Ten simple rules to run a successful BioHackathon

This proposal is about a study we recently published in the IEEE Transaction of Software Engineering journal [4]. Context: Collaborative software engineering (CoSE) deals with methods, processes and tools for enhancing collaboration, communication, and co-ordination (3C) among team members [5]. CoSE can be employed to conceive different kinds of artifacts during the development and evolution of software systems. For instance, when focusing on software design, multiple stakeholders with different expertise and responsibility collaborate on the system design. Model-Driven Software Engineering (MDSE) provides suitable techniques and tools for specifying, manipulating, and analyzing modeling artifacts including metamodels, models, and transformations [1]. Collaborative MDSE consists of methods or techniques in which multiple stakeholders manage, collaborate, and are aware of each others' work on a set of shared models. A collaborative MDSE approach is composed of three main complementary dimensions: (i) a model management infrastructure for managing the life cycle of the models, (ii) a set of collaboration means for allowing involved stakeholders to work on the modelling artifacts collaboratively, and (iii) a set of communication means for allowing involved stakeholders to exchange, share, and communicate information within the team. Collaborative MDSE is attracting several research efforts from different research areas (e.g., model-driven engineering, global software engineering, etc.), resulting in a variegated scientific body of knowledge on the topic. Objective: In this study we aim at identifying, classifying, and understanding existing collaborative MDSE approaches. More specifically, our goal is to assess (i) the key characteristics of collaborative MDSE approaches (e.g., model editing environments, model versioning mechanisms, model repositories, support for communication and decision making), (ii) their faced challenges and limitations, and (iii) the interest of researchers in collaborative MDSE approaches over time and their focus on the three dimensions of collaborative MDSE. Method: In order to achieve this, we designed and conducted a systematic mapping study [6] on collaborative MDSE. Starting from over 3,000 potentially relevant studies, we applied a rigorous selection procedure [3] resulting in 106 selected papers, further clustered into 48 primary studies, along a time span of nineteen years. A suitable classification framework has been empirically defined and rigorously applied for extracting key information from each selected study. We collated, summarized, and analyzed extracted data by applying scientifically sound data synthesis techniques. Results: In addition to a number of specific insights, our analysis revealed the following key findings: (i) there is a growing scientific interest on collaborative MDSE in the last years; (ii) multi-view modeling, validation support, reuse, and branching are more rarely covered with respect to other aspects about collaborative MDSE; (iii) different primary studies focus differently on individual dimensions of collaborative MDSE (i.e., model management, collaboration, and communication); (iv) most approaches are language-specific, with a prominence of UML-based approaches; (v) few approaches support the interplay between synchronous and asynchronous collaboration. Conclusion: This study gives a solid foundation for a thorough identification and comparison of existing and future approaches for collaborative MDSE [2]. Those results can be used by both researchers and practitioners for identifying existing research/technical gaps to attack, better scoping their own contributions to the field, or better understanding or refining existing ones.

Agile software development methodologies, including Scrum, have become popular for their flexibility and collaborative approach. However, the success of Scrum teams heavily depends on the dynamics among team members. This study explores the challenges related to Agile software development, specifically focusing on the influence of human skills on the Scrum team. While Scrum encompasses various well-defined aspects, it does not explicitly address personality traits. Consequently, this study seeks to explore how teams' performance is influenced by the human skills possessed by their members during the implementation of Agile methodologies. This study investigated eight teams of software engineering students engaged in software development projects by observing impacted team processes in each iteration. The results show that soft skills and J/P significantly influence team processes. However, their impact on the team's product varies across cycles. Additionally, soft skills interact with the Feeling (F)/ Thinking (T) and Judging (J)/Perceiving (P), affecting team processes and products.

Agile in software development is a blanket term that covers many different tools, techniques and ways of working. Like Lean, it has at its core a focus on customer value, the promotion of continuous improvement and the reduction of waste from the software development process. The Kanban board has significantly improved our daily stand-up providing team members a visual cue for discussions and making it clearer across the team exactly what they have been working on. Prior to use of the board, the online system's ticket numbers were frequently referenced at our stand-up meetings. In a university for example, users tend to be students with their own learning commitments, or front-facing staff where budgets or business requirements do not allow them to be seconded. The chapter discusses the bottlenecks at the next retrospective to identify the cause and find solutions to prevent this happening in future.

