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We present a finite-volume, genuinely fourth-order accurate numerical method for solving the equations of resistive relativistic magnetohydrodynamics in Cartesian coordinates. In our formulation, the magnetic field is evolved in time in terms of face-average values via the constrained-transport method, while the remaining variables (density, momentum, energy, and electric fields) are advanced as cell volume averages. Spatial accuracy employs fifth-order accurate WENO-Z reconstruction from point values (as described in a companion paper) to obtain left and right states at zone interfaces. Explicit flux evaluation is carried out by solving a Riemann problem at cell interfaces, using the Maxwell–Harten–Lax–van Leer with contact wave resolution. Time-stepping is based on the implicit–explicit Runge–Kutta (RK) methods, of which we consider both the third-order strong stability preserving SSP3(4,3,3) and a recent fourth-order additive RK scheme, to cope with the stiffness introduced by the source term in Ampere's law. Numerical benchmarks are presented in order to assess the accuracy and robustness of our implementation. [ABSTRACT FROM AUTHOR]

In this paper, we present CALSAGOS : Clustering ALgorithmS Applied to Galaxies in Overdense Systems which is a PYTHON package developed to select cluster members and to search, find, and identify substructures. CALSAGOS is based on clustering algorithms, and was developed to be used in spectroscopic and photometric samples. To test the performance of CALSAGOS , we use the S-PLUS's mock catalogues, and we found an error of 1–6 per cent on member selection depending on the function that is used. Besides, CALSAGOS has a F 1-score of 0.8, a precision of 85 per cent and a completeness of 100 per cent in the identification of substructures in the outer regions of galaxy clusters (r > r 200). The F 1-score, precision, and completeness of CALSAGOS fall to 0.5, 75, and 40 per cent when we consider all substructure identifications (inner and outer) due to the function that searches, finds, and identifies the substructures works in 2D, and cannot resolve the substructures projected over others. [ABSTRACT FROM AUTHOR]

It is commonly believed that human-centred design (HCD) approach is very beneficial to interactive systems development. However, not much is known about the state of HCD practice in developing countries, especially the sub-Saharan Africa. This paper explores the state of HCD practice in three Nigerian software companies. We used the interview technique to explore two key issues. First, the perception of humans as a component of sociotechnical systems, and second, how HCD process is being approached in software companies. A cross-case analysis of the three companies was performed and the usability maturity model-human-centredness scale was used to determine the state of maturity of the three companies. The outcomes of this study reveal that HCD practice is currently at the least stage of maturity in the three companies and user involvement is not practiced in the right manner. The outcomes of the study suggest the need for reflective HCD practice and localizing human–computer interaction approaches to contexts. [ABSTRACT FROM AUTHOR]

Motivation Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and scripting of software that are mostly not user friendly and lack basic GUIs. As the researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines truly speeding up the learning curve to build software workstations. Therefore, this paper aims to provide MetumpX, a software package that eases in the installation of 103 software by automatically resolving their individual dependencies and also allowing the users to choose which software works best for them. Results MetumpX is a Ubuntu-based software package that facilitate easy download and installation of 103 tools spread across the standard metabolomics pipeline. As far as the authors know MetumpX is the only solution of its kind where the focus lies on automating development of software workstations. Availability and implementation https://github.com/hasaniqbal777/MetumpX-bin. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Triggered by our occasionally tense field experiences relating to the implementation and institutionalization of usability in design engineering organizations that are characterized by traditional engineering education and thinking, we have earlier suspected that the activities associated with human-centered design were orthogonal to the design engineering practices otherwise in place. While noting that other human factors professionals have had comparable challenges relating to multidisciplinary design, we have, however, reached a point where we rather are suggesting that the ontological, epistemological and methodological grounding of classic design engineering, under some circumstances, could be the direct cause for friction between that discipline and that of human factors. In a way taking our own medicine, we have thus arrived at a place where we are realizing the need for an ethnographical exploration and improved understanding of classic design engineering fundamentals, appreciating that a more successful and fruitful interaction and cooperation with that essential discipline very well could spring from a deeper and more nuanced understanding of the mindset of the classic design engineer. The main part of the present paper pivots around developing such an insight, hoping to contribute to the effective, efficient and satisfactory outcome of multidisciplinary cooperation for those who find themselves being tasked with human-centric work in traditional engineering organizations. [ABSTRACT FROM AUTHOR]

