An empirical study evaluating depth of inheritance on the maintainability of object-oriented software

This empirical research was undertaken as part of a multi-method programme of research to investigate unsupported claims made of object-oriented technology. A series of subject-based laboratory experiments, including an internal replication, tested the effect of inheritance depth on the maintainability of object-oriented software. Subjects were timed performing identical maintenance tasks on object-oriented software with a hierarchy of three levels of inheritance depth and equivalent object-based software with no inheritance. This was then replicated with more experienced subjects. In a second experiment of similar design, subjects were timed performing identical maintenance tasks on object-oriented software with a hierarchy of five levels of inheritance depth and the equivalent object-based software. The collected data showed that subjects maintaining object-oriented software with three levels of inheritance depth performed the maintenance tasks significantly quicker than those maintaining equivalent object-based software with no inheritance. In contrast, subjects maintaining the object-oriented software with five levels of inheritance depth took longer, on average, than the subjects maintaining the equivalent object-based software (although statistical significance was not obtained). Subjects' source code solutions and debriefing questionnaires provided some evidence suggesting subjects began to experience diffculties with the deeper inheritance hierarchy. It is not at all obvious that object-oriented software is going to be more maintainable in the long run. These findings are sufficiently important that attempts to verify the results should be made by independent researchers

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

Automated Fixing of Programs with Contracts

This paper describes AutoFix, an automatic debugging technique that can fix faults in general-purpose software. To provide high-quality fix suggestions and to enable automation of the whole debugging process, AutoFix relies on the presence of simple specification elements in the form of contracts (such as pre- and postconditions). Using contracts enhances the precision of dynamic analysis techniques for fault detection and localization, and for validating fixes. The only required user input to the AutoFix supporting tool is then a faulty program annotated with contracts; the tool produces a collection of validated fixes for the fault ranked according to an estimate of their suitability. In an extensive experimental evaluation, we applied AutoFix to over 200 faults in four code bases of different maturity and quality (of implementation and of contracts). AutoFix successfully fixed 42% of the faults, producing, in the majority of cases, corrections of quality comparable to those competent programmers would write; the used computational resources were modest, with an average time per fix below 20 minutes on commodity hardware. These figures compare favorably to the state of the art in automated program fixing, and demonstrate that the AutoFix approach is successfully applicable to reduce the debugging burden in real-world scenarios.Comment: Minor changes after proofreadin