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

2021 ◽  
Vol 17 (8) ◽  
pp. e1009227
Author(s):  
Kai Budde ◽  
Jacob Smith ◽  
Pia Wilsdorf ◽  
Fiete Haack ◽  
Adelinde M. Uhrmacher
Keyword(s):  
Simulation Model ◽  
Web Application ◽  
Model Simulation ◽  
Research Question ◽  
Simulation Models ◽  
Simulation Studies ◽  
Provenance Information ◽  
Provenance Data ◽  
Starting Point ◽  
Wet Lab

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.

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

2021 ◽  
Author(s):  
Kai Budde ◽  
Jacob Smith ◽  
Pia Wilsdorf ◽  
Fiete Haack ◽  
Adelinde M. Uhrmacher
Keyword(s):  
Simulation Model ◽  
Wnt Signaling ◽  
Model Simulation ◽  
Research Question ◽  
Simulation Models ◽  
Simulation Studies ◽  
Provenance Information ◽  
Starting Point ◽  
Wet Lab ◽  
The Creation

AbstractFor 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 inWebProv, 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.Author summaryWe revise a provenance ontology for simulation studies of cellular biochemical models. Provenance information is useful for understanding the creation of a simulation model, because it does not only contain information about the entities and activities that have led to a simulation model but also the relations of these, which can be visualized. It provides additional structure as research questions, assumptions, and requirements are singled out and explicitly related along with data, qualitative models, simulation models, and simulation experiments through a small set of predefined but extensible activities.We have applied our concept to a family of 19 Wnt signaling models and implemented a web-based tool (WebProv) to store the provenance information of these studies. The resulting provenance graph visualizes the story line within simulation studies and demonstrates the creation and calibration of simulation models, the successive attempts of validation and extension, and shows, beyond an individual simulation study, how the Wnt models are related. Thereby, the steps and sources that contributed to a simulation model are made explicit.Our approach complements other approaches aimed at facilitating the reuse and assessment of simulation products in systems biology such as model repositories as well as annotation and documentation guidelines.

scholarly journals Guidelines to Calibrate a Multi-Residential Building Simulation Model Addressing Overheating Evaluation and Residents’ Influence

Buildings ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 242
Author(s):  
Christoph Schünemann ◽  
David Schiela ◽  
Regine Ortlepp
Keyword(s):  
Simulation Model ◽  
Time Window ◽  
Residential Building ◽  
Simulation Models ◽  
Building Simulation ◽  
Night Time ◽  
Building Performance Simulation ◽  
Starting Point ◽  
3D Simulation Model ◽  
Building Physics

Can building performance simulation reproduce measured summertime indoor conditions of a multi-residential building in good conformity? This question is answered by calibrating simulated to monitored room temperatures of several rooms of a multi-residential building for an entire summer in two process steps. First, we did a calibration for several days without the residents being present to validate the building physics of the 3D simulation model. Second, the simulations were calibrated for the entire summer period, including the residents’ impact on evolving room temperature and overheating. As a result, a high degree of conformity between simulation and measurement could be achieved for all monitored rooms. The credibility of our results was secured by a detailed sensitivity analysis under varying meteorological conditions, shading situations, and window ventilation or room use in the simulation model. For top floor dwellings, a high overheating intensity was evoked by a combination of insufficient use of night-time window ventilation and non-heat-adapted residential behavior in combination with high solar gains and low heat storage capacities. Finally, the overall findings were merged into a process guideline to describe how a step-by-step calibration of residential building simulation models can be done. This guideline is intended to be a starting point for future discussions about the validity of the simplified boundary conditions which are often used in present-day standard overheating assessment.

Development of a Simulation Model for Optimization of Business Process

2018 ◽  
pp. 1-25
Keyword(s):  
Simulation Model ◽  
Business Process ◽  
Mathematical Analysis ◽  
Business Processes ◽  
Research Question ◽  
Simulation Models ◽  
Customer Behavior ◽  
The Novel ◽  
Realistic Simulation ◽  
Key Concepts

Earning profits in business promotes optimization of business processes. For the analysis of business processes, realistic simulation models are an important prerequisite. The research question is as follows: What is business process based on gap processes? The aim of the research is to carry out mathematical analysis of gap processes underpinning elaboration of a simulation model for optimization of a bursty business process. The meanings of such key concepts as “bursty business process,” “binary customer behavior,” “gap,” and “gap processes” are studied. In this chapter, a new simulation model is presented that allows a realistic analysis of business process based on gap processes. The model is based on the assumption that the gaps between two buyers are statistically independent on each other, which has been proofed as a good practical approximation. The novel contribution of the manuscript is revealed in the newly created simulation model based on gap processes. Directions of further research are indicated.

scholarly journals Modeling Patterns of Land Use in Chinese Cities Using an Integrated Cellular Automata Model

