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Digital technology is now pervasive, however, not all groups have uniformly benefitted from technological changes and some groups have been left behind or digitally excluded. Comprehensive data from the 2017 Current Population Survey shows that older people and persons with disabilities still lag behind in computer and internet access. Furthermore unique ethical, privacy and safety implications exist for the use of technology for older persons and people with disabilities and careful reflection is required to incorporate these aspects, which are not always part of a traditional software lifecycle. In this paper we present the Inclusion4EU project that aims to co-design a new framework, guidelines and checklists for inclusive software design and development with end-users from excluded categories, academics with expertise in human-computer interaction and industry practitioners from software engineering.

Genome-scale metabolic modeling is widely used to study the impact of metabolism on the phenotype of different organisms. While substrate modeling reflects the potential distribution of carbon and other chemical elements within the model, the additional use of omics data, e.g., transcriptome, has implications when researching the genotype-phenotype responses to environmental changes. Several algorithms for transcriptome analysis using genome-scale metabolic modeling have been proposed. Still, they are restricted to specific objectives and conditions and lack flexibility, have software compatibility issues, and require advanced user skills. We classified previously published algorithms, summarized transcriptome pre-processing, integration, and analysis methods, and implemented them in the newly developed transcriptome analysis tool IgemRNA , which (1) has a user-friendly graphical interface, (2) tackles compatibility issues by combining previous data input and pre-processing algorithms in MATLAB, and (3) introduces novel algorithms for the automatic comparison of different transcriptome datasets with or without Cobra Toolbox 3.0 optimization algorithms. We used publicly available transcriptome datasets from Saccharomyces cerevisiae BY4741 and H4-S47D strains for validation. We found that IgemRNA provides a means for transcriptome and environmental data validation on biochemical network topology since the biomass function varies for different phenotypes. Our tool can detect problematic reaction constraints.

Agile development processes are increasing their consideration of usability by integrating various user-centered design techniques throughout development. One such technique is Personas, which proposes the creation of fictitious users with real preferences to drive application design. Since applying this technique conflicts with the time constraints of agile development, Personas has been adapted over the years. Our objective is to determine the adoption level and type of integration, as well as to propose improvements to the Personas technique for agile development. A systematic mapping study was performed, retrieving 28 articles grouped by agile methodology type. We found some common integration strategies regardless of the specific agile approach, along with some frequent problems, mainly related to Persona modelling and context representation. Based on these limitations, we propose an adaptation to the technique in order to reduce the creation time for a preliminary persona. The number of publications dealing with Personas and agile development is increasing, which reveals a growing interest in the application of this technique to develop usable agile software.

The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the confusion is due in part to a misunderstanding of the function of code when applied to the life sciences. Code has many roles, and in this paper we present a three-dimensional taxonomy to classify those roles and map them specifically to the life sciences. We identify a "sweet spot" in the taxonomy-a convergence where bioinformaticians should concentrate their efforts in order to derive the most value from the time they spend using code. We suggest the use of the "inverse Conway maneuver" to shape a research team so as to allow dedicated software engineers to interface with researchers working in this "sweet spot." We conclude that in order to address current issues in the use of software in life science research such as reproducibility and scalability, the field must reevaluate its relationship with software engineering, and adapt its research structures to overcome current issues in bioinformatics such as reproducibility, scalability and productivity.

There are many tangled normative and technical questions involved in evaluating the quality of software used in epidemiological simulations. In this paper we answer some of these questions and offer practical guidance to practitioners, funders, scientific journals, and consumers of epidemiological research. The heart of our paper is a case study of the Imperial College London (ICL) covid-19 simulator, set in the context of recent work in epistemology of simulation and philosophy of epidemiology.

Today, thanks to advances in cloud computing, it is possible for small teams of software developers to produce internet-scale products, a feat that was previously the preserve of large organizations. Herein, we describe how these advances in software engineering can be made more readily available to bioinformaticians. In the same way that cloud computing has democratized access to distributed systems engineering for generalist software engineers, access to scalable and reproducible bioinformatic engineering can be democratized for generalist bioinformaticians and biologists. We present solutions, based on our own efforts, to achieve this goal., (© The Author(s) 2020. Published by Oxford University Press.)

HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background and Objective: The evaluation of musculo-articular stiffness (MAS) is an increasingly demanded procedure with applications in different fields, such as sports performance and lower limbs injury prevention. However, this task is non-automated, time-consuming and error-prone due to manual handling of data streams and files across several software applications. Despite the fact that process automation of validated procedures helps to prevent errors, there is still a lack of easy-to-use tools for analysis, management and visualization of MAS trials., Methods: In the present work a tool called FLEXOR has been developed which applies mathematical methods and novel algorithms to automatically adjust curves of data streams for MAS analysis decreasing substantially time employed and errors. This tool permits to define different adjustment parameters, detect curve peaks and valleys, and display the results on the fly. FLEXOR has been implemented through a component-based software development (CBSD) process. All physiological fundamentals for the biomechanical measurement have been included in the tool developed. To describe the integration of all required components a 4 + 1 view model architecture has been used. The installation guide, the FLEXOR software and some data samples can be found on its GitHub repository (https://github.com/FlexorSoftware/flexor)., Results: A multiplatform software tool to simplify traditional complex and manual procedures for MAS analysis is obtained. The tool turns them into a simple all-in-one procedure, reducing processing times from hours to a few minutes. The methodology was tested on multiple datasets generated by previous tools in former procedures as well as on real-time trials in the laboratory, showing identical results., Conclusion: The results show that the developed tool can accomplish an unfilled essential task in the analysis, management and visualization of MAS measurement. The presented software tool empowers analysts to handle the different studies, investigate different parameters related to each experiment and even test with different output parameters in each experiment, enabling real-time trials and shared studies between different analysts., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The quality of software is high in medical devices due to the strict regulatory requirements and their implementation in the software development processes through the use of the IEC 62304 standard. The goal of this standard revision project was to extend the scope of the standard to all health software and also to bring the requirements of the 12 year old standard back to the state-of-the-art including provisions for cybersecurity. The joint IEC/SC62A and ISO/TC215 project team revised the standard and adapted its risk management, usability, and security requirements to serve both the medical device industry and the overall health software industry. The resulting second version of the standard has gone through a multistage global voting process to achieve a consensus of the requirements to serve both these communities. The resulting standard has potential to have a major impact on the quality of software used in health care globally.

The increasing complexity of data and analysis methods has created an environment where scientists, who may not have formal training, are finding themselves playing the impromptu role of software engineer. While several resources are available for introducing scientists to the basics of programming, researchers have been left with little guidance on approaches needed to advance to the next level for the development of robust, large-scale data analysis tools that are amenable to integration into workflow management systems, tools, and frameworks. The integration into such workflow systems necessitates additional requirements on computational tools, such as adherence to standard conventions for robustness, data input, output, logging, and flow control. Here we provide a set of 10 guidelines to steer the creation of command-line computational tools that are usable, reliable, extensible, and in line with standards of modern coding practices., (© The Author(s) 2019. Published by Oxford University Press.)

Systematic reviewers are simultaneously unable to produce systematic reviews fast enough to keep up with the availability of new trial evidence while overproducing systematic reviews that are unlikely to change practice because they are redundant or biased. Although the transparency and completeness of trial reporting has improved with changes in policy and new technologies, systematic reviews have not yet benefited from the same level of effort. We found that new methods and tools used to automate aspects of systematic review processes have focused on improving the efficiency of individual systematic reviews rather than the efficiency of the entire ecosystem of systematic review production. We use software engineering principles to review challenges and opportunities for improving the interoperability, integrity, efficiency, and maintainability. We conclude by recommending ways to improve access to structured systematic review results. Major opportunities for improving systematic reviews will come from new tools and changes in policy focused on doing the right systematic reviews rather than just doing more of them faster., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Clinical reading centers provide expertise for consistent, centralized analysis of medical data gathered in a distributed context. Accordingly, appropriate software solutions are required for the involved communication and data management processes. In this work, an analysis of general requirements and essential architectural and software design considerations for reading center information systems is provided. The identified patterns have been applied to the implementation of the reading center platform which is currently operated at the Center of Ophthalmology of the University Hospital of Tübingen.

