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An object-oriented framework for evolutionary pangenome analysis

CELL REPORTS METHODS 2021年第5期1卷 100085页

作者： Ferres, Ignacio Iraola, Gregorio Inst Pasteur Montevideo Microbial Genom Lab Montevideo Uruguay Inst Pasteur Montevideo Ctr Innovat Epidemiol Surveillance Montevideo Uruguay Wellcome Sanger Inst Hinxton England Univ Mayor Ctr Integrat Biol Santiago Chile

Pangenome analysis is fundamental to explore molecular evolution occurring in bacterial populations. Here, we introduce Pagoo, an R framework that enables straightforward handling of pangenome data. The encapsulated nature of Pagoo allows the storage of complex molecular and phenotypic information using an object-oriented approach. This facilitates to go back and forward to the data using a single programming environment and saving any stage of analysis (including the raw data) in a single file, making it sharable and reproducible. Pagoo provides tools to query, subset, compare, visualize, and perform statistical analyses, in concert with other microbial genomics packages available in the R ecosystem. As working examples, we used 1,000 Escherichia coli genomes to show that Pagoo is scalable, and a global dataset of Campylobacter fetus genomes to identify evolutionary patterns and genomic markers of host-adaptation in this pathogen.

关键词： pangenome analysis bacterial comparative genomics bacterial evolution data visualization object-oriented programming R pangenome reconstruction

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An efficient variable-node XFEM for modeling multiple crack growth: A Matlab object-oriented implementation

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ADVANCES IN ENGINEERING SOFTWARE 2020年第0期140卷 102750-000页

作者： Ding, Junlei Yu, Tiantang Yang, Yin Tinh Quoc Bui Hohai Univ Dept Engn Mech Nanjing 211100 Peoples R China Hydraul Res Inst Jiangsu Prov Lake Res Inst Nanjing 210017 Peoples R China Duy Tan Univ Inst Res & Dev Da Nang City Vietnam Tokyo Inst Technol Dept Civil & Environm Engn Meguro Ku 2-12-1-W8-22 Ookayama Tokyo 1528552 Japan

We present a Matlab object-oriented implementation of an efficient variable-node extended finite element method (XFEM) for multiple crack growth simulation in brittle materials. To enhance the accuracy of the present method, not only the local mesh refinement strategy is used, but also the variable-node elements are adopted to directly link different scale elements, saving the computational cost. In order to efficiently conduct coalescence detection, a modification is also presented. A stability analysis is performed to determine active crack tips, and the crack length control scheme is employed to model multiple crack growth. Mesh is locally refined simultaneously with the extension of cracked area via a straightforward manner. A general computer program structure for the Matlab object-oriented programming code for the variable-node XFEM is described. All those desirable features of the present work are demonstrated through five numerical examples with branching in linear-elastic fracture mechanics. In addition, this work provides an efficient computer code written by Matlab programming language for computational fracture simulation, which is for educational and academic uses.

关键词： XFEM Local mesh refinement Variable-node elements Fracture object-oriented programming Matlab

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A tutorial-driven introduction to the parallel finite element library FEMPAR v1.0.0

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COMPUTER PHYSICS COMMUNICATIONS 2020年第0期248卷 107059-000页

作者： Badia, Santiago Martin, Alberto F. Monash Univ Sch Math Clayton Vic 3800 Australia Ctr Int Metodes Numer Enginyeria Esteve Terrades 5 E-08860 Castelldefels Spain Univ Politecn Cataluna Jordi Girona 1-3Edifici C1 E-08034 Barcelona Spain

This work is a user guide to the FEMPAR scientific software library. FEMPAR is an open-source object-oriented framework for the simulation of partial differential equations (PDEs) using finite element methods on distributed-memory platforms. It provides a rich set of tools for numerical discretization and built-in scalable solvers for the resulting linear systems of equations. An application expert that wants to simulate a PDE-governed problem has to extend the framework with a description of the weak form of the PDE at hand (and additional perturbation terms for non-conforming approximations). We show how to use the library by going through three different tutorials. The first tutorial simulates a linear PDE (Poisson equation) in a serial environment for a structured mesh using both continuous and discontinuous Galerkin finite element methods. The second tutorial extends it with adaptive mesh refinement on octree meshes. The third tutorial is a distributed-memory version of the previous one that combines a scalable octree handler and a scalable domain decomposition solver. The exposition is restricted to linear PDEs and simple geometries to keep it concise. The interested user can dive into more tutorials available in the FEMPAR public repository to learn about further capabilities of the library, e.g., nonlinear PDEs and nonlinear solvers, time integration, multi-field PDEs, block preconditioning, or unstructured mesh handling. Program summary Program Title: FEMPAR Program Files doi: http://***/10.17632/dtx487wp57.1 Licensing provisions: GNU General Public License 3 programming language: MPI, Fortran2003/2008 (object-oriented programming features) Nature of problem: Computational simulation of a broad range of large-scale application problems governed by Partial Differential Equations Solution method: Arbitrary-order grad-, curl-, and div-conforming finite elements on n-cube and n-simplex meshes. Continuous and Discontinuous Galerkin FEM. Adaptive Mesh Refi

