Version 1
: Received: 14 October 2023 / Approved: 16 October 2023 / Online: 19 October 2023 (04:47:55 CEST)
How to cite:
Luís, M.; Vaz, C.; Francisco, A.P. FLOWViZ: An Airflow Based Workflow Middleware for Computational Phylogenetics. Preprints2023, 2023101211. https://doi.org/10.20944/preprints202310.1211.v1
Luís, M.; Vaz, C.; Francisco, A.P. FLOWViZ: An Airflow Based Workflow Middleware for Computational Phylogenetics. Preprints 2023, 2023101211. https://doi.org/10.20944/preprints202310.1211.v1
Luís, M.; Vaz, C.; Francisco, A.P. FLOWViZ: An Airflow Based Workflow Middleware for Computational Phylogenetics. Preprints2023, 2023101211. https://doi.org/10.20944/preprints202310.1211.v1
APA Style
Luís, M., Vaz, C., & Francisco, A.P. (2023). FLOWViZ: An Airflow Based Workflow Middleware for Computational Phylogenetics. Preprints. https://doi.org/10.20944/preprints202310.1211.v1
Chicago/Turabian Style
Luís, M., Cátia Vaz and Alexandre P. Francisco. 2023 "FLOWViZ: An Airflow Based Workflow Middleware for Computational Phylogenetics" Preprints. https://doi.org/10.20944/preprints202310.1211.v1
Abstract
Epidemiological surveillance and phylogenetic studies rely nowadays on processing and analysing huge volumes of data. Processing tasks consist on running and refining a series of intertwined computational tasks. And, despite of existing several web applications for data processing and interactive visualization for phylogenetic studies, integrating many different tools and algorithms, their execution is total or partially on the client side, making them unsuitable for dealing with huge volumes of data. Studies are often also not easy to reproduce. On the other hand, in recent years, data-centric workflow systems have been proposed, allowing to deal better with increasingly larger datasets. The integration of these systems within phylogenetic tools will allow to scale them as required, and will contribute also to promote studies reproducibility. We propose then the FLOWViZ middleware for facilitating the integration of a state of the art data-centric workflow system, Apache Airflow, within web applications for phylogenetic analyses. This framework abstracts contracts and a core API for defining tools and workflows, where tools are assumed to be containerized. FLOWViZ has been tested and evaluated within the PHYLOViZ web application, a tool supporting phylogenetic inference and data visualization.
Keywords
software integration; middleware; data centric workflows; computational phylogenetics
Subject
Computer Science and Mathematics, Software
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
