Relating simulation studies by provenance-Developing a family of Wnt signaling models.

For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one. A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To a...

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Auteurs principaux:	Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M Uhrmacher
Format:	article
Langue:	EN
Publié:	Public Library of Science (PLoS) 2021
Sujets:	Biology (General) QH301-705.5
Accès en ligne:	https://doaj.org/article/5774682ad6014f3e9b72a7f581b2d14f
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spelling	oai:doaj.org-article:5774682ad6014f3e9b72a7f581b2d14f2021-12-02T19:58:08ZRelating simulation studies by provenance-Developing a family of Wnt signaling models.1553-734X1553-735810.1371/journal.pcbi.1009227https://doaj.org/article/5774682ad6014f3e9b72a7f581b2d14f2021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009227https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one. A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To answer this question, we need to identify entities and activities that contributed to the development of a simulation model. Therefore, we exploit the provenance data model, PROV-DM, of the World Wide Web Consortium and, building on previous work, continue developing a PROV ontology for simulation studies. Based on a case study of 19 Wnt/β-catenin signaling models, we identify crucial entities and activities as well as useful metadata to both capture the provenance information from individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, a web application for inserting and querying provenance information. Our specialization of PROV-DM contains the entities Research Question, Assumption, Requirement, Qualitative Model, Simulation Model, Simulation Experiment, Simulation Data, and Wet-lab Data as well as activities referring to building, calibrating, validating, and analyzing a simulation model. We show that most Wnt simulation models are connected to other Wnt models by using (parts of) these models. However, the overlap, especially regarding the Wet-lab Data used for calibration or validation of the models is small. Making these aspects of developing a model explicit and queryable is an important step for assessing and reusing simulation models more effectively. Exposing this information helps to integrate a new simulation model within a family of existing ones and may lead to the development of more robust and valid simulation models. We hope that our approach becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models.Kai BuddeJacob SmithPia WilsdorfFiete HaackAdelinde M UhrmacherPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 8, p e1009227 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Kai Budde Jacob Smith Pia Wilsdorf Fiete Haack Adelinde M Uhrmacher Relating simulation studies by provenance-Developing a family of Wnt signaling models.
description	For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one. A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To answer this question, we need to identify entities and activities that contributed to the development of a simulation model. Therefore, we exploit the provenance data model, PROV-DM, of the World Wide Web Consortium and, building on previous work, continue developing a PROV ontology for simulation studies. Based on a case study of 19 Wnt/β-catenin signaling models, we identify crucial entities and activities as well as useful metadata to both capture the provenance information from individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, a web application for inserting and querying provenance information. Our specialization of PROV-DM contains the entities Research Question, Assumption, Requirement, Qualitative Model, Simulation Model, Simulation Experiment, Simulation Data, and Wet-lab Data as well as activities referring to building, calibrating, validating, and analyzing a simulation model. We show that most Wnt simulation models are connected to other Wnt models by using (parts of) these models. However, the overlap, especially regarding the Wet-lab Data used for calibration or validation of the models is small. Making these aspects of developing a model explicit and queryable is an important step for assessing and reusing simulation models more effectively. Exposing this information helps to integrate a new simulation model within a family of existing ones and may lead to the development of more robust and valid simulation models. We hope that our approach becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models.
format	article
author	Kai Budde Jacob Smith Pia Wilsdorf Fiete Haack Adelinde M Uhrmacher
author_facet	Kai Budde Jacob Smith Pia Wilsdorf Fiete Haack Adelinde M Uhrmacher
author_sort	Kai Budde
title	Relating simulation studies by provenance-Developing a family of Wnt signaling models.
title_short	Relating simulation studies by provenance-Developing a family of Wnt signaling models.
title_full	Relating simulation studies by provenance-Developing a family of Wnt signaling models.
title_fullStr	Relating simulation studies by provenance-Developing a family of Wnt signaling models.
title_full_unstemmed	Relating simulation studies by provenance-Developing a family of Wnt signaling models.
title_sort	relating simulation studies by provenance-developing a family of wnt signaling models.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/5774682ad6014f3e9b72a7f581b2d14f
work_keys_str_mv	AT kaibudde relatingsimulationstudiesbyprovenancedevelopingafamilyofwntsignalingmodels AT jacobsmith relatingsimulationstudiesbyprovenancedevelopingafamilyofwntsignalingmodels AT piawilsdorf relatingsimulationstudiesbyprovenancedevelopingafamilyofwntsignalingmodels AT fietehaack relatingsimulationstudiesbyprovenancedevelopingafamilyofwntsignalingmodels AT adelindemuhrmacher relatingsimulationstudiesbyprovenancedevelopingafamilyofwntsignalingmodels
_version_	1718375778444378112

Relating simulation studies by provenance-Developing a family of Wnt signaling models.

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