关键词： Mathematical software Finite elements object-oriented programming Partial Differential Equations

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A Genetic Algorithm-Based Personalized Remedial Learning System for Learning object-oriented Concepts of Java

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IEEE TRANSACTIONS ON EDUCATION 2019年第4期62卷 237-245页

作者： Lin, Che-Chern Liu, Zi-Cheng Chang, Chih-Lin Lin, Yu-Wen Natl Kaohsiung Normal Univ Dept Software Engn & Management Kaohsiung Taiwan Natl Sun Yat Sen Univ Kaohsiung Taiwan Natl Cheng Kung Univ Tainan Taiwan Natl Kaohsiung Normal Univ Kaohsiung Taiwan

Contribution: An online genetic algorithm-based remedial learning system is presented in order to strengthen students' understanding of object-oriented programming (OOP) concepts by tailoring personalized learning materials according to each student's strengths and weaknesses. Background: Prior studies on computer programming education have analyzed methods of learning OOP, and shown that teaching this topic is a challenge. A simple and personalized learning system for generating remedial learning materials would therefore be valuable, but had yet to be designed. Intended Outcomes: Students' grasp of OOP concepts is expected to improve through study of the tailored remedial learning materials generated by the system. Application Design: Students who had previously studied OOP were recruited to test the learning system in a two-semester pre-experiment using a one-group pre-test-post-test design. The students first took a pre-test that determined their individual strengths and weaknesses in these concepts. They then read three sets of quiz-based remedial learning materials;each set was generated by the system according to the individual student's answers in the pre-test and previous quizzes. Findings: 1) Overall, the changes between learners' pre-and post-test scores were significant;2) Score changes for different learners (junior, senior, low-achievement, and high-achievement learners) and for different learning styles (intensive and non-intensive) were also significant;and 3) Score changes for low-achievement learners were greater than those for high-achievement learners.

关键词： Java Genetic algorithms Learning systems Biological cells programming profession Education Adaptive computer learning computer science educational software genetic algorithms individual differences object-oriented programming remedial learning

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Augmented Reality App for Teaching OOP

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INTERNATIONAL JOURNAL OF ADVANCED COMPUTER SCIENCE AND APPLICATIONS 2019年第9期10卷 51-54页

作者： Rizwan, Sana Aslam, Arslan Usman, Sobia Ghauri, Muhammad Moeez COMSATS Univ Islamabad Dept Comp Sci Lahore Campus Lahore Pakistan

Now a days, there is demanding needs of developing interactive mediums of study. As our conventional methods of learning are not very effective. programming has become one of the core subjects of every field of study due to their vast use. However, introducing computer programming to those students who's are not familiar with programming is a tough task. Use interactive learning through visual effects using AR (Augmented Reality) developed to provide a platform for new students to interact more in learning environment. As this learning environment becomes more effective it is easier for new comers to understand key concepts of programming more effective way.

关键词： Augmented reality object-oriented programming unity visualization human computer interaction Vuforia rendering compiler

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Modeling strong/weak discontinuities by local mesh refinement variable-node XFEM with object-oriented implementation

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THEORETICAL AND APPLIED FRACTURE MECHANICS 2020年第0期106卷 102434-000页

作者： Ding, Junlei Yu, Tiantang Tinh Quoc Bui Hohai Univ Dept Engn Mech Nanjing 211100 Peoples R China Duy Tan Univ Inst Res & Dev Da Nang City Vietnam Tokyo Inst Technol Dept Civil & Environm Engn Meguro Ku 2-12-1-W8-22 Ookayama Tokyo 1528552 Japan

In this paper, we present a Matlab object-oriented implementation of the variable-node extended finite element method (XFEM), which is enhanced by local mesh refinement technique, for modeling strong and weak discontinuities such as cracks, inclusions, and voids. An easy-to-use local mesh refinement scheme is thus proposed, in which the variable-node elements play an important role as they are integrated into the model for the purpose of connecting/linking different scale meshes. For efficiency, the fine-scale mesh is generated near discontinuities, and the refinement is controlled by three parameters: the number of extension layers, the number of subdivision scales, and the number of refinement levels. We detail the implementation of integrating the variable-node elements into the local mesh refinement XFEM codes in a seamless way. The concept of object-oriented programming (OOP) and strategy design pattern promote the extensibility of computer codes. We consider several numerical examples to show the applicability and accuracy of the current computer codes for mutiple crack growths, crack-hole interactions, multiple inclusions, and a rock slope with one interface and two faults.