There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. To this end, simple flexible strategies are needed for interconnecting heterogeneous software tools and enabling data exchange between them. Drawing on our own work and that of others, we present several strategies for interoperability and their consequences, in particular, a set of simple data structures--list, matrix, network, table and tuple--that have proven sufficient to achieve a high degree of interoperability. We provide a few guidelines for the development of future software that will function as part of an interoperable community of software tools for biological data analysis and visualization., (© The Author 2012. Published by Oxford University Press.)

The document discusses the contributions to systems software and service process improvement and innovation based on recent advances. It highlights the EuroSPI initiative, which organizes annual conferences and collaborates with various projects in the automotive and battery industries. The special issue includes selected papers from the EuroSPI 2022 conference, focusing on topics such as blockchain-enabled traceability management, quality risks, gamification in software development, sustainable software engineering, and process compliance with legislation. The papers offer insights into cutting-edge practices and methodologies in software engineering and process improvement. [Extracted from the article]

This study was carried out with the aim of developing a software program that will enable the breeder to decide easily during the preparation of the feasibility for livestock enterprises. For this purpose, 63 enterprises in Gaziantep and Sanliurfa provinces/Turkey were visited between the years 2021-2022 and all the data obtained were evaluated. The "C#" programming language was used in the development of the software program. "Microsoft SQL Server" database was used to store the obtained data. This feasibility program is a software program where productivity checks are performed for enterprises and their personnel. It is a program that can be used easily from a small-capacity enterprises to a large-capacity enterprises. The cost calculations are not included in the program due to the economic conditions of the market. As a result, this program, which was prepared by taking into account software engineering techniques, will provide great advantages and conveniences for enterprises. Risk factors will be determined and alternatives will be presented with this software program that performs enterprises efficiency testing. It has been concluded that this software will be a program that can be preferred by the breeder since it can be used on all computers and offers different alternatives in enterprises establishments. [ABSTRACT FROM AUTHOR]

Software quality is becoming a momentous challenge in software engineering processes, and software testing has a pivotal role in its measurements. Nature-inspired metaheuristic methods play an essential role in software testing, in which various studies have been conducted in this field; however, due to a lack of wide-ranging papers reviewing these methods, conducting a comprehensive systematic review to examine an array of crucial mechanisms in this field has become a necessity. This study aims to present a detailed analysis and taxonomically classifies the metaheuristic methods inspired by nature. This paper compromises a systematic literature review of 65 chosen studies published between 2015 and 2022. Genetic algorithm-based, hybrid, ant colony optimization-based, cuckoo search-based, firefly algorithm-based, artificial bee colony-based, and other metaheuristic methods constitute this systematic study's stratification. Evaluation methods, applied tools, merits, and demerits of each reviewed article are investigated. Additionally, future directions and open issues are addressed. This conducted paper not only expounds on software testing strengths, open issues, and future works, but also recognizes the quest for optimizing the insufficient metrics in software testing, such as mutation score, complexity, and scalability, which would be the propulsion of the testing process if consummated. [ABSTRACT FROM AUTHOR]

Copyright of Revista Cubana de Ciencias Informáticas is the property of Universidad de las Ciencias Informaticas (UCI) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This scientific paper aims to explore the identification and quantification of the knowledge level within a team working on a software engineering project. The knowledge level of a team plays a crucial role in the success and efficiency of project outcomes. To achieve this objective, a comprehensive review of existing literature on knowledge management, team dynamics, and software engineering practices was conducted. This article reveals insights into the knowledge dynamics within software engineering teams. The research methodology consists of different quantitative and qualitative methods for data collection and analysis. The identified knowledge gaps and strengths can inform strategies for improving team performance, such as targeted training programs or knowledge sharing initiatives. Furthermore, the quantification of knowledge levels can serve as a benchmark for future projects, allowing for better resource allocation and team composition. Overall, this research is bringing benefits to the field of software engineering by providing a systematic approach to identify and quantify the knowledge level of teams, enabling organizations to optimize their team structures and enhance project outcomes. [ABSTRACT FROM AUTHOR]

