Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework

Abstract Background A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks are either too cumbersome to apply genome-wide or unable to model a number of important experimental conditions in ChIP-seq. Results We present ChIPs, a toolkit for rapidly simulating ChIP-seq data using statistical models of key experimental steps. We demonstrate how ChIPs can be used for a range of applications, including benchmarking analysis tools and evaluating the impact of various experimental parameters. ChIPs is implemented as a standalone command-line program written in C++ and is available from https://github.com/gymreklab/chips. Conclusions ChIPs is an efficient ChIP-seq simulation framework that generates realistic datasets over a flexible range of experimental conditions. It can serve as an important component in various ChIP-seq analyses where ground truth data are needed.

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The impact of future cities on commuting patterns: An agent-based approach

Environment and Planning B Urban Analytics and City Science ◽

10.1177/2399808317751145 ◽

2018 ◽

Vol 46 (6) ◽

pp. 1079-1096

Author(s):

Marcello Marini ◽

Anna P Gawlikowska ◽

Andrea Rossi ◽

Ndaona Chokani ◽

Hubert Klumpner ◽

...

Keyword(s):

Urban Areas ◽

Simulation Models ◽

Single Family ◽

Simulation Framework ◽

Agent Based ◽

Commercial Activities ◽

Transportation Sector ◽

Commuting Time ◽

Commuting Patterns ◽

The Impact

Over the next 35 years, the population of Switzerland is expected to grow by 25%. One possible way to accommodate this larger population is to transform smaller cities in Switzerland through the direct intervention of urban planners. In this work, we integrate agent-based simulation models of people flow, mobility and urban infrastructure with models of the electricity and gas systems to examine the increase of the density of existing residential zones and the creation of new workplaces and commercial activities in these urban areas. This novel simulation framework is used to assess, for the year 2050, two different scenarios of urbanization in a region with small urban areas. It is shown that a densification scenario, with a preference for multi-dwelling buildings, consumes 93% less land than a sprawl scenario, with a preference for single-family houses. The former scenario also accommodates 27% more people than the latter scenario, as there is a higher penetration of battery electric vehicles – and therefore reduced air pollution from the transportation sector – and also a larger shift of commuters to the use of public transport. However, in the former scenario, the commuting time is 20% longer. The outcome of this work demonstrates how this novel simulation framework can be used to support the formulation of policies that can direct the transformation of urban areas.

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Modeling Energy Portfolio Scoring

International Journal of Business Analytics ◽

10.4018/ijban.2015100101 ◽

2015 ◽

Vol 2 (4) ◽

pp. 1-22 ◽

Cited By ~ 1

Author(s):

Rafael Diaz ◽

Joshua G. Behr ◽

Rafael Landaeta ◽

Francesco Longo ◽

Letizia Nicoletti

Keyword(s):

Renewable Energy ◽

Production Method ◽

Economic Benefits ◽

Dynamics Simulation ◽

Electricity Production ◽

Simulation Framework ◽

Renewable Electricity ◽

Hampton Roads ◽

Support Policy ◽

The Impact

U.S. regions are expected to follow the national trend towards investment in renewable energy as part of their electricity portfolio. The progress of energy portfolios that typically involves traditional methods, such as centralized nuclear and coal-fired generation, and towards cleaner- and renewable-source generation will impact economic growth and public health. Renewable electricity production must strike a balance among cost, reliability, and compatibility. The economic and health benefits obtained from developing an efficient energy portfolio make renewable energy alternatives an important consideration for regions endowed with natural resources. A portfolio mix of production method that considers the economic benefits while limiting adverse health and environmental impacts is attractive. This research proposes a System Dynamics simulation framework to support policy-making efforts in assessing the impact of energy portfolios. The authors demonstrate the utility of the framework by means of analyzing data that pertain to the U.S. Hampton Roads - Peninsula Region.

