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Many science advances have been possible thanks to the use of research software, which has become essential to advancing virtually every Science, Technology, Engineering and Mathematics (STEM) discipline and many non-STEM disciplines…
Advancements in digital technologies have a bootstrapping effect. The past fifty years of technological innovations from the computer architecture community have brought innovations and orders-of-magnitude efficiency improvements that…
Most of the scientific software is developed in the same manner: It starts at a lab and the scientist says "This part of software is only for my private use". But the software grows and grows, and it comes the time, that other scientists…
For decades, the use of HPC systems was limited to those in the physical sciences who had mastered their domain in conjunction with a deep understanding of HPC architectures and algorithms. During these same decades, consumer computing…
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…
Software has eaten the world with many of the necessities and quality of life services people use requiring software. Therefore, tools that improve the software development experience can have a significant impact on the world such as…
ChatGPT, a recently developed product by openAI, is successfully leaving its mark as a multi-purpose natural language based chatbot. In this paper, we are