Gebiedsgericht Voorraadbeleid van Woningcorporaties; Een analyse van planningsbenaderingen in Vogelaarwijken

The goal of this study was to show the extent to which electronic accounting information systems in the public and private universities in Jordan can provide quantitative indicators of financial performance. Represented by seven indicators, these quantitative indicators are: the amounts and rates related to scientific research and conferences, the development of software and hardware, and the purchase of books, references and periodicals, Earnings per share (EPS), return on assets (ROA), the annual average cost of the student, and comparison between the cost of a teaching member and its’ revenue. To achieve the objective of the study, two tools were used presented by questionnaire and a personal interview, (26) questionnaires were distributed on the CFOs in (26) public and private universities in Jordan, and (20) questionnaire were recovered in a (76.9%) response rate, interviews were also performed with (8) directors to confirm the data collected from the questionnaire. The findings and recommendations that the study came out with are traced at the end.

Software development is a knowledge intensive activity and software developers are knowledge workers. Knowledge needed for software development is often distributed among different developers. Supporting efficient knowledge collaboration and transfer is thus essential for software development organizations to remain competitive. This paper proposes a new theory /sub y/namic community to support knowledge collaboration and discusses its application in software development. Dynamic community integrates the traditional knowledge management approach in which knowledge is formalized and accumulated in knowledge repositories, and the community-based knowledge collaboration approach in which knowledge is transferred through informal community participation and human contacts. The dynamic community theory takes into full consideration individual knowledge workers' ever-changing needs for new knowledge as well as the role of social relationship of knowledge workers in effective knowledge collaboration. This paper introduces the dynamic community theory, a general system architecture of sociotechnical environments in support of dynamic community, and its application in software development.

In many of today's small companies and startups, developers may not give enough attention to the importance of UX/UI design for the product under development. Moreover, such small teams may lack the required organization skills that help them to collaborate and work together. As a result, such teams usually face problems with delivering the “right” product, as well as not being able to follow a sustainable development process. In a similar context, CS students in programming classes are facing almost the same problems of small teams in industry. To tackle these problems, various approaches for integrating agile development methods and UX design methods have been proposed to help developers carefully consider the UX requirements, and to be able to organize their work environment. In this paper, we explore how such integration can be a good fit for both CS students and software developers, especially for those who work on mobile development. We present our proposed set of integration guidelines, and then we focus on Pair Programming (PP) as an agile practice that promotes a collaborative work environment. The expert reviews conducted in this paper helped us exlore how PP can be introduced to CS students (and later, to developers in the market) to support collaborative work environments. Moreover, Using PP in class provides an adaptive and collaborative teaching approach that can be used in CS programming labs. We also discuss the pitfalls that can affect developers during PP sessions, and how to avoid such negative effects. We conclude by providing a set of recommended practices that can be applied to introduce PP for developers in both academic and industrial contexts.