BackgroundAn image sharing framework is important to support downstream data analysis especially for pandemics like Coronavirus Disease 2019 (COVID-19). Current centralized image sharing frameworks become dysfunctional if any part of the framework fails. Existing decentralized image sharing frameworks do not store the images on the blockchain, thus the data themselves are not highly available, immutable, and provable. Meanwhile, storing images on the blockchain provides availability/immutability/provenance to the images, yet produces challenges such as large-image handling, high viewing latency while viewing images, and software inconsistency while storing/loading images.ObjectiveThis study aims to store chest x-ray images using a blockchain-based framework to handle large images, improve viewing latency, and enhance software consistency.Basic proceduresWe developed a splitting and merging function to handle large images, a feature that allows previewing an image earlier to improve viewing latency, and a smart contract to enhance software consistency. We used 920 publicly available images to evaluate the storing and loading methods through time measurements.Main findingsThe blockchain network successfully shares large images up to 18 MB and supports smart contracts to provide code immutability, availability, and provenance. Applying the preview feature successfully shared images 93% faster than sharing images without the preview feature.Principal conclusionsThe findings of this study can guide future studies to generalize our framework to other forms of data to improve sharing and interoperability.

Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 "rules" centered on 2 best practice components: clean code and testing. These 2 areas are relatively straightforward and provide substantial utility relative to the learning investment. Adopting clean code practices helps to standardize and organize software code in order to enhance readability and reduce cognitive load for both the initial developer and subsequent contributors; this allows developers to concentrate on core functionality and reduce errors. Clean coding styles make software code more amenable to testing, including unit tests that work best with modular and consistent software code. Unit tests interrogate specific and isolated coding behavior to reduce coding errors and ensure intended functionality, especially as code increases in complexity; unit tests also implicitly provide example usages of code. Other forms of testing are geared to discover erroneous behavior arising from unexpected inputs or emerging from the interaction of complex codebases. Although conforming to coding styles and designing tests can add time to the software development project in the short term, these foundational tools can help to improve the correctness, quality, usability, and maintainability of open-source scientific software code. They also advance the principal point of scientific research: producing accurate results in a reproducible way. In addition to suggesting several tips for getting started with clean code and testing practices, we recommend numerous tools for the popular open-source scientific software languages Python, R, and Julia.

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.

Several institutions have developed image feature extraction software to compute quantitative descriptors of medical images for radiomics analyses. With radiomics increasingly proposed for use in research and clinical contexts, new techniques are necessary for standardizing and replicating radiomics findings across software implementations. We have developed a software toolkit for the creation of 3D digital reference objects with customizable size, shape, intensity, texture, and margin sharpness values. Using user-supplied input parameters, these objects are defined mathematically as continuous functions, discretized, and then saved as DICOM objects. Here, we present the definition of these objects, parameterized derivations of a subset of their radiomics values, computer code for object generation, example use cases, and a user-downloadable sample collection used for the examples cited in this paper.

Radiomic features are being increasingly studied for clinical applications. We aimed to assess the agreement among radiomic features when computed by several groups by using different software packages under very tightly controlled conditions, which included standardized feature definitions and common image data sets. Ten sites (9 from the NCI's Quantitative Imaging Network] positron emission tomography-computed tomography working group plus one site from outside that group) participated in this project. Nine common quantitative imaging features were selected for comparison including features that describe morphology, intensity, shape, and texture. The common image data sets were: three 3D digital reference objects (DROs) and 10 patient image scans from the Lung Image Database Consortium data set using a specific lesion in each scan. Each object (DRO or lesion) was accompanied by an already-defined volume of interest, from which the features were calculated. Feature values for each object (DRO or lesion) were reported. The coefficient of variation (CV), expressed as a percentage, was calculated across software packages for each feature on each object. Thirteen sets of results were obtained for the DROs and patient data sets. Five of the 9 features showed excellent agreement with CV < 1%; 1 feature had moderate agreement (CV < 10%), and 3 features had larger variations (CV ≥ 10%) even after attempts at harmonization of feature calculations. This work highlights the value of feature definition standardization as well as the need to further clarify definitions for some features.