2018 ◽  
Vol 7 (10) ◽  
pp. 403 ◽  
Author(s):  
Yanlei Feng ◽  
Yi Qi
Keyword(s):  
Land Use ◽  
Cellular Automata ◽  
Simulation Model ◽  
Large Scale ◽  
Driving Forces ◽  
Simulation Models ◽  
Simulation Studies ◽  
Cellular Automata Model ◽  
Urban Simulation ◽  
Land Use And Cover

This paper introduces an urban growth simulation model applied to the full scope of China. The model uses a multicriteria decision analysis to calculate the land conversion probability and then integrates it with a cellular automata model. A nonlinear relationship is incorporated in to the model to interpret the impacts of different Land Use and Cover Change driving forces. The Analytical Hierarchical Process is also implemented to compute the variance between weights of different factors. Multiple sizes of neighborhood and different urban ratios in the model rules are tested, and a 5 × 5 neighborhood and an urban threshold of 0.33 are chosen. The study demonstrates the importance of spatial analysis on socioeconomic factors, population, and Gross Domestic Product in land use change simulation modeling. The model fills the gap between the purely economic theory simulation model and the geographic simulation model. The nationwide urban simulation is an example that addresses the lack of urban simulation studies in China and among large-scale simulation models.

scholarly journals Living lab on sharing and circular economy: The case of Turin

2021 ◽  
Vol 27 (1) ◽  
pp. 146045822098727
Author(s):  
Federico Cuomo ◽  
Nadia Lambiase ◽  
Antonio Castagna
Keyword(s):  
Circular Economy ◽  
Common Ground ◽  
Swot Analysis ◽  
Research Question ◽  
Environmental Benefits ◽  
Production Cycle ◽  
Living Lab ◽  
Starting Point ◽  
Living Labs ◽  
Past Experiences

Cities with their innovative capacity are key places to address critical climate, environmental and health challenges. Urban experimentations, such as Living Labs, can represent a starting point to reintroduce resources into the production cycle and reduce environmental impacts, embracing the paradigm of the circular economy (CE). According to recent studies, Living Labs at a city scale could generate significant environmental benefits, improvements in quality of life and positive impacts on citizens’ health.1 This paper aims at presenting the case of the Torino Living Lab on Sharing and Circular Economy (LLSC) to point out possible future scenarios of urban sustainable policies. The case study is analysed in five sections: (1) the description of the new permanent laboratory proposed by the City of Turin; (2) the past experiences of Living Labs in Turin; (3) the birth of LLSC and the involvement strategy; (4) the introduction of the eight admitted experimentations. In the light of the results collected, the last paragraph (5) came up with the Strengths, Weaknesses, Opportunities, Treaths (SWOT) analysis in the LLSC. Eventually, it deals with the research question by offering a common ground for global and local policies focused on sustainability and CE.

scholarly journals A Simulation Model of Construction Projects Executed in Random Conditions with the Overlapping Construction Works

2021 ◽  
Vol 13 (11) ◽  
pp. 5795
Author(s):  
Sławomir Biruk ◽  
Łukasz Rzepecki
Keyword(s):  
Simulation Model ◽  
Technological Process ◽  
Construction Projects ◽  
Working Time ◽  
Simulation Studies ◽  
Construction Methods ◽  
The Impact ◽  
Construction Works

Reducing the duration of construction works requires additional organizational measures, such as selecting construction methods that assure a shorter realization time, engaging additional resources, working overtime, or allowing construction works to be performed simultaneously in the same working units. The simultaneous work of crews may affect the quality of works and the efficiency of construction processes. This article presents a simulation model aimed at assessing the impact of the overlap period on the extension of the working time of the crews and the reduction of a repetitive project’s duration in random conditions. The purpose of simulation studies is to provide construction managers with guidelines when deciding on the dates of starting the sequential technological process lines realized by specialized working crews, for sustainable scheduling and organization of construction projects.

scholarly journals Implications of Lesson Study for Tertiary-Level EFL Teachers’ Professional Development: A Case Study From Turkey

SAGE Open ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 215824402110237
Author(s):  
İlknur Bayram ◽  
Fatma Bıkmaz
Keyword(s):  
Professional Development ◽  
Lesson Study ◽  
English Language ◽  
Research Question ◽  
Teaching Style ◽  
Language Teachers ◽  
Student Thinking ◽  
Pedagogical Content ◽  
Starting Point

This qualitative case study carried out at a Turkish university with four English language teachers aims to explore what teachers experience in the planning, implementation, analysis, and reporting phases of the lessons study process and what the implications of lesson study for teacher professional development can be. Data in this four-month study were gathered through observations, interviews, whole group discussions, and reflective reports. Findings revealed that lesson study had potential challenges and benefits for the professional development of teachers. The model poses challenges in finding a topic and research question, determining the lesson design and teaching style, making student thinking observable and analyzing qualitative data. On the other hand, it benefited teachers in terms of increasing their pedagogical content knowledge, reflectivity, research skills, collaboration, and collegiality. This study suggests that lesson study might be a good starting point for institutions wishing to adopt a more teacher-led, inquiry-driven and collaborative perspective for professional development.