Rational: Lymphangioleiomyomatosis (LAM) is a rare, progressive interstitial lung disease (ILD) predominantly affecting women of reproductive age. Improving access to structured exercise through home-based programs is attractive in LAM and other ILDs, but monitoring exercise pulse oximetry and outcomes can be challenging for patients far from specialized pulmonology centres. A preliminary study of a remotely-monitored exercise program demonstrated improvement in 6-minute walk test (6MWT) distance without safety incident, indicating mobile technology with remote monitoring may provide a feasible solution for broader access. For use during LAMFit, a fully-remote, structured exercise program for LAM, we aimed to develop and test a mobile health application to enable remote assessment of 6MWT and home monitoring of pulse oximetry during exercise. Methods: Application development involved multi-stakeholder engagement and collaboration between LAMFit investigators, patient representatives, LAM care providers, and software developers. Feature design was informed by 2002 American Thoracic Society (ATS) guidelines for the 6MWT. The application was deployed in a 28-week LAMFit pilot in 25 women with LAM (mean±SD, age 52.6±14 years). Weekly exercise sessions were remotely monitored via the application, and remote 6MWT and validated patient questionnaires were completed at weeks 2, 14, and 27. System Usability Scale (SUS) scores, a standardized metric to assess user perceptions and ease of system use, were collected at weeks 2 and 28.Results: Collaborative co-design facilitated the creation of a mobile application for the LAMFit program. Iterative design, testing and refinement, guided by steering team feedback, incorporated adjustments in language, font size, icons, and audio prompts, and enabled 6MWT to continue during brief connection-loss with the Bluetooth-enabled pulse oximeter. All 25 patients successfully used the application to complete surveys and multiple 6MWT. System usability (SUS) at week 2 was 50.625 (SD 3.227), and 52.62 (SD 4.292) at week 28. On exit survey, 88% of participants found it feasible to conduct a remote 6MWT at home using the mobile health app. Conclusion: A collaborative co-design approach enabled alignment of the application with users’ needs, enabling successful implementation of the technology. SUS scores increased during the study, suggesting improvements in perceptions of usability with increasing familiarity. However, both scores are below the industry average SUS of 68, indicating potential for further improvement in application usability. Examination of application usability during LAMFit's pilot study provides insights to inform the refinement of the application prior to scaling up the program, optimizing a digital-health solution that supports patients with LAM exercise routines

This study implements a conflict management training approach guided by principles of transformative learning and conflict management practice simulated via an LLM. Transformative learning is more effective when learners are engaged mentally and behaviorally in learning experiences. Correspondingly, the conflict management training approach involved a three-step procedure consisting of a learning phase, a practice phase enabled by an LLM, and a reflection phase. Fifty-six students enrolled in a systems development course were exposed to the transformative learning approach to conflict management so they would be better prepared to address any potential conflicts within their teams as they approached a semester-long software development project. The study investigated the following: (1) How did the training and practice affect students’ level of confidence in addressing conflict? (2) Which conflict management styles did students use in the simulated practice? (3) Which strategies did students employ when engaging with the simulated conflict? The findings indicate that: (1) 65% of the students significantly increased in confidence in managing conflict by demonstrating collaborative, compromising, and accommodative approaches; (2) 26% of the students slightly increased in confidence by implementing collaborative and accommodative approaches; and (3) 9% of the students did not increase in confidence, as they were already confident in applying collaborative approaches. The three most frequently used strategies for managing conflict were identifying the root cause of the problem, actively listening, and being specific and objective in explaining their concerns.

We propose a metric for meeting quality in software development. Meeting is important in order to share knowledge and experience among developers and stakeholders. Most frequent and important meetings are in software requirement analysis phase. System engineers and stakeholders discuss software requirements. However, meeting quality is various. Sometimes, stakeholders feel vague decision and suspicious discussion. It is difficult to measure quantitatively the vagueness and suspicion because the vagueness and suspicion are based on human feeling. Therefore, to measure the vagueness and suspicion, our proposed metric is useful. A feature of the metric is to measure only when and who speaks in meetings, not depending on what was said. Hence, the metric does not require software domain knowledge and development experience. The metric consists of system engineers’ speaking time and the number of stakeholders’ speaking within one question by a system engineer. The metric is applied to a practical project. As a result, we automatically extract vague discussion and suspicious discussion in quantitative analysis using the metric. The number of extracted doubtful topic is 37 in all 69 topics. After that, we confirmed that the metric can predict doubtful topics that cause software faults in precision 59.5%, recall 84.5%. In addition, we found that a repeatable topic may cause software faults in requirement meetings.