We describe JBrowse Connect, an optional expansion to the JBrowse genome browser, targeted at developers. JBrowse Connect allows live messaging, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present example applications of JBrowse Connect that allow users 1) to specify and execute BLAST searches by either running on the same host as the webserver, with a self-contained BLAST module leveraging NCBI Blast+ commands, or via a managed Galaxy instance that can optionally run on a different host, and 2) to run the primer design service Primer3. JBrowse Connect allows users to track job progress and view results in the context of the browser. The software is available under a choice of open source licenses including LGPL and the Artistic License.

Interpretations of elevated blood levels of alanine aminotransferase (ALT) for drug-induced liver injury often assume that the biomarker is released passively from dying cells. However, the mechanisms driving that release have not been explored experimentally. The usefulness of ALT and related biomarkers will improve by developing mechanism-based explanations of elevated levels that can be expanded and elaborated incrementally. We provide the means to challenge the ability of closely related model mechanisms to generate patterns of simulated hepatic injury and ALT release that scale (or not) to be quantitatively similar to the wet-lab validation targets, which are elevated plasma ALT values following acetaminophen (APAP) exposure in mice. We build on a published model mechanism that helps explain the generation of characteristic spatiotemporal features of APAP hepatotoxicity within hepatic lobules. Discrete event and agent-oriented software methods are most prominent. We instantiate and leverage a small constellation of concrete model mechanisms. Their details during execution help bring into focus ways in which particular sources of uncertainty become entangled with cause-effect details within and across several levels. We scale ALT amounts in virtual mice directly to target plasma ALT values in individual mice. A virtual experiment comprises a set of Monte Carlo simulations. We challenge the sufficiency of four potentially explanatory theories for ALT release. The first of the tested model theories failed to achieve the initial validation target, but each of the three others succeeded. Results for one of the three model mechanisms matched all target ALT values quantitatively. It explains how ALT externalization is the combined consequence of lobular-location-dependent drug-induced cellular damage and hepatocyte death. Falsification of one (or more) of the model mechanisms provides new knowledge and incrementally shrinks the constellation of model mechanisms. The modularity and biomimicry of our explanatory models enable seamless transition from mice to humans.

BackgroundOntologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool.ResultsROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems.ConclusionsROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.

Context. With the development of the software industry, the number of applied methodologies and hybrid approaches based on them constantly increases, that is why, the choice of the most suitable/optimal methodology for the project is an urgent problem of software engineering, since the selection process is poorly formalized, requires sufficient experience of the person who will make this decision and depends on many related factors. Objective. The support of decision-making in the process of choosing a methodology for the software project development and increase of the level of adequacy of the above choice. Method. Based on the previously developed algorithm by the author, a generalized method for selecting the best software development methodology is proposed, which consists of 14 steps and takes into account the characteristics of the project, based on the multi-criteria analysis approaches, taking into consideration the opinions of experts for a more reasonable choice of the most suitable methodology for this project. The method uses the aggregated expert evaluation. It was decided to use the AHP to calculate the criteria weights. Based on the established values of criteria, their weights and expert evaluation, the score is calculated for each methodology using the weighted sum and TOPSIS methods. Results. The application of the developed method to the data of actual projects showed a match in 83% of cases (in five out of six cases, the application of the method resulted in the selection of methodology that corresponded to the one actually used in an existing project). In cases when the methodology chosen by the proposed method differed from the one that was actually used, the application of the proposed method recommends going to the stage of the initial determination of criteria and their weights, which will allow making a more adequate choice of methodology. Conclusions. The proposed method can be applied in practice by software project managers to support the decision-making process, and will allow reducing time spent on project management. [ABSTRACT FROM AUTHOR]

