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Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from execution of a…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
The number of studies focusing on onboarding in software organizations has increased significantly during the last years. However, current literature overlooks onboarding in Software Product Lines (SPLs). SPLs have been proven effective in…
Towards understanding the ecosystem gap of fixed-release Linux that is caused by the evolution of mirrors, we conducted a comprehensive study of the Debian ecosystem. This study involved the collection of Debian packages and the…
In the near future, autonomous space systems will compose many of the deployed spacecraft. Their tasks will involve autonomous rendezvous and proximity operations with large structures, such as inspections, assembly, and maintenance of…
Backpropagation is the default algorithm for training deep neural networks due to its simplicity, efficiency and high convergence rate. However, its requirements make it impossible to be implemented in a human brain. In recent years, more…
In the 1980s, high-performance computing (HPC) became another tool for research in the open (non-defense) science and engineering research communities. However, HPC came with a high price tag; the first Cray-2 machines, released in 1985,…
In software development there is a constant pressure to produce code faster and faster without compromising on quality. New tools supporting developers are created in response to this demand. Currently a new generation of such solutions is…
This paper presents Boomerang, an I/O system that integrates a legacy non-real-time OS with one that is customized for timing-sensitive tasks. A relatively small RTOS benefits from the pre-existing libraries, drivers and services of the…
Software is a great enabler for a number of projects that otherwise would be impossible to perform. Such projects include Space Exploration, Weather Modeling, Genome Projects, and many others. It is critical that software aiding these…
This work details a hardware-assisted approach for information flow tracking implemented on reconfigurable chips. Current solutions are either time-consuming or hardly portable (modifications of both sofware/hardware layers). This work…
Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or…
We introduce SciWING, an open-source software toolkit which provides access to pre-trained models for scientific document processing tasks, inclusive of citation string parsing and logical structure recovery. SciWING enables researchers to…
Identity-based software signing tools aim to make software artifact provenance verifiable while reducing the operational burden of long-lived key management. However, there is limited cross-tool longitudinal evidence about which usability…
Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…
Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication…