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The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data (vol 13, 2365, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-11页

作者： Reiff, Sarah B. Schroeder, Andrew J. Kirli, Koray Cosolo, Andrea Bakker, Clara Mercado, Luisa Lee, Soohyun Veit, Alexander D. Balashov, Alexander K. Vitzthum, Carl Ronchetti, William Pitman, Kent M. Johnson, Jeremy Ehmsen, Shannon R. Kerpedjiev, Peter Abdennur, Nezar Imakaev, Maxim Ozturk, Serkan Utku Camoglu, Ugur Mirny, Leonid A. Gehlenborg, Nils Alver, Burak H. Park, Peter J. Department of Biomedical Informatics Harvard Medical School Boston MA 02115 USA Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA 02139 USA Karya SMD Software Solutions İzmir 35040 Turkey Department of Physics Massachusetts Institute of Technology Cambridge MA 02139 USA

The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (https://***/), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.

关键词： Computational platforms and environments Genetic databases Genomics

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Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learning

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Frontiers of Computer Science 2024年第2期18卷 217-229页

作者： Yizheng WANG Xin ZHANG Ying JU Qing LIU Quan ZOU Yazhou ZHANG Yijie DING Ying ZHANG Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengdu 610054China Yangtze Delta Region Institute(Quzhou) University of Electronic Science and Technology of ChinaQuzhou 324000China Beidahuang Industry Group General Hospital Harbin 150088China School of Informatics Xiamen UniversityXiamen 361005China Department of Anesthesiology Hospital(T.C.M)Affiliated to Southwest Medical UniversityLuzhou 646000China Software Engineering College Zhengzhou University of Light IndustryZhengzhou 450002China

Numerous studies have demonstrated that human microRNAs(miRNAs)and diseases are associated and studies on the microRNA-disease association(MDA)have been *** developed a model using a low-rank approximation-based link propagation algorithm with Hilbert–Schmidt independence criterion-based multiple kernel learning(HSIC-MKL)to solve the problem of the large time commitment and cost of traditional biological experiments involving miRNAs and diseases,and improve the model *** constructed three kernels in miRNA and disease space and conducted kernel fusion using *** propagation uses matrix factorization and matrix approximation to effectively reduce computation and time *** results of the experiment show that the approach we proposed has a good effect,and,in some respects,exceeds what existing models can do.

关键词： human miRNA-disease association multiple kernel learning link propagation miRNA similarity disease similarity

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Patterns of Remote Work Environments 27

Patterns of Remote Work Environments

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2022 27th European Conference on Pattern Languages of Programs, EuroPLoP 2022

作者： Toldy, Kristian Sulaiman Khail, Waheedullah Vranic, Valentino Institute of Informatics Faculty of Informatics and Information Technologies Information Systems and Software Engineering Slovak University of Technology in Bratislava Bratislava Slovakia Helmholtz-Zentrum Berlin fur Materialien und Energie Gmbh Berlin Germany

ISBN: (纸本)9781450395946

People are more and more in a position to work remotely. They face the same problems of establishing and running remote work environments over and over again. In order to help them a bit, six organizational patterns of remote work environments are presented in this paper: Unofficial Meetings, Remote Mentor, Unified Communication Channels, Standard Operating Procedures, Information Hub, and Cut Meetings. The patterns come from a firsthand remote work experience obtained in a company focusing on quality assurance through a crowd testing methodology where software companies get real users to test their newest products. © 2022 ACM.

关键词： Quality assurance

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Modeling and Analysis of the Kinetics of the Pyrolysis Process of Biomass with Influence Raw Material Composition on Comsol Multiphysics 4

Modeling and Analysis of the Kinetics of the Pyrolysis Proce...