Functional and nonfunctional characteristics of software systems are defined by their architecture. Therefore, research streams such as Internet-of-Things (IoT) or component-based software engineering provide researchers and practitioners with construction guidelines for selected architectural characteristics. Current systems can be categorized in delivering services to the user and being engineered in a smart way. For example, services being provided by IoT-Systems must fulfill users’ goals in a highly dynamic and ad-hoc way. Consequently, this survey aims at answering various research questions regarding the methodical composition of system components and services. Furthermore, new research opportunities are sketched that should be tackled to make the scientific progress available to practitioners. Based on a systematic literature review from a software architecture point of view, in this paper we identify 75 primary studies for domain-specific IoT component composition approaches and architectures. Initial results show that current integration approaches mainly focus on performance evaluation of their integration solutions, which may be too narrow for fulfilling user goals by utilizing of IoT architectures. [ABSTRACT FROM AUTHOR]

The development process of on-board software applications can benefit from model-driven engineering techniques. Model validation and model transformations can be applied to drive the activities of specification, requirements definition, and system-level validation and verification according to the space software engineering standards ECSS-E-ST-40 and ECSS-Q-ST-80. This paper presents a model-driven approach to completing these activities by avoiding inconsistencies between the documents that support them and providing the ability to automatically generate the system-level validation tests that are run on the Ground Support Equipment and the matrices required to complete the software verification. A demonstrator of the approach has been built using as a proof of concept a subset of the functionality of the software of the control unit of the Energetic Particle Detector instrument on-board Solar Orbiter. [ABSTRACT FROM AUTHOR]

Practical studies show that, in order for users to use smart devices more, use smart applications more often for different purposes, applications must meet the requirements of use. their application, must be easy to use, stable and reliable. The era of information technology development with countless advancements and economic development. This is the same thing that requires an increasing human capacity to process and store information based on two factors: efficiency and accuracy. However, in the process of using smart applications, there are many problems that have been encountered related to the quality of the software. In the article, some challenges facing Software Engineering industry are mentioned through comparison of data and some solutions mentioned are most practical to solve the problem. [ABSTRACT FROM AUTHOR]

A significant portion of bone fractures fail to heal properly, increasing healthcare costs. Advances in fracture management have slowed because translation barriers have limited generation of mechanism-based explanations for the healing process. When uncertainties are numerous, analogical modeling can be an effective strategy for developing plausible explanations of complex phenomena. We demonstrate the feasibility of engineering analogical models in software to facilitate discovery of biomimetic explanations for how fracture healing may progress. Concrete analogical models-Callus Analogs-were created using the MASON simulation toolkit. We designated a Target Region initial state within a characteristic tissue section of mouse tibia fracture at day-7 and posited a corresponding day-10 Target Region final state. The goal was to discover a coarse-grain analog mechanism that would enable the discretized initial state to transform itself into the corresponding Target Region final state, thereby providing an alternative way to study the healing process. One of nine quasi-autonomous Tissue Unit types is assigned to each grid space, which maps to an 80×80 μm region of the tissue section. All Tissue Units have an opportunity each time step to act based on individualized logic, probabilities, and information about adjacent neighbors. Action causes transition from one Tissue Unit type to another, and simulation through several thousand time steps generates a coarse-grain analog-a theory-of the healing process. We prespecified a minimum measure of success: simulated and actual Target Region states achieve ≥ 70% Similarity. We used an iterative refinement protocol to explore many combinations of Tissue Unit logic and action constraints. Workflows progressed through four stages of analog mechanisms. Similarities of 73-90% were achieved for Mechanisms 2-4. The range of Upper-Level similarities increased to 83-94% when we allowed for uncertainty about two Tissue Unit designations. We have demonstrated how Callus Analog experiments provide domain experts with a fresh medium and tools for thinking about and understanding the fracture healing process.