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On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation

BMC Bioinformatics ◽

10.1186/s12859-018-2269-0 ◽

2018 ◽

Vol 19 (S9) ◽

Cited By ~ 2

Author(s):

Soumya Kundu ◽

Mukul S. Bansal

Keyword(s):

Gene Tree ◽

The Impact

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A Multi-Criteria Simulation Framework for Civil Aircraft Trajectory Optimisation

Volume 1: Advances in Aerospace Technology ◽

10.1115/imece2010-38237 ◽

2010 ◽

Cited By ~ 1

Author(s):

Hasan Zolata ◽

Cesar Celis ◽

Vishal Sethi ◽

Riti Singh ◽

David Zammit-Mangion

Keyword(s):

Computational Models ◽

New Technologies ◽

Oxides Of Nitrogen ◽

Simulation Framework ◽

Short Term ◽

Commercial Aviation ◽

Flight Profile ◽

Aircraft Trajectory ◽

The Impact ◽

Trajectory Optimisation

Over the past few years, great concern has been raised about the impact of commercial aviation on the environment. In a Business As Usual approach, the expected growth in air traffic is going to affect climate change even more unless mitigation policies are devised and implemented. Although there is a tendency to focus on long-term technological solutions and breakthroughs, short-term improvements applicable to existing aircraft/engine configurations are also very important to fully realise the benefits of new technologies. Aircraft trajectory optimisation presents the opportunity to effectively reduce fuel consumption and pollutants emitted providing a feasible short-term strategy to be applied to the existing aircraft fleet. The present study focuses on preliminary results obtained using a multi-disciplinary aircraft trajectory optimisation simulation framework. Three in-house computational models are implemented in the framework to model the aircraft and engine performance, as well as to predict the level of gaseous emissions produced. A commercially available optimiser is integrated within the framework to analyse and optimise single flight path elements (e.g., climb), as well as the entire flight profile. For the purpose of this study, the climb and the whole flight profile are divided in four and eight segments respectively. Trajectory optimisation processes are then carried out in order to minimise three different objective functions: flight time, fuel burned, and mass of oxides of nitrogen (NOx) emitted. The results of the trajectory optimisation processes performed confirm the validity, effectiveness, and flexibility of the methodology proposed. In future, it is expected that these types of approaches are utilised to efficiently compute complete, optimum and ‘greener’ aircraft trajectories, which help to minimise the impact of commercial aviation on the environment. Other computational models that simulate several other aspects such as aircraft and engine noise, weather conditions and contrails formation, among others, need to be also included in the optimisation processes.

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High-Efficiency Simulation Framework to Analyze the Impact of Exhaust Air from COVID-19 Temporary Hospitals and its Typical Applications

Applied Sciences ◽

10.3390/app10113949 ◽

2020 ◽

Vol 10 (11) ◽

pp. 3949 ◽

Cited By ~ 2

Author(s):

Donglian Gu ◽

Zhe Zheng ◽

Pengju Zhao ◽

Linlin Xie ◽

Zhen Xu ◽

...

Keyword(s):

High Efficiency ◽

Adverse Impact ◽

Simulation Framework ◽

Levels Of Detail ◽

Surrounding Environment ◽

Building Information ◽

Simulation Results ◽

Medical Infrastructure ◽

The Impact ◽

Different Levels

The outbreak of COVID-19 resulted in severe pressure on the existing medical infrastructure in China. Several Chinese cities began to construct temporary hospitals for the centralized treatment of COVID-19 patients. The harmful exhaust air from the outlets of these hospitals may have a significant adverse impact on the fresh-air intakes and surrounding environment. Owing to the need to rapidly construct these hospitals within 6–10 days, just a few hours are allowed for the analysis of the impact of this exhaust air on the environment. To overcome this difficulty, a high-efficiency simulation framework is proposed in this study. Based on the open-source computational fluid dynamics software, FDS, the proposed framework is adaptive and incorporates building information with different levels of detail during various design phases of the hospital, and has been applied in the design of the Wuhan Huoshenshan Hospital, the first typical COVID-19 temporary hospital in China. According to the simulation results, neither the fresh-air intakes nor the surrounding buildings would be polluted by the harmful air discharged from the air outlets of the Huoshenshan hospital. The proposed simulation framework can provide a reference for the design and overall planning of similar hospitals in China and other affected countries.

