The Evolution of the Linux Build System

Software evolution entails more than just redesigning and reimplementing functionality of, fixing bugs in, or adding new features to source code. These evolutionary forces induce similar changes on the software's build system too, with far-reaching consequences on both overall developer productivity as well as software configurability. In this paper we take a look at this phenomenon in the Linux kernel from its inception up until present day. We do this by analysing the kernel's build traces with MAKAO, our re(verse)-engineering framework for build systems. This helps us in detecting interesting idioms and patterns in the dynamic build behaviour. Finding a good balance between obtaining a fast, correct build system and migrating in a stepwise fashion turns out to be the general theme throughout the evolution of the Linux build system

Ant Build Maintenance with Formiga

A build system produces a set of deliverables from a software project\u27s source code and resources. Build maintenance refers to the changes made to the build system as a software project evolves over time. It has been shown to impose a significant overhead on overall development costs, in part because changes to source code often require parallel changes in the build system. However, little tool support exists to assist developers with build maintenance, particularly for those changes that must accompany changes to the source code. Formiga is a build maintenance and dependency discovery tool for the Ant build system. Formiga\u27s primary uses are to automate build changes as the source code is updated, to identify the build dependencies within a software project, and to assist with build refactoring. Formiga is implemented as an IDE plugin, which allows it to recognize when project resources are updated and automatically update the build system accordingly. This implementation also allows it to leverage existing metaphors used by developers to maintain source code, thus making it easier to use. A controlled experiment was conducted to assess Formiga\u27s ability to assist developers with build maintenance. Formiga was shown to signficantly reduce the time required to perform build maintenance while increasing the correctness with which it can be performed

Experiences with workflows for automating data-intensive bioinformatics

High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.Pubblicat