Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic

Vera, Julio; Lischer, Christopher; Nenov, Momchil; Николов, Светослав; Lai, Xin; Eberhardt, Martin

doi:10.3390/ijms22020547

Cited by 12 publications

(6 citation statements)

References 40 publications

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“…The Building Simulation Model activity, also called model derivation [ 86 ], can use all entity types as any entity described above can contribute to the model building process, but it needs to have at least one link to a Research Question or Simulation Model. The only result of the building simulation activity is a Simulation Model entity.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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“…Modern biological science in the past 50 years has made a spectacular journey providing us fascinating insights into the nature of living organisms, and leading to accumulation of incredible amount of information. Nowadays, we observe introduction of the new systems approaches, that allow us to supplement the qualitative nature of the life sciences by quantitative and mechanism-driven analysis [1]. More and more scientists are becoming attracted by the unique opportunities that are provided by the novel synthetic approaches encompassed by the systems biology, systems physiology and systems pharmacology in various fields [2][3][4][5][6].…”

Section: Articlementioning

confidence: 99%

Systems approaches meet biology and physiology: why do we need yet another journal?

Panteleev

2021

SBPR

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“…The Building Simulation Model activity, also called model derivation [84], can use all entities types, as any entity described above can contribute to the model building process, but it needs to have at least a link to a Research Question or Simulation Model. The only result of the building simulation activity is an entity Simulation Model.…”

Section: Building Simulation Model [Bsm]mentioning

confidence: 99%

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

Budde

Smith

Wilsdorf

et al. 2021

Preprint

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For many cell-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 and look at entities and activities that contributed to the development of a simulation model. Therefore, we exploit the PROV Data Model (PROV-DM) and, building on previous work, continue developing a PROV ontology for simulation models. Based on a concrete 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 of individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, which allows one to insert and query 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 Simulation Models is small. Making these aspects of developing a model explicit and queryable is a crucial step for assessing and reusing simulation models more effectively. The unambiguous specification of information helps to integrate a new simulation model within the family of existing ones. Our approach opens up a wealth of knowledge that may lead to the development of more robust and valid simulation models. We hope that it becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models.

show abstract

Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic

Cited by 12 publications

References 40 publications

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

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

Systems approaches meet biology and physiology: why do we need yet another journal?

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

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