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Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.

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Domain-specific standards and documents heavily regulate safety-critical systems. One example is the DO-178C standard for aerospace, which guides organizations to achieve system safety and evidence for their certification. Under such regulated contexts, most organizations use traditional development processes, in contrast to the massive adoption of Agile in the software industry. Among other benefits, Agile methods promise faster delivery and better flexibility to address customer needs. Adopting Agile methods and practices are possible in aerospace because the DO-178C standard does not prescribe concrete software development methods. In spite of that, Agile development is not used in DO-178C contexts. To help change that, our research aims to understand whether and how organizations engineering safety-critical software systems for aerospace may benefit from Agile methods and practices. We analyzed the DO-178C standard and confirm that it is compatible with Agile methods. Then, we present a systematic literature mapping of adopting Agile in software development for aerospace, where we identified significant concerns, recurrent issues, and several challenges. Some real industry aerospace projects provided us with important data and the perspective of domain experts about the pros and cons of Agile methods in this context. We conclude by proposing an agenda of research opportunities to improve safety-critical software development towards agility that we consider worthy of further research, application and confirmation in wider contexts.

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Reading, adapting, and maintaining complex software can be a daunting task. We might need to refactor it to streamline the process and make the code cleaner and self-explanatory. Traditional refactoring tools guide developers to achieve better-quality code. However, the feedback and assistance they provide can take considerable time. To tackle this issue, we explored the concept of Live Refactoring. This approach focuses on delivering real-time, visually-driven refactoring suggestions. That way, we prototyped a Live Refactoring Environment that visually identifies, recommends, and applies several refactorings in real-time. To validate its effectiveness, we conducted a set of experiments. Those showed that our approach significantly improved various code quality metrics and outperformed the results obtained from manually refactoring code. © 2024 IEEE Computer Society. All rights reserved.