abstract

To popularise in silico trials for development of new medical devices, drugs, or treatment procedures, we present the modelling framework des-ist (Discrete Event Simulation framework for In Silico Trials). This framework supports discrete event-based simulations. Here, events are collected in an acyclic, directed graph, where each node corresponds to a component of the overall in silico trial. A simple API and data layout are proposed to easily couple numerous simulations by means of containerised environments, i.e. Docker and Singularity. An example in silico trial is highlighted studying treatment of acute ischemic stroke, as considered in the INSIST project.

The proposed framework enables straightforward coupling of the discrete models, reproducible outcomes by containerisation, and easy parallel execution by GNU Parallel. Furthermore, des-ist supports the user in creating, running, and analysing large numbers of virtual cohorts, automating repetitive user interactions. In future work, we aim to provide a tight integration with validation, verication and uncertainty quantication analyses, to enable sensitivity analysis of individual components of in silico trials and improve trust in the computational outcome to successfully augment classical medical trials and thereby enable faster development of treatment procedures.

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Notes

  1. 1.

    Non-Python code is included using Python’s subprocess library https://docs.python.org/3.10/library/subprocess.html.

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Authors and Affiliations

  1. Computational Science Laboratory, Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands

    Max van der Kolk, Claire Miller, Raymond Padmos & Alfons Hoekstra

  2. Netherlands eScience Center, Science Park 140, 1098 XG, Amsterdam, The Netherlands

    Victor Azizi

Authors
  1. Max van der Kolk
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  2. Claire Miller
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  3. Raymond Padmos
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  4. Victor Azizi
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  5. Alfons Hoekstra
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Corresponding author

Correspondence to Max van der Kolk .

Editor information

Editors and Affiliations

  1. AGH University of Science and Technology, Krakow, Poland

    Maciej Paszynski

  2. Ludwig-Maximilians-Universität München, Munich, Germany

    Dieter Kranzlmüller

  3. University of Amsterdam, Amsterdam, The Netherlands

    Valeria V. Krzhizhanovskaya

  4. University of Tennessee at Knoxville, Knoxville, TN, USA

    Jack J. Dongarra

  5. University of Amsterdam, Amsterdam, The Netherlands

    Peter M.A. Sloot

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van der Kolk, M., Miller, C., Padmos, R., Azizi, V., Hoekstra, A. (2021). des-ist: A Simulation Framework to Streamline Event-Based In Silico Trials. In: Paszynski, M., Kranzlmüller, D., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M. (eds) Computational Science – ICCS 2021. ICCS 2021. Lecture Notes in Computer Science(), vol 12744. Springer, Cham. https://doi.org/10.1007/978-3-030-77967-2_53

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  • DOI: https://doi.org/10.1007/978-3-030-77967-2_53

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-77966-5

  • Online ISBN: 978-3-030-77967-2

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