Evaluation of phenotype-driven gene prioritization approaches for Mendelian diseases could facilitate the software development and method selection for the workflow configuration and clinical practice. In our original article, the performance of 10 well-recognized causal-gene prioritization methods was benchmarked using 305 cases from the deciphering developmental disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results showed that LIRICAL and AMELIE were two of the best methods in our benchmark experiments, and the possible integrative approach of these two methods may enhance the diagnostic efficiency. However, some methodological critiques were raised by the authors of Exomiser and PhenIX, so we revisited our benchmarking studies to answer their comments in this letter. [ABSTRACT FROM AUTHOR]

We present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities—universality (support for all common genomic file formats), high compression ratios, speed, feature-richness and extensibility. Genozip delivers high-performance compression for widelyused genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space. Availability and implementation Genozip is written in C. The code is open-source and available on http://www.genozip.com. The package is free for non-commercial use. It is distributed through the Conda package manager, github, and as a Docker container on DockerHub. Genozip is tested on Linux, Mac and Windows. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

This article explores the emergence of Automated Vehicles (AVs) in Australia. It will investigate the legal and regulatory terrain. International and domestic approaches are examined to determine potential responses. The regulatory issues emerge partly due to the varied nature of artificial intelligence systems and processes that enable AVs to function. The variations may be due to the chosen domain model, software development processes, or the development of biases that may occur during code development for the underlying artificial intelligence system. Such variations can create difficulties in the application of road rules, safety requirements, and the legal and regulatory requirements. They may give rise to significant issues relating to driver classification and licensing for AVs, due to the varied levels of control and involvement in the driving process. For this reason, legislative reform at specific jurisdictional levels is suggested together with clearer international standards as a pathway to ensure the safe and effective integration of autonomous vehicles into society. [ABSTRACT FROM AUTHOR]

Modern geopolitics includes measures short of armed conflict designed to control decision-making in, and action by, target states. One increasingly significant category of these measures involves attacks by foreign states against civil society institutions in target states. Liberal states that seek to protect their civil societies from this interference seek to bolster civil society defences, to determine the origin of and respond to attacks and to deny relevant tools to potential attackers. With the rise of cyberspace, target states using purely territorial measures are increasingly impotent to protect their civil societies from foreign governmental hacking. Denying access to advanced hacking software by antagonist foreign states may assist in protecting target state civil societies. This article explores the possibility of denying hacking tools to potential attackers, identifies some of the problems and proposes a refinement of export controls that will permit greater protection with less disruption of desirable software development. [ABSTRACT FROM AUTHOR]

Do human–computer interaction (HCI) researchers agree about which HCI approaches should be used in the development of an interactive system? To address this question, we performed a study based on the engineering process areas (requirements development, technical solution, product integration, verification and validation) of the CMMI-DEV (Capability Maturity Model Integration for Development), a software engineering model commonly used in the industry. To carry out this study, a literature review was performed, a specific instrument was designed based on CMMI-DEV and interviews with 20 researchers from the HCI domain were conducted. Analyzing the interview data with monovariate and multivariate statistical approach (Multiple Correspondence Analysis - MCA), we find the greatest agreement occurred among researchers for HCI approaches that support verification and validation phases and the use of functional prototypes in some activities of the last phases of software development (technical solution and product integration). However, we identified lack of agreement among researchers regarding requirements development activities. [ABSTRACT FROM AUTHOR]

Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others. [ABSTRACT FROM AUTHOR]

A crucial part of the design of mobile user interfaces is their evaluation with users. Although user studies are widely used for measuring the usability of a software system, they are time-consuming and expensive. In this study, we propose a novel approach which is based on the computational analysis of an app's visual appearance. By calculating metrics which measure the complexity of the user interface, it should be possible to draw conclusions about the perceived usability. Automating this practice would be beneficial to developers and designers, as it would help to find usability issues early and reliably in the software development life cycle. However, there is no tool available yet which allows to automatically quantify the complexity of a mobile application's user interface with metrics. We analyze the complexity based on screenshots of the user interface as well as on interaction data, without the need to access the source code of the application. We introduce a set of complexity metrics, which are partially based on existing metrics for the visual appearance of a user interface. In order to evaluate the quality of our metrics, we conducted a user study with several mobile apps. The results show that there are significant correlations between some of the proposed metrics and the perceived usability and workload. [ABSTRACT FROM AUTHOR]

