Provenance in modeling and simulation studies — Bridging gaps

Ruscheinski, Andreas; Uhrmacher, Adelinde M.

doi:10.1109/wsc.2017.8247839

Cited by 27 publications

(15 citation statements)

References 32 publications

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“…Capturing provenance (i.e. information about how a product has been generated) helps to assess the products of simulation studies, such as simulation data or simulation models (Ruscheinski and Uhrmacher, 2017). Fig.…”

Section: Provenance Of the Developed Simulation Modelsmentioning

confidence: 99%

Exploring the mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling

Haack

Budde

Uhrmacher

2020

Journal of Cell Science

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Endocytosis plays a pivotal regulatory role in canonical WNT signaling. Internalization of the low-density lipoprotein receptor-related protein 6 (LRP6) receptor complex can either promote or attenuate canonical WNT signaling, depending on the employed internalization pathway. Detailed analysis of the mechanism of LRP6 internalization and its temporal regulation is crucial for understanding the different cellular responses to WNT stimulation under varying conditions and in various cell types. Here, we elucidate the mechanisms involved in the internalization of LRP6 and re-evaluate existing, partly contradicting, theories on the regulation of LRP6 receptor internalization. We utilize a computational approach that aims at finding a set of mechanisms that accounts for the temporal dynamics of LRP6 receptor internalization upon WNT stimulation. Starting with a simple simulation model, we successively extend and probe the model's behavior based on quantitative measurements. The final model confirms that LRP6 internalization is clathrin independent in vertebrates, is not restricted to microdomains, and that signalosome formation delays LRP6 internalization within the microdomains. These findings partly revise the current understanding of LRP6 internalization in vertebrates.

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Section: Provenance Of the Developed Simulation Modelsmentioning

confidence: 99%

Exploring the mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling

Haack

Budde

Uhrmacher

2020

Journal of Cell Science

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“…rather than "How has it been developed?". To capture the provenance of simulation models, i.e., how a model has been developed, in Ruscheinski and Uhrmacher (2017) data, simulation model, and simulation experiments have been identified as central processes and products within a simulation study and mapped to processes and artifacts within an Open Provenance Model profile (Moreau et al 2011). In this triangle of interrelated artifacts, exploiting roles in relating artifacts and processes provides additional semantics that can be queried.…”

Section: Provenance Information About Simulation Models -Structured Annotations Roles and Relationsmentioning

confidence: 99%

CRISIS, WHAT CRISIS – DOES REPRODUCIBILITY IN MODELING & SIMULATION REALLY MATTER?

Taylor¹,

Eldabi²,

Monks³

et al. 2018

2018 Winter Simulation Conference (WSC)

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How important it is to our discipline that we can reproduce the results of Modeling & Simulation (M&S) research? How important is it to be able to (re)use the models, data, and methods described in simulation publications to reproduce published results? Is it really that important or are the lessons and experiences described in a paper enough for us to build on the work of others? At the 2016 Winter Simulation Conference, a panel considered opinions on reproducibility in discrete-event simulation. This article builds on these and asks if there really is a reproducibility crisis in M&S? A diverse range of views on the subject are presented including reflections on the reproducibility in terms of the art and science of simulation, the frustrations of poor reproducibility, perspectives from the industrial production & logistics community, the wider context of open science and artefact sharing, and the role of provenance beyond reproducibility. INTRODUCTIONWhat does reproducibility mean in terms of Modeling & Simulation? Does reproducibility matter? To what degree is reproducibility possible? Could reproducibility policies have a negative impact on publishing in M&S? These questions were amongst some initially posed to our panelists as a starting point to gather a range of views on this potentially important topic. This panel paper presents a range of views on the subject and contributes to the on-going debate about the role of reproducibility in our discipline.

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“…Semantic annotations can also be used to quantify the similarity between model elements 27,28,[50][51][52][53][54] , helping to ensure that the user is presented with the most relevant models following a search. Other types of annotations, such as those that capture provenance information [55][56][57][58] , can also help researchers determine which models best meet their research needs and make comparisons between different model versions 59 .…”

Section: Challenges In Model Reuse and Integrationmentioning

confidence: 99%

Harmonizing semantic annotations for computational models in biology

Neal

König

Nickerson

et al. 2018

Preprint

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Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition, and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current semantic annotation practices among the COmputational Modeling in BIology NEtwork (COMBINE) community and provide a set of recommendations for building a consensus approach to semantic annotation.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

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Provenance in modeling and simulation studies — Bridging gaps

Cited by 27 publications

References 32 publications

Exploring the mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling

Exploring the mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling

CRISIS, WHAT CRISIS – DOES REPRODUCIBILITY IN MODELING & SIMULATION REALLY MATTER?

Harmonizing semantic annotations for computational models in biology

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