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Container-Based Platform for Computational Medicine

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Part of the Lecture Notes in Networks and Systems book series (LNNS,volume 451)

Abstract

In recent years the concept of “containerization” thanks to commercial software development has become a very promising paradigm also for e-science. In this paper, we present how this paradigm may significantly facilitate the creation of platforms for advanced scientific simulations. We present how with currently available containerization technologies, you can design a platform for simulation in the field of computational medicine with the same functionality as cloud system called Atmosphere, developed in 2011-14 ACK Cyfronet AGH for the Virtual Physiological Human community. The Atmosphere, based on the virtualization concept, provides support thanks to an intuitive interface that performs workflows on-demand cloud computing as well as access to cloud storage. After careful analysis of the Atmosphere structure, a redesign of the platform was subsequently carried out using container-based technologies, in particular Kubernetes. After architectural remodeling based on analysis of requirements and containerization possibilities, an implementation has followed through a Maven project in Java using the Kubernetes API. All this was followed by a validation phase to verify the actual operation.

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Acknowledgements

The authors would like to thank their colleagues from ACC Cyfronet Marek Kasztelnik, Maciej Malawski, Jan Meizner and Piotr Nowakowski for their help in understanding the structure of the Atmosphere platform and for valuable discussions and suggestions regarding the Kubernetes. The work was carried out during the GJP’s stay at AGH under the Erasmus+ program. MB research was partially supported by EU H2020 grant Sano 857533 and IRAP FNP project.

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Correspondence to Gennaro Junior Pezzullo .

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Pezzullo, G.J., Di Martino, B., Bubak, M. (2022). Container-Based Platform for Computational Medicine. In: Barolli, L., Hussain, F., Enokido, T. (eds) Advanced Information Networking and Applications. AINA 2022. Lecture Notes in Networks and Systems, vol 451. Springer, Cham. https://doi.org/10.1007/978-3-030-99619-2_13

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