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software Package: An Advanced Theoretical Tool for Inhomogeneous Fluids(Atif)

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Chinese Journal of Polymer Science 2022年第2期40卷 220-230页

作者： Jian Jiang Beijing National Laboratory for Molecular Sciences State Key Laboratory of Polymer Physics and ChemistryInstitute of ChemistryChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China

In spite of the impending flattening of Moore’s law,the complexity and size of the systems we are interested in keep on increasing.This challenges the computer simulation tools due to the expensive computational cost.Fortunately,advanced theoretical methods can be considered as alternatives to accurately and efficiently capture the structural and thermodynamic properties of complex inhomogeneous fluids.In the last decades,classical density functional theory(cDFT)has proven to be a sophisticated,robust,and efficient approach for studying complex inhomogeneous fluids.In this work,we present a pedagogical introduction to a broadly accessible open-source density functional theory software package named"an advanced theoretical tool for inhomogeneous fluids"(Atif)and of the underlying theory.To demonstrate Atif,we take three cases as examples using a typical laptop computer:(i)electric double-layer of asymmetric electrolytes;(ii)adsorptions of sequencedefined semiflexible polyelectrolytes on an oppositely charged surface;and(iii)interactions between surfaces mediated by polyelectrolytes.We believe that this pedagogical introduction will lower the barrier to entry to the use of Atif by experimental as well as theoretical groups.A companion website,which provides all of the relevant sources including codes and examples,is attached.

关键词： Polyelectrolytes Complex fluids software Density functional theory Self-defined sequence

software debugging analysis based on developer behavior data

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Frontiers of Computer Science 2021年第1期15卷 233-235页

作者： Bo YANG Qian YU Huai LIU Yuze HE Chao LIU School of Information Science and Technology North China University of TechnologyBeijing 100144China Department of Computer Science and software Engineering Swinburne University of TechnologyHawthorn VIC 3122Australia School of Computer Science and Engineering Beihang UniversityBeijing 100191China

1 Introduction software debugging is one of the most costly activities in sof-ware development process.It mainly consists of four core tasks,namely fault detection,fault localization,fault understanding and fault fixi... 详细信息

关键词： fault process. software

software defined industrial network architecture for edge computing offloading

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The Journal of China Universities of Posts and Telecommunications 2019年第1期26卷 49-58页

作者： Xu Fangmin Ye Huanyu Cui Shaohua Zhao Chenglin Yao Haipeng School of Telecommunication Engineering Beijing University of Posts and Telecommunications China Petroleum Technology and Development Corporation

The integration of the Internet and the traditional manufacturing industry makes the industrial Internet of things(IIoT) as a popular research topic. However, traditional industrial networks continue to face challenges of resource management and limited raw data storage and computation capacity. A novel software defined industrial network(SDIN) architecture was proposed to address the existing drawbacks in IIoT such as resource utilization, data processing and storage, and system compatibility. The architecture is developed based on the software defined network(SDN) architecture, combining hierarchical cloud and fog computing and content-aware caching technologies. Based on the SDIN architecture, two types of edge computing strategies in industrial applications are discussed. Different scenarios and service requirements are considered. The simulation results confirm that the SDIN architecture is feasible and effective in the application of edge computing offloading.

关键词： software defined industrial network(SDIN) industrial Internet of things(IIoT) edge computing computing offloading time delay

software testing without the oracle correctness assumption

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Frontiers of Computer Science 2020年第3期14卷 221-224页

作者： Tun LI Wanwei LIU Xinrui GUO Ji WANG School of Computer National University of Defense TechnologyChangsha 410073China Laboratory of software Engineering for Complex Systems Changsha 410073China Microsoft STCA Beijing 100080China

1 Introduction When testing programs,the oracle correctness assumption(OCA)implies that there are no errors in the test oracles,such as the expected outputs are always correctly designed and written in unit testing assertions.Guo's work[1]is the first piece of work that investigated the influences on fault localization caused by errors in test oracles and proposed a method to identify potential incorrect oracles.However,no systematic discussions are availed.

关键词： oracle testing software

Intelligent analysis for software data:research and applications

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Frontiers of Information Technology & Electronic Engineering 2022年第5期23卷 661-663页

作者： Tao ZHANG Xiaobing SUN Zibin ZHENG Ge LI School of Computer Science and Engineering Macao University of Science and TechnologyMacaoChina School of Information Engineering Yangzhou UniversityYangzhou 225127China School of software Engineering Sun Yat-sen UniversityZhuhai 519082China School of Computer Science Peking UniversityBeijing 100871China

Over the last few decades,software has been one of the primary drivers of economic growth in the world.Human life depends on reliable software;therefore,the software production process(i.e.,software design,development,testing,and maintenance)becomes one of the most important factors to ensure the quality of software.During the production process,large amounts of software data(e.g.,source code,bug reports,logs,and user reviews)are generated.