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4th International Conference on Technological Advancements in Computational Sciences, ICTACS 2024

作者： Gulyamovna, Mamatkulova Sayyora Norboyevich, Uzakov Gulom Ug'ii, Qodirov Farrux Ergash Tagayevna, Ulasheva Shaxlo Department Alternative Energy Sources Karshi Engineering Economic Institute Karshi City Uzbekistan The Department Alternative Energy Sources Karshi Engineering Economic Institute Karshi City Uzbekistan Shakhrisabz State Pedagogical Institute Department of Informatics and its Teaching Methodology Kashkadarya Uzbekistan Karshi Branch of the Tashkent University of Information Technologies named after Muhammad Al-Khwarizmi The Department of Information Technology Software Uzbekistan

ISBN: (纸本)9798350387490

In this article, the modeling and analysis of the kinetics of the pyrolysis process is carried out, which allows us to determine the rate of chemical reactions occurring during the decomposition of the material, as well as to identify key factors affecting the speed and efficiency of pyrolysis. The simulation was performed using Comsol Multiphysics software based on the kinetic mechanisms of the reaction of biomass of corn cob particles at a temperature of 500°C. The pyrolysis process of plant biomass was analyzed at a residence time of 0 to 10 minutes. The resulting models describe temperature changes well, especially in the center of the biomass. It was found that pyrolysis of corncob biomass occurred in the temperature range from 190 to 432°, at 190°C mass loss began, which ended at 432 °C. The kinetic parameters were calculated using the Kissinger method, and the least squares method and correlation analysis were used to calculate the kinetic constants. The study results will be useful for optimizing the conditions of the biomass pyrolysis process in the future. © 2024 IEEE.

关键词： Pyrolysis

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Towards Modeling Process Mining for Graphical Editors

Towards Modeling Process Mining for Graphical Editors

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Conference on Model Driven engineering Languages and Systems Companion (MODELS-C)

作者： MohammadHadi Dehghani Luca Berardinelli Manuel Wimmer Institute of Business Informatics - Software Engineering & CDL-MINT Johannes Kepler University Linz Austria

engineering tools typically offer graphical environments to help modelers deal with the complexity of designing software-intensive systems. Collecting and analyzing how different users perform modeling actions is a valuable asset to improve the user experience, the quality of the modeled system, and the evolution of the modeling language and accompanying tool support. This tool paper presents a novel tool that captures user interaction events in graphical modeling editors and enables mining modeling processes. Modeling events from Sirius-based graphical editors and GLSP-compliant editors are saved in IEEE eXtensible Event Stream (XES) format and integrated with the open-source ProM process mining tool as one example. By importing modeling traces into process mining tools, analysts can visualize and gain insights into the underlying modeling processes, enabling informed decision-making for designing modeling language and tool improvements. Initial experimental results demonstrate the applicability of our tool in capturing and analyzing user interactions on desktop and Web editors in solo and collaborative modeling sessions.

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Composite metamorphic relations for integration testing 22

Composite metamorphic relations for integration testing

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8th International Conference on Computer Technology Applications, ICCTA 2022

作者： Iakusheva, Sofia Khritankov, Anton Phystech School of Applied Mathematics and Informatics Moscow Institute of Physics and Technology Russia Faculty of Computer Science Dept. of Software Engineering Hse University Russia

ISBN: (纸本)9781450396226

Metamorphic testing is a testing method for problems without test oracles. Integration testing allows for detecting errors in complex systems that may not be found during the testing of their components. In this paper, we propose a novel approach that applies metamorphic testing in integration testing. The main idea is to develop a composite metamorphic relation for the system represented as an acyclic graph. This relation is a logical function of metamorphic relations for the parts of the system (vertices of the graph). It takes into account the features of the parts. Also, it can simplify the search for failure by identifying the subsystem with error. In this paper's theoretical part, we describe an algorithm of relation design. Then, we apply our method to a bioinformatics system for comparative genetic analysis of tissues using production tools. This experiment proves our method can be applied to real-life pipelines and find errors in them. © 2022 ACM.

关键词： Integration testing

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On-lattice Approximation of a Grid-free Individual-based Model of Growing Cell Populations 10

On-lattice Approximation of a Grid-free Individual-based Mod...

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10th IEEE Jubilee International Conference on Computational Cybernetics and Cyber-Medical Systems, ICCC 2022

作者： Kiss, Dániel Lovrics, Anna Software Engineering Institute John von Neumann Faculty of Informatics Óbuda University Budapest Hungary Institute of Enzymology Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary

ISBN: (数字)9781665481779

ISBN: (纸本)9781665481779

We compare a lattice-based computational model to an off-lattice individual-based approach for growing cell populations. After summarizing the fundamental properties of the existing off-lattice model, we present its on-lattice approximation and a possible way of their simulation. By performing in silico experiments, including single-cell and multicellular simulations, we show that the collective behavior of the agents is similar in both models, even though there are differences in the individual-level attributes. © 2022 IEEE.