An empirical study of the effect of knowledge integration on software development performance

The article analyzes the approach to teaching the software design and work-out methods in the framework of "Business-informatics". It proposes developing the teaching process proceeding from the analysis of software reliability criterion. Support of software reliability requirements follows all the steps of software life cycle and implementation of this requirement guarantees the high-quality software development. Special aspects of teaching data engineering within the frame of "Business-Informatics" specialty are described. The thesis considering the used IT relating rather to typical "basic" technologies than to unique IT is analyzed. At the same time the main property of academic activity is its engineering not scientific character. Higher school outputs primarily "the basic" knowledge and qualification in a definite subject domain of modern economic life. Opinion is advanced that in the "Business-Informatics" framework the typical widespread "basic" IT should be taught. The subject steering documents are proposed to be revised toward increase in study hours on IT introduction, backing and practical application and decrease in hours for developing and designing the info systems and IT. Proposal of configuring the software development method study process on the basis of maintenance of reliability criterion instead of now spread in-depth study of all software development is derived from this approach. Such approach is built around basic knowledge of the software life cycle without detailed and in-depth study of the software every life cycle. It is suspected that the business IT specialist mastering such approach will govern successfully the processes of high-quality software designing and developing.Capacity of Specs for software development is analyzed. It is proposed to include a description of quality parameters, clear for the end user, in the Specs to ensure the software reliability. Description of the main reliability provision requirements is given herein.

Objectives: Presenting the results of an Egyptian branch of an international company as a case study. The existing gap in the knowledge types and the impact of the lack interaction was investigated within the structure of the company team. Methods: This study is an exploratory case study. To enhance the data collection process and to answer the study’ questions, the following three phases were performed: interviews, online survey, and interviews. A descriptive statistical analysis and root – cause analysis were used to analyze the online survey in quantitative and qualitative attributes and a general framework coding for a thematic analysis to analyze the interviews. Finding: The results explore that: (1) the current structure of the Egyptian branch of an international company case study distributed teams faces an existing gap in the knowledge types (domain, technical, and application). (2) The existing gap in both of domain and technical knowledge leads to a gap in the application knowledge. (3) The lack of using qualified document, recording audio and video meetings between the distributed teams, Co-located practice, wikis (asynchronous tool) besides email, and the yearly planned formal training and training course create root causes for the existing knowledge gap. (4) Qualified document is standardized and contains the both test cases and user stories. (5) Recording audio and video meetings between the distributed teams especially in complex project is an excellent feedback. (6) The strategy of the Co-located practice, where the designers (offshore members) travel to collocate with Client engagement team (onshore team) during the requirements document preparing, is preferred by the most participants than the opposite. Application/Improvement: Capturing the existing gap in knowledge types for the agile partial offshoring model will lead to improving this model. Which increase the software quality and decrease delivery time and cost for international software development companies and software development’ clients. Keywords: AGSD, Communication, Coordination, Distributed Teams, Knowledge Sharing, Knowledge Types

This research assessed the implementation of the Think-Pair-Share (TPS) strategy and its performance on students’ understanding on Climate for Junior High School (JHS) Grade 9 at Pagsabungan National High School, Division of Mandaue City, during the third quarter of school year 2024-2025. The research aimed to evaluate the effectiveness of TPS as a collaborative learning approach and used the findings to develop lesson exemplars for Junior High School Science 9. The pre-test and post-test results analysis demonstrate a significant improvement in students’ climate competencies following instructional interventions. In the pre-test, many students were categorized under Average Mastery and Low Mastery, with many scoring between 0 and 4. However, the post-test results indicate that no students remained in the lower tiers and most advanced too. Closely Approximating Mastery or Mastered levels. Specifically, 38.46% of students Mastered explaining how various factors influence climate, compared to none in the pre-test, while 51.92% Closely Approximating Mastery. Similarly, 42.31% Mastered describing global climatic phenomena, with 30.77% Closely Approximating Mastery. The mean scores and low standard deviation increase suggest consistent student learning gains. The absence of students in the Low Mastery category in the post-test highlights the effectiveness of instructional strategies, such as technology-enhanced learning and differentiated instruction, in addressing learning deficiencies. The Think-Pair-Share (TPS) strategy was crucial in boosting student performance across genders, as evidenced by the overall score improvements and reduced variability. These findings reinforce the positive impact of structured and engaging teaching methods in fostering more profound climate-related knowledge and emphasize the need for continued implementation to support all learners, particularly those requiring additional assistance. Addressing these issues through structured facilitation, equitable participation, and scaffolding techniques can enhance TPS implementation. The findings highlight the necessity for adaptive, student-centered pedagogies to ensure comprehensive climate literacy among all learners.