Settings, Experimentation and Evaluation of the Simulation Models

2013 ◽  
Vol 309 ◽  
pp. 366-371 ◽  
Author(s):  
František Manlig ◽  
Radek Havlik ◽  
Alena Gottwaldova
Keyword(s):  
Simulation Model ◽  
New Technology ◽  
Simulation Models ◽  
Manufacturing Processes ◽  
Customer Requirements ◽  
Evaluation Functions ◽  
Operational Management ◽  
Minimum Number ◽  
User Friendly ◽  
Setting Parameters

This paper deals with research in computer simulation of manufacturing processes. The paper summarizes the procedures associated with developing the model, experimenting with and evaluating the model results. The key area is of experimentation with the simulation model and evaluation using indicators or multi-criteria functions. With regards to the experiment the crucial variables are the simulation model. The key ideas are to set the number of variables, depending on what a given simulation will be. For example, when introducing new technology into production, modify the type of warehouse, saving workers, thus economizing. The simulation models for the operational management uses simplified models, if possible, a minimum number of variables to obtain the result in shortest possible time. These models are more user friendly and the course will be conducted mostly in the background. An example of a criteria function is the number of parts produced or production time. Multi-criteria function has given us the opportunity to make better quality decisions. It is based on the composition of several parameters, including their weight to one end point. The type of evaluation functions, whether it is an indicator or criteria function is selected and based on customer requirements. In most cases it is recommended to use the multi-dimensional function. It gives us a more comprehensive view of the results from the model and facilitates decision-making. The result of this paper is a display of setting parameters for the experimentation on a sample model. Furthermore, the comparisons of results with a multi-criteria objective function and one-criterion indicator.

A Method to Define the Best Weld Sequence Using a Limited Number of Welding Simulation Analysis

2015 ◽  
Author(s):  
Mahyar Asadi ◽  
Ghazi Alsoruji
Keyword(s):  
Simulation Model ◽  
Surrogate Model ◽  
Simulation Analysis ◽  
Combinatorial Problem ◽  
Fem Analysis ◽  
Simulation Models ◽  
Computational Time ◽  
Optimal Sequence ◽  
Welded Structure ◽  
Welding Sequence

Weld sequence optimization, which is determining the best (and worst) welding sequence for welding work pieces, is a very common problem in welding design. The solution for such a combinatorial problem is limited by available resources. Although there are fast simulation models that support sequencing design, still it takes long because of many possible combinations, e.g. millions in a welded structure involving 10 passes. It is not feasible to choose the optimal sequence by evaluating all possible combinations, therefore this paper employs surrogate modeling that partially explores the design space and constructs an approximation model from some combinations of solutions of the expensive simulation model to mimic the behavior of the simulation model as closely as possible but at a much lower computational time and cost. This surrogate model, then, could be used to approximate the behavior of the other combinations and to find the best (and worst) sequence in terms of distortion. The technique is developed and tested on a simple panel structure with 4 weld passes, but essentially can be generalized to many weld passes. A comparison between the results of the surrogate model and the full transient FEM analysis all possible combinations shows the accuracy of the algorithm/model.

Rotorcraft Lateral-Directional Oscillations: The Anatomy of a Nuisance Mode

2021 ◽  
Author(s):  
Dheeraj Agarwal ◽  
Linghai Lu ◽  
Gareth D. Padfield ◽  
Mark D. White ◽  
Neil Cameron
Keyword(s):  
Simulation Model ◽  
Simulation Models ◽  
Flight Test ◽  
Flight Simulation ◽  
Stability And Control ◽  
Systems Research ◽  
Control Derivatives ◽  
Research Aircraft ◽  
Level Of Understanding ◽  
And Control

High-fidelity rotorcraft flight simulation relies on the availability of a quality flight model that further demands a good level of understanding of the complexities arising from aerodynamic couplings and interference effects. One such example is the difficulty in the prediction of the characteristics of the rotorcraft lateral-directional oscillation (LDO) mode in simulation. Achieving an acceptable level of the damping of this mode is a design challenge requiring simulation models with sufficient fidelity that reveal sources of destabilizing effects. This paper is focused on using System Identification to highlight such fidelity issues using Liverpool's FLIGHTLAB Bell 412 simulation model and in-flight LDO measurements from the bare airframe National Research Council's (Canada) Advanced Systems Research Aircraft. The simulation model was renovated to improve the fidelity of the model. The results show a close match between the identified models and flight test for the LDO mode frequency and damping. Comparison of identified stability and control derivatives with those predicted by the simulation model highlight areas of good and poor fidelity.

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