关键词： Cell proliferation

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SBFT Tool Competition 2024 - Cyber-Physical Systems Track

SBFT Tool Competition 2024 - Cyber-Physical Systems Track

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Search-Based and Fuzz Testing (SBFT), IEEE/ACM International Workshop on

作者： Matteo Biagiola Stefan Klikovits Università della Svizzera italiana Lugano Switzerland Institute for Business Informatics - Software Engineering Johannes Kepler University Linz Austria

ISBN: (数字)9798400705625

ISBN: (纸本)9798350376012

This report summarizes the results of the fourth edition of the 2024 Cyber-Physical Systems tool competition, held as part of the SBFT’24 workshop. Three tools (AmbieGenVAE, CRAG, and OptAngle) competed with the aim of triggering out-of-bounds errors of two autonomous driving agents. The competitors were evaluated based on the effectiveness in exposing failures and the diversity of the discovered faulty tests. As in previous years, we report on the experiment methodology, the competitors and the results.

关键词： Conferences Cyber-physical systems Fuzzing Autonomous vehicles

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Towards Integrating Emerging AI Applications in SE Education

arXiv

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arXiv 2024年

作者： Vierhauser, Michael Groher, Iris Antensteiner, Tobias Sauerwein, Clemens University of Innsbruck Department of Computer Science Austria Johannes Kepler University Linz Institute of Business Informatics – Software Engineering Austria

Artificial Intelligence (AI) approaches have been incorporated into modern learning environments and software engineering (SE) courses and curricula for several years. However, with the significant rise in popularity of large language models (LLMs) in general, and OpenAI’s LLM-powered chatbot ChatGPT in particular in the last year, educators are faced with rapidly changing classroom environments and disrupted teaching principles. Examples range from programming assignment solutions that are fully generated via ChatGPT, to various forms of cheating during exams. However, despite these negative aspects and emerging challenges, AI tools in general, and LLM applications in particular, can also provide significant opportunities in a wide variety of SE courses, supporting both students and educators in meaningful ways. In this early research paper, we present preliminary results of a systematic analysis of current trends in the area of AI, and how they can be integrated into university-level SE curricula, guidelines, and approaches to support both instructors and learners. We collected both teaching and research papers and analyzed their potential usage in SE education, using the ACM Computer Science Curriculum Guidelines CS2023. As an initial outcome, we discuss a series of opportunities for AI applications and further research areas. © 2024, CC BY-NC-ND.

关键词： Adversarial machine learning

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Green data, green future? How data spaces enable the product carbon footprint calculation for the automotive industry : A case study on Catena-X

Green data, green future? How data spaces enable the product...

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2024 Lock-in or log out? Wie digitale Souveranitat gelingt, INFORMATIK 2024

作者： Gieß, Anna Neumann, Jenny Jussen, Ilka Schweihoff, Julia Fraunhofer Institute for Software and Systems Engineering IT Service Providers Speicherstraße 6 Dortmund44147 Germany TU Braunschweig University Institute for Business Informatics Mühlenpfordtstraße 23 Braunschweig38106 Germany TU Dortmund University Joseph-von-Fraunhofer-Straße 2-4 Dortmund44227 Germany

ISBN: (纸本)9783885797463

Society and politics are increasingly demanding a shift to more sustainable behavior, especially from manufacturing companies. This can be a major challenge as they face technological, regulatory, economic, supply chain, and cultural hurdles when transitioning to more sustainable practices. However, data spaces offer new ways to sharing data can help to accurately calculate CO2 emissions and develop new business models based on it. To illustrate the impact of data spaces on sustainability we considered the example of the product carbon footprint. Doing so, we analyzed public data of the automotive network Catena-X and highlighted the added value for each actor in the ecosystem using the e3value modeling language. Supplementary, we transferred our findings into business model elements (value proposition, value creation and delivery, and value capture). © 2024 Gesellschaft fur Informatik (GI). All rights reserved.

关键词： Carbon sequestration

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