Related papers: Impacting the bioscience progress by backporting s…
In year 2006 Biolinux inter alia with the work of Tim Booth gives its rise and provide an operating system that was and is specialized in providing an environment for the needs of bioinformatics. Since than some years have been seen and the…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
As computer systems become more and more complex, software and tools lag more and more behind. This is especially true for scientific software that often demands high performance, and thus needs to take advantage of parallelisms, memory…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Open-source software is increasingly reused, complicating the process of patching to repair bugs. In the case of Linux, a distinct ecosystem has formed, with Linux mainline serving as the upstream, stable or long-term-support (LTS) systems…
Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing. This is despite the fact that the Windows is the most popular operating system used among life…
A timeline is presented which shows the stages involved in converting a bioinformatics software application from a set of standalone algorithms through to a simple web based tool then to a web based portal harnessing Grid technologies and…
Documentation is one of the most neglected activities in Software Engineering, although it is an important method of assuring quality and understanding. Bioinformatics software is generally written by researchers from fields other than…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
Innovation is slowing greatly in the pharmaceutical sector. It is considered here how part of the problem is due to overly limiting intellectual property relations in the sector. On the other hand, computing and software in particular are…
Contemporary bioinformatics has seen in profound new visibility into the composition, structure, and history of the natural world around us. Arguably, the central pillar of bioinformatics is phylogenetics -- the study of hereditary…
Scientific software projects evolve rapidly in their initial development phase, yet at the end of a funding period, the completion of a research project, thesis, or publication, further engagement in the project may slow down or cease…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
Real-time operating systems employ spatial and temporal isolation to guarantee predictability and schedulability of real-time systems on multi-core processors. Any unbounded and uncontrolled cross-core performance interference poses a…
Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
In the past decade, enormous progress has been made in advancing the state-of-the-art in bioimage analysis - a young computational field that works in close collaboration with the life sciences on the quantitative analysis of scientific…