关键词： XFEM Local mesh refinement Variable-node elements Cracks Voids Inclusions object-oriented programming

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Development of an object-oriented framework for the vibration characteristic computation of multibody systems

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ADVANCES IN ENGINEERING SOFTWARE 2020年 148卷 102874-102874页

作者： Chen, Gangli Rui, Xiaoting Gu, Junjie Zeng, Xiaoyun Liu, Xingbao China Acad Engn Phys Inst Machinery Mfg Technol Mianyang 621900 Sichuan Peoples R China Nanjing Univ Sci & Technol Inst Launch Dynam Nanjing 210094 Peoples R China

Vibration characteristic is one of the most important properties for structures and mechanical systems. Transfer matrix method for linear multibody systems (linear MSTMM) is an efficient approach to computing the vibration characteristics of such systems due to its following features: easy to formulate, high programming, and low-order matrix without system global dynamic equations. In this work, a vibration characteristic solver based on linear MSTMM is developed by adopting object-oriented programming (OOP) technique. Binary tree is employed to describe multibody system topology. Then, a novel approach combining sequence and chain storage structures is proposed to store the element data and topology of multibody system. A recursive formula is proposed to derive the overall transfer matrix of multibody system, and its automatic deduction and computation by computer are achieved. The object-oriented framework of the solver is developed to realize the vibration characteristic computation. Furthermore, the numerical study for a Stewart parallel mechanism as well as the practical engineering example of an ultra-precision fly cutting machine tool are performed to validate the solver.

关键词： Vibration characteristic solver Transfer matrix method object-oriented programming Data structure Automatic deduction

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Study Case of an Adaptive Educational Tool oriented to University Students for an object Orientation Course 11th

Study Case of an Adaptive Educational Tool Oriented to Unive...

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11th International Conference on Social Computing and Social Media (SCSM) Held as Part of the 21st International Conference on Human-Computer Interaction (HCI International)

作者： Gonzalez, Ninozka Cubillos, Claudio Roncagliolo, Silvana Mellado, Rafael Pontificia Univ Catolica Valparaiso Valparaiso Chile

ISBN: (纸本)9783030219055;9783030219048

The use of e-learning for educational purposes has been the focus of researchers for a long time, because of the difficulty to determine if a tool based on this concept is able to instruct the educational content that a professor can easily teach on a classroom. In this document the available tools and teaching methods to deliver Adaptive Learning to each user are investigated. Through the development of this paper, the adaptive techniques to be implemented to the Educational Tool are proposed;how and which contents will be presented to the students and which adaptation model will be applied to that content. Thanks to the investigations on the topic, and the analysis of the performance of the students on the object Orientation course, from the Pontificia Universidad Catolica de Valparaiso (PUCV), preliminary models for the Educational and Adaptive Tool have been defined, with promising results.

关键词： E-learning Adaptive learning system Educational tool Adaptive Hypermedia System object-oriented programming Java language

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object-oriented Software for Fitness-For-Service Assessment of Cracked Cylinder Based on API RP 579

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FRATTURA ED INTEGRITA STRUTTURALE 2020年第52期14卷 163-180页

作者： Kasivitamnuay, Jirapong Singhatanadgid, Pairod Chulalongkorn Univ Bangkok Thailand

Fitness-for-service assessment of a cracked component intends to evaluate its remaining strength and remaining life to support the implementation of a maintenance plan. This research aims to develop a fitness-for-service assessment software to facilitate the task. The software development process included identifying the software specifications, designing the software structure, manipulating the information in the standard for programming, the graphical user interface design, and finally verification. The assessment procedure employed in this study was the third edition of the standard API RP 579. The software structure was designed using an object-oriented concept. The software can perform integrity assessment levels 1, 2, and 3 option B, leak-before-break assessment, and remaining life assessment for a cracked cylinder that has a through-thickness crack or semi-elliptical surface crack oriented in an axial or circumferential direction. The applied loads could be a nominal axial force, bending moment, and internal pressure, as well as stress profiles perpendicular to the crack plane due to mechanical, thermal, and residual stresses. Accuracy of the software was demonstrated by applying it to example problems. Some aspects of the software extensibility were conceptually discussed.

关键词： API 579 Fitness-for-Service Fracture mechanics object-oriented programming Pressure vessel

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Java Stream Fusion: Adapting FP mechanisms for an OO setting 19

Java Stream Fusion: Adapting FP mechanisms for an OO setting

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23rd Brazilian Symposium on programming Languages (SBLP)

作者： Ribeiro, Francisco Saraiva, Joao Pardo, Alberto Univ Minho INESC TEC HASLab Braga Portugal Univ Republica Inst Computac Montevideo Uruguay

ISBN: (纸本)9781450376389

In this paper, we show how stream fusion, a program transformation technique used in functional programming, can be adapted for an object-oriented setting. This makes it possible to have more Stream operators than the ones currently provided by the Java Stream API. The addition of more operators allows for a greater deal of expressiveness. To this extent, we show how these operators are incorporated in the stream setting. Furthermore, we also demonstrate how a specific set of optimizations eliminates overheads and produces equivalent code in the form of for loops. In this way, programmers are relieved from the burden of writing code in such a cumbersome style, thus allowing for a more declarative and intuitive programming approach.

关键词： object-oriented programming Functional programming Program Fusion

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