Contribution: In this study, we accumulated the knowledge and generated evidence on how and in what context CDIO framework has been used in software engineering (SE) education. The aggregated evidence will enable SE academics in making informed decisions while adopting CDIO for SE education and build upon it. Background: CDIO framework is relevant for SE as it focuses on enabling engineering graduates in conceiving, designing, implementing, and operating complex systems and products. We were not able to find any study that identifies and aggregates the evidence on the use of CDIO for SE education. Research Questions: This study attempts to answer the following research questions: 1) how CDIO has been used in SE education? and 2) what are the experiences of academics in applying the CDIO framework in SE education? Methodology: Using a mixed-method approach (systematic mapping study and interview study with experienced academics in SE), we established the state of the art and practice on the use of CDIO in SE education. Findings: Getting a commitment from the higher management, teachers, and students is a major challenge in the adoption of the CDIO initiative followed by a lack of competence, finance, and resources. Ownership, motivation, persistence, and training of teachers and students are required not only to adopt CDIO for SE but also to sustain it. [ABSTRACT FROM AUTHOR]

Contribution: This article compares the effectiveness for online software engineering education of video-based learning and game-based learning using teacher-authored educational video games created by using authoring tools. Background: Although substantial research has evaluated the impact of video-based and game-based learning versus traditional teaching approaches, little research has been done comparing the effectiveness of video-based learning and video game-based learning. Furthermore, the few studies that performed this comparison did not compare the effectiveness for online education or examined teacher-authored video games. Research Questions: Is game-based learning using teacher-authored video games more effective than video-based learning in terms of knowledge acquisition for software engineering students in online settings? Is game-based learning using teacher-authored video games more effective than video-based learning in terms of motivation for software engineering students in online settings? Methodology: A quasi-experimental design with control and experimental groups and pre- and post-tests was employed. A total of 180 software engineering students participated in this study, 81 of which belonged to the control group while the other 99 were part of the experimental group. The students in the control group took an online lesson in which they learned exclusively by watching videos, whereas the students in the experimental group took the same lesson but learned exclusively by playing an educational video game created by a teacher through an authoring tool. Findings: The results show that game-based learning using teacher-authored educational video games was more effective than video-based learning in terms of both knowledge acquisition and motivation. [ABSTRACT FROM AUTHOR]

Contribution: This article identifies the participation of external stakeholders as a key contributing factor for positive outcomes in project-based software engineering courses. A model for overlapping virtuous circles of lasting positive impact on both stakeholders and students from such courses is proposed. Background: Project-based courses are widespread in software engineering education, and there are numerous designs for such courses presented in literature. It is found that the needs and motivations of external stakeholders, from industry and government sectors, in these courses has received limited attention in related work. Intended Outcomes: A course design that prepares students for graduate level studies and professional life, through close proximity to external stakeholders in a highly realistic setting, working on “live” projects. Application Design: Building on a long tradition of university-industry collaboration dating back to 1977, as well as findings in related work, students are assigned to live projects proposed by external stakeholders from industry and government, working in close proximity with their respective stakeholders throughout the project. The course places great emphasis on coaching over instruction, treating the many unforeseen challenges of such projects as a valuable part of the learning experience. Findings: Based on interviews with stakeholders and students, it is found that stakeholder and student outcomes are interdependent and build upon one another, and that positive outcomes for both groups are necessary for the sustainability of the course over multiple iterations. [ABSTRACT FROM AUTHOR]

U.S. national research laboratories and agencies play an integral role in advancing science and technology for the public good. The authors of this article, as research software engineers (RSEs) and allies from eight unique national R&D organizations, came together to explore RSE needs from the perspective of national institutions. We identified three key areas of improvement for future RSEs to pursue science in the national interest: community establishment, hiring and retention, and recognition. To retain and cultivate this essential talent, U.S. national institutions must evolve to support appropriate career pathways for RSEs, and to recognize and reward RSEs' work. [ABSTRACT FROM AUTHOR]

