A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.

Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing. While there are good examples if the use of scientific workflows in bioinformatics, medical informatics, biomedical imaging and data analysis, there are fewer examples in multi-scale computational modeling in general and cardiac electrophysiology in particular. Cardiac electrophysiology simulation is a mature area of multi-scale computational biology that serves as an excellent use case for developing and testing new scientific workflows. In this article, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale cardiac cell and tissue model that is expandable, modular and portable. The workflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing. During all stages of the workflow design, we rely on freely available open-source tools, to make our workflow freely usable by scientists.

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PID https://www.doi.org/10.1371/journal.pcbi.1006856
PID pmc:PMC6426265
PID pmid:30849072
URL https://doaj.org/toc/1553-734X
URL https://doi.org/10.1371/journal.pcbi.1006856
URL https://academic.microsoft.com/#/detail/2921130302
URL https://doaj.org/toc/1553-7358
URL https://pubmed.ncbi.nlm.nih.gov/30849072/
URL https://pesquisa.bvs.br/brasil/resource/pt/mdl-30849072
URL https://escholarship.org/uc/item/52k7q9pn
URL http://dx.plos.org/10.1371/journal.pcbi.1006856
URL https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006856
URL https://www.ncbi.nlm.nih.gov/pubmed/30849072
URL https://ucdavis.pure.elsevier.com/en/publications/a-demonstration-of-modularity-reuse-reproducibility-portability-a
URL https://dblp.uni-trier.de/db/journals/ploscb/ploscb15.html#YangPIJDVMAAC19
URL http://europepmc.org/articles/PMC6426265
URL https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006856&type=printable
URL http://dx.doi.org/10.1371/journal.pcbi.1006856
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Access Right Open Access
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Author Yang, Pei-Chi, 0000-0002-5753-1131
Author Purawat, Shweta, 0000-0002-5183-2750
Author Ieong, Pek U.
Author Jeng, Mao-Tsuen, 0000-0003-4454-4299
Author DeMarco, Kevin R.
Author Vorobyov, Igor, 0000-0002-4767-5297
Author McCulloch, Andrew D., 0000-0002-1708-5675
Author Altintas, Ilkay
Author Amaro, Rommie E.
Author Clancy, Colleen E., 0000-0001-6849-4885
Contributor Sauro, Herbert
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Collected From PubMed Central; eScholarship - University of California; ORCID; Datacite; UnpayWall; DOAJ-Articles; Crossref; Microsoft Academic Graph
Hosted By Europe PubMed Central; eScholarship - University of California; PLoS Computational Biology
Publication Date 2019-03-08
Publisher eScholarship, University of California
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Country United States
Description Author summary We present a computational workflow as a proof of concept for integration and implementation of a reusable and reproducible cardiac multi-scale electrophysiology model that is expandable, modular and portable. This framework enables scientists to create intuitive, user-friendly and flexible end-to-end automated scientific workflows using a graphical user interface. Kepler is an advanced open-source platform that supports multiple models of computation. The underlying workflow engine handles scalability, provenance, reproducibility aspects of the code, performs orchestration of data flow, and automates execution on heterogeneous computing resources. One of the main advantages of workflow utilization is the integration of code written in multiple languages Standardization occurs at the interfaces of the workflow elements and allows for general applications and easy comparison and integration of code from different research groups or even multiple programmers coding in different languages for various purposes from the same group. A workflow driven problem-solving approach enables domain scientists to focus on resolving the core science questions, and delegates the computational and process management burden to the underlying Workflow. The workflow driven approach allows scaling the computational experiment with distributed data-parallel execution on multiple computing platforms, such as, HPC resources, GPU clusters, Cloud etc. The workflow framework tracks software version information along with hardware information to allow users an opportunity to trace any variation in workflow outcome to the system configurations.
Format application/pdf
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Resource Type Other literature type; Article
keyword keywords.Ecology, Evolution, Behavior and Systematics
system:type publication
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Source https://science-innovation-policy.openaire.eu/search/publication?articleId=dedup_wf_001::4334fa1e6ed12c75063383d8d6881de5
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Last Updated 23 December 2020, 03:16 (CET)
Created 23 December 2020, 03:16 (CET)