关键词： software bug testing

Data Comparison and software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 937-948页

作者： Yi Wang Fatma Lecourieux Rui Zhang Zhanwu Dai David Lecourieux Shaohua Li Zhenchang Liang Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant ResourcesInstitute of Botanythe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China Ecophysiology and Functional Genomics of Vine Bordeaux Sciences AgroINRAEUniversity of BordeauxInstitute of Vine and Wine Sciences Bordeaux-AquitaineVillenave d’Ornon 33140France College of Plant Protection Shandong Agricultural UniversityTaian 271018China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China

CRISPR-based genome editing systems have been successfully and effectively used in many organisms.However,only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome applications.Although many web-based toolkits are available,there is still a shortage of comprehensive,user-friendly,and plant-specific CRISPR databases and desktop software.In this study,we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif(PAM)sites,the effects of GC content,optimal proto-spacer length,potential universality within the plant kingdom,PAM-rich region(PARR)inhibiting ratio,and the effects of G-quadruplex(G-Q)structures.Using this information,we built a comprehensive CRISPR database(including 138 plant genome data sources,***/pc/index.html),which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 systems.We also developed a desktop software on the basis of the Perl/Tk tool,which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows platform.Therefore,this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.

关键词： CRISPR/Cas PAM-rich region G-Q software Database

Evaluation indicators for open-source software:a review

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Cybersecurity 2021年第1期4卷 292-315页

作者： Yuhang Zhao Ruigang Liang Xiang Chen Jing Zou SKLOIS Institute of Information EngineeringChinese Academy of SciencesBeijing 100093China School of Cyber Security University of Chinese Academy of SciencesBeijing 100049China School of Information Science and Technology Nantong UniversityNantong 226019China State Grid Economic and Technological Research Institute Co.Ltd. Beijing 102209China

In recent years,the widespread applications of open-source software(OSS)have brought great convenience for software developers.However,it is always facing unavoidable security risks,such as open-source code defects and security vulnerabilities.To find out the OSS risks in time,we carry out an empirical study to identify the indicators for evaluating the OSS.To achieve a comprehensive understanding of the OSS assessment,we collect 56 papers from prestigious academic venues(such as IEEE Xplore,ACM Digital Library,DBLP,and Google Scholar)in the past 21 years.During the process of the investigation,we first identify the main concerns for selecting OSS and distill five types of commonly used indicators to assess OSS.We then conduct a comparative analysis to discuss how these indicators are used in each surveyed study and their differences.Moreover,we further undertake a correlation analysis between these indicators and uncover 13 confirmed conclusions and four cases with controversy occurring in these studies.Finally,we discuss several possible applications of these conclusions,which are insightful for the research on OSS and software supply chain.

关键词： Open-source software Evaluation Indicator Correlation Vulnerability License

Forecasting of software Reliability Using Neighborhood Fuzzy Particle Swarm Optimization Based Novel Neural Network

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IEEE/CAA Journal of Automatica Sinica 2019年第6期6卷 1365-1383页

作者： Pratik Roy Ghanshaym Singha Mahapatra Kashi Nath Dey Department of Computer Science and Engineering University of CalcuttaKolkata-700106India Department of Mathematics National Institute of TechnologyPuducherryKaraikal-609609India

This paper proposes an artificial neural network(ANN) based software reliability model trained by novel particle swarm optimization(PSO) algorithm for enhanced forecasting of the reliability of software. The proposed ANN is developed considering the fault generation phenomenon during software testing with the fault complexity of different levels. We demonstrate the proposed model considering three types of faults residing in the software. We propose a neighborhood based fuzzy PSO algorithm for competent learning of the proposed ANN using software failure data. Fitting and prediction performances of the neighborhood fuzzy PSO based proposed neural network model are compared with the standard PSO based proposed neural network model and existing ANN based software reliability models in the literature through three real software failure data sets. We also compare the performance of the proposed PSO algorithm with the standard PSO algorithm through learning of the proposed ANN. Statistical analysis shows that the neighborhood fuzzy PSO based proposed neural network model has comparatively better fitting and predictive ability than the standard PSO based proposed neural network model and other ANN based software reliability models. Faster release of software is achievable by applying the proposed PSO based neural network model during the testing period.

关键词： Artificial neural network(ANN) fuzzy particle swarm optimization(PSO) reliability prediction software reliability

A new hierarchical software architecture towards safety-critical aspects of a drone system

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Frontiers of Information Technology & Electronic Engineering 2019年第3期20卷 353-362页

作者： Xiao-rui ZHU Chen LIANG Zhen-guo YIN Zhong SHAO Meng-qi LIU Hao CHEN Department of Mechanical Engineering and Automation Harbin Institute of Technology (Shenzhen) Department of Computer Science Yale University

A new hierarchical software architecture is proposed to improve the safety and reliability of a safetycritical drone system from the perspective of its source code. The proposed architecture uses formal verification methods to ensure that the implementation of each module satisfies its expected design specification, so that it prevents a drone from crashing due to unexpected software failures. This study builds on top of a formally verified operating system kernel, certified kit operating system(CertiKOS). Since device drivers are considered the most important parts affecting the safety of the drone system, we focus mainly on verifying bus drivers such as the serial peripheral interface and the inter-integrated circuit drivers in a drone system using a rigorous formal verification method. Experiments have been carried out to demonstrate the improvement in reliability in case of device anomalies.

关键词： Safety-critical Drone software architecture Formal verification