The Princeton Research Software Engineering Group has grown rapidly since its inception in late 2016. The group is housed in the central Research Computing Department, comprises professional research software engineers (RSEs), and works directly with researchers to create high-quality research software. As the group has matured, so has the need for formalizing operational details and procedures. The Research Software Engineering Group uses an RSE partnership model, where RSEs work long term with a designated academic department, institute, center, consortium, or individual principal investigator. This article describes the operation of the central Princeton Research Software Engineering Group, including funding, partner and project selection, and best practices for defining expectations for a successful partnership with researchers. [ABSTRACT FROM AUTHOR]

Research software engineers (RSE) play a vital role in scientific discoveries worldwide. They lead the core development of the applications, libraries, and tools that enable today's supercomputers to process the vast volumes of data generated from the world's most extensive and complicated scientific instruments and facilities. This article describes the mission, culture, and practices of RSE teams at Oak Ridge National Laboratory (ORNL), including their team dynamics and composition, work ethics, standard practices, and ever-evolving skill sets vital to pursuing scientific innovations and implementing novel ideas. We describe the lessons learned from specific activities that contribute to shaping the identity and growth of RSE roles at ORNL. Finally, we provide our view for the near future on effective strategies for establishing, leading, and nurturing RSE teams and building a thriving community in collaboration with science stakeholders. [ABSTRACT FROM AUTHOR]

Background: Peer evaluation in software engineering (SE) project courses enhances the learning experience of students. It also helps instructors monitor and assess both teams and individual students. Peer evaluations might influence the way individual students and teams work; therefore, the quality of the peer evaluations should be tracked through the project course. Contribution: In this article, we analyzed the quality and scoring behavior of students in peer evaluation in an undergraduate SE project course over three years. Research Questions: RQ1: What is the quality of peer evaluation of undergraduate students in a SE project course? RQ2: How do undergraduate students in an SE project course score each other? Methodology: The quality of peer evaluation (length, level of detail, etc.) and scoring of peers based on various aspects of peer evaluations of third-year students in a year-long SE project course were studied. Taking into account the grade students received at the end of the course (A, B, C, and F-calibers), peer evaluations were categorized, analyzed over time, and compared between students calibers. Findings: After analyzing 6854 peer evaluations from 193 students, it was found that the quality of peer evaluations across students was mostly consistent throughout the course. Also, it was observed that quantitative aspects of the peer evaluation were scored similarly across student calibers. However, the qualitative aspects of the peer evaluation were impacted by the caliber of students. These findings suggest that weaker students (i.e., C-caliber students) generally receive better quality peer evaluations than stronger students (i.e., A-caliber students). Finally, a preliminary analysis showed a positive connotation of emotions and sentiments found in the textual feedback delivered by students. [ABSTRACT FROM AUTHOR]

Contribution: Determine and analyze the gap between software practitioners’ education outlined in the 2014 IEEE/ACM software engineering education knowledge (SEEK) and industrial needs pointed by Wikipedia articles referenced in Stack Overflow (SO) posts. Background: Previous work has uncovered deficiencies in the coverage of computer fundamentals, people skills, software processes, and human–computer interaction, suggesting rebalancing. Research Questions: 1) To what extent are developers’ needs, in terms of Wikipedia articles referenced in SO posts, covered by the SEEK knowledge units? 2) How does the popularity of Wikipedia articles relate to their SEEK coverage? 3) What areas of computing knowledge can be better covered by the SEEK knowledge units? 4) Why are Wikipedia articles covered by the SEEK knowledge units cited on SO? Methodology: Wikipedia articles were systematically collected from SO posts. The most cited were manually mapped to the SEEK knowledge units, assessed according to their degree of coverage. Articles insufficiently covered by the SEEK were classified by hand using the 2012 ACM computing classification system (CCS). A sample of posts referencing sufficiently covered articles was manually analyzed. A survey was conducted on software practitioners to validate the study findings. Findings: SEEK appears to cover sufficiently computer science fundamentals, software design, and mathematical concepts, but less so areas, such as the World Wide Web, software engineering (SE) components, and computer graphics. Developers seek advice, best practices and explanations about software topics, and code review assistance. Future SEEK models and the computing education could dive deeper in information systems, design, testing, security, and soft skills. [ABSTRACT FROM AUTHOR]