In human-based computation, the machine outsources certain steps of an algorithm to humans to optimize computation by making an equilibrium of human and machine computation advantages. Software testing is an important part of the software development life cycle that aims to reveal failures in software. One of the most important activities in the software testing is test data generation. Although many automatic methods have been introduced to generate effective test data, humans are still extensively used in the software industry, due to the challenges of the proposed automatic methods. Assuming that software companies still need the help of humans, in this research, we hypothesize that a game with a purpose can be utilized to improve the process of human-based test data generation by making test data generation more cost-effective and fun. To investigate this hypothesis, we implemented a game with a purpose, Rings, to improve the process of human-based test data generation for program units. We also performed an experiment to evaluate this idea as entertainment as well as a mean for test data generation. The results show that by crowd-sourcing test data generation of program units to typical players of a game, we can make test data generation more cost-effective and fun. [ABSTRACT FROM AUTHOR]

Background: The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets. Results: Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in <6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd-based contest a combination of computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project. Conclusions: Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics. [ABSTRACT FROM AUTHOR]

In recent years, research into gender differences has established that individual differences in how people problem-solve often cluster by gender. Research also shows that these differences have direct implications for software that aims to support users' problem-solving activities, and that much of this software is more supportive of problem-solving processes favored (statistically) more by males than by females. However, there is almost no work considering how software practitioners--such as User Experience (UX) professionals or software developers--can find genderinclusiveness issues like these in their software. To address this gap, we devised the GenderMag method for evaluating problem-solving software from a gender-inclusiveness perspective. The method includes a set of faceted personas that bring five facets of gender difference research to life, and embeds use of the personas into a concrete process through a gender-specialized Cognitive Walkthrough. Our empirical results show that a variety of practitioners who design software-- without needing any background in gender research--were able to use the GenderMag method to find gender-inclusiveness issues in problem-solving software. Our results also show that the issues the practitioners found were real and fixable. This work is the first systematic method to find gender-inclusiveness issues in software, so that practitioners can design and produce problemsolving software that is more usable by everyone. [ABSTRACT FROM AUTHOR]

In this article, we report from a case study of an agile software development organization and we study in particular the developers' and product managers' attitudes towards integrating usability work into software development. We offer explanations based on system justification theory illuminating what would-be integrators might be up against. The analysis shows how the developers only pay lip service to usability work and how they treat users superficially. It further shows how that leads to stereotyping of usability designers and users in order to preserve status quo, and how internalization of inequality between the developers and usability designers rationalizes the preservation of status quo. These findings will have significant implications for managers of software development. [ABSTRACT FROM AUTHOR]

Motivation: Next-generation sequencing technologies have enabled the large-scale assessment of the impact of rare and low-frequency genetic variants for complex human diseases. Gene-level association tests are often performed to analyze rare variants, where multiple rare variants in a gene region are analyzed jointly. Applying gene-level association tests to analyze sequence data often requires integrating multiple heterogeneous sources of information (e.g. annotations, functional prediction scores, allele frequencies, genotypes and phenotypes) to determine the optimal analysis unit and prioritize causal variants. Given the complexity and scale of current sequence datasets and bioinformatics databases, there is a compelling need for more efficient software tools to facilitate these analyses. To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related individuals. RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection. We illustrate the advantages of RVTESTS in functionality and efficiency using the 1000 Genomes Project data. [ABSTRACT FROM AUTHOR]

The security of software is becoming increasingly important. Open source software forms much of our digital infrastructure. It, however, contains vulnerabilities which have been exploited, attracted public attention, and caused large financial damages. This article proposes a solution to shortcomings in the current economic situation of open source software development. The main idea is to introduce price signals into the peer production of software. This is achieved through a trading market for futures contracts on the status of software issues. Users, who value secure software, gain the possibility to predict outcomes and incentivize work, strengthening collaboration and information sharing in open source software development. The design of such a trading market is discussed and a prototype introduced. The feasibility of the trading market design is corroborated in a proof-of-concept implementation and simulation. Preliminary results show that the implementation works and can be used for future experiments. Several directions for future research result from this article, which contributes to peer production, software development practices, and incentives design. [ABSTRACT FROM AUTHOR]

The article reports on the development of the Autolens software by the University of Nottingham researchers to be used in handling data about the mass in the universe obtained by the European Space Agency's Euclid space observatory.

The article reports on the development of a software, called the Automated CME Triangulation, by researchers at Aberystwyth University that tracks coronal mass ejections from the Sun in three dimensions.