Four years ago, at BOSC 2019, the Forome Platform team first presented AnFiSA, an open-source variant curation and interpretation tool for analysis of the data produced from genome sequencing. In the last year the work has been published in the Journal of Biomedical Informatics1. One of the focuses of the paper was the creation of a community comprising clinicians, researchers, and professional software developers to reach our goals. We received contributions from numerous organizations and dozens of individual contributors to facilitate this effort. It became evident that for a community to operate efficiently, there must be a shared language that comes naturally to all members. Back in 2019, we argued that representing variant curation guidelines in the form of manually curated decision trees would align the guidelines development workflow with that of software development. We also suggested that developers of these guidelines would benefit from utilizing an Integrated Development Environment (IDE) that offers functionalities such as syntax highlighting, error checking, and visual debugging. Over the past four years, we have made significant progress towards creating such an IDE. We replaced the Vue.js client with one based on React.js and introduced IDE-like features. As the guidelines are often articulated as free-text English prose, we contend that developing a more structured domain-specific language (DSL) that can be grasped by both clinicians and engineers/researchers would be immensely advantageous for the community as well as helpful in mimicking software development process. Our development of the DSL and its corresponding visual representations for editing and debugging allowed us to condense decision trees into ordered sequences of inclusion and exclusion criteria. In this talk, we aim to present our systematic approach for converting free text into complex logical statements and extensive decision trees, which can be further translated into inclusion and exclusion criteria depicted by graphical widgets. We will also demonstrate the utilization of these widgets and dashboards in a debugging process for a particular corpus of data. We would like to emphasize that we view the visualization of the ordered sequences of inclusion and exclusion criteria as a valuable tool, extending beyond variant curation to areas such as patient recruitment and population health research. Our DSL utilizes genetic and sequencing annotations as variables, which encompass both technical and biological information. Technical annotations include provenance and confidence data for specific calls, while biological annotations summarize evidence pertaining to the potential impact of mutations on molecular function and phenotype. These annotations collectively provide clinicians and researchers with information on provenance, confidence, and evidence to aid in decision making. Our work on the DSL revealed the need to structure annotation types systematically to help answer three critical questions: 1) How confident am I that the variant is present in my patient? 2) How confident am I that it affects the phenotype? 3) What evidence supports the association between the observed genotype change and the phenotype? In order to accomplish this objective, in the latest version of AnFiSA we have implemented a classification system for annotations based on their scale and resolution, knowledge domain, and method. Genetic and biological annotations gather relevant evidence from public and proprietary sources about the potential mutation effects on molecular function and phenotype, combining multiple inputs to provide a summary. The strength of evidence heavily relies on the level of resolution of a specific annotation, as well as the knowledge domain and the method of an annotation2. The resolution ranges from granular transcript and variant specific to broader functional units. The knowledge domain refers to areas such as human or animal genetics, or molecular function described by experimental or computational techniques. The methods used for generating annotations vary among statistical genetics inference, bioinformatics predictions, and in vivo and in vitro experiments. The initial implementation of this classification is accessible on GitHub and can be tested in the most recent versions of AnFiSA. Our proposal is to initiate a conversation regarding the semantic and syntax of the DSL for variant curation and interpretation, as well as the most effective and intuitive way to structure annotation types. We believe that developing a standard or at least a guideline, for representation of variant curation rules will help in establishing a unified and systematic approach to reporting clinically relevant and actionable variants and ultimately will bring us closer to evidence based medicine. 1. Bouzinier, M. A. et al. AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease. J. Biomed. Inform. 133, 104174 (2022). 2. Hufeng Zhou et al. FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome. Nucleic Acids Res 2022 Nov 9; gkac966. PMID: 36350676. DOI: 10.1093/nar/gkac966