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A stochastic roadmap method to model protein structural transitions

Robotica ◽

10.1017/s0263574715001058 ◽

2015 ◽

Vol 34 (8) ◽

pp. 1705-1733 ◽

Cited By ~ 8

Author(s):

Kevin Molloy ◽

Rudy Clausen ◽

Amarda Shehu

Keyword(s):

Protein Structure ◽

Molecular Basis ◽

Structure And Function ◽

Structural Transitions ◽

Simulation Framework ◽

Human Disorders ◽

Model Protein ◽

And Function ◽

The Impact

SUMMARYEvidence is emerging that the role of protein structure in disease needs to be rethought. Sequence mutations in proteins are often found to affect the rate at which a protein switches between structures. Modeling structural transitions in wildtype and variant proteins is central to understanding the molecular basis of disease. This paper investigates an efficient algorithmic realization of the stochastic roadmap simulation framework to model structural transitions in wildtype and variants of proteins implicated in human disorders. Our results indicate that the algorithm is able to extract useful information on the impact of mutations on protein structure and function.

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Terraces in Gene Tree Reconciliation-Based Species Tree Inference

10.1101/2020.04.17.047092 ◽

2020 ◽

Author(s):

Michael J. Sanderson ◽

Michelle M. McMahon ◽

Mike Steel

Keyword(s):

Incomplete Lineage Sorting ◽

Gene Tree ◽

Solution Space ◽

Species Tree ◽

Gene Trees ◽

Species Trees ◽

Lineage Sorting ◽

Data Set ◽

Tree Reconciliation ◽

The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

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The Analyst Model Performance Multi-tier for Increase of Efficiency Virtual Machine In Moodle Application

International Journal of Scientific Research in Computer Science Engineering and Information Technology ◽

10.32628/cseit206473 ◽

2020 ◽

pp. 94-101

Author(s):

Raka Yusuf ◽

Harni Kusniyati

Keyword(s):

Model Performance ◽

Single Server ◽

College Courses ◽

Application Layer ◽

Simulation Framework ◽

Application Performance ◽

Interval Timer ◽

Second Tier ◽

The Impact ◽

The Ideal

The use of multi-tier schema has become general phenomena in moodle application on web base in nowadays. Usually is layer presentation on the first tier. On the second tier of the application layer and layer data on the third tier. This is modelling on this paper to looking application performance on web base who is using three-tier model and the impact of value amount in the server who is controlling of each on the tier for the performance. The example in the case who is used for this modelling is the application of Moodle for the college courses in XYZ University. The framework of modelling who is used is Simply which is the simulation framework activity base on the district is using phyton language programming. The simulation on simply can using to a certain interval timer or unlimited (the ideal until for the work all is serviced). The results of the simulation are showing the best obtained by using a single server on each of layer by optimizing the speed of process on the server.

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Demonstration of the “Work Models that Compute” Simulation Framework for Objective Function Allocation

Proceedings of the Human Factors and Ergonomics Society Annual Meeting ◽

10.1177/1541931218621074 ◽

2018 ◽

Vol 62 (1) ◽

pp. 321-324 ◽

Cited By ~ 1

Author(s):

Martijn IJtsma ◽

Lanssie M. Ma ◽

Karen M. Feigh ◽

Amy R. Pritchett

Keyword(s):

Traffic Management ◽

Information Transfer ◽

Computational Simulation ◽

Objective Evaluation ◽

Air Traffic Management ◽

Simulation Framework ◽

Trade Offs ◽

Function Allocation ◽

Physical Resources ◽

The Impact

This document describes a demonstration of the computational simulation framework Work Models that Compute (WMC). WMC is a framework for the objective evaluation of function allocation between humans and robots. The WMC framework has been used to study the impact of function allocation on both the air traffic management and spacecraft operations work domains. Recent advances include modeling of human-robot control modes, locomotion, failures and physical resources. We propose a demonstration of WMC showcasing how WMC can provide useful, objective and quantitative insight in the trade-offs asso-ciated with function allocation. In the demonstration, we will analyze function allocation for an on-orbit maintenance scenario. We will first show how minor changes to a function allocations can have major ef-fects on the emergent work patterns that result from the simulation framework. Second, we will demon-strate an analysis of 10-15 possible function allocations (defined in advance) and cross-compare their char-acteristics based on measures such as the idle time, taskload for each agent, information transfer require-ments, physical resources exchanges and others. This will show the framework’s capability to rapidly ex-plore the function allocation trade-space and allow the designer to make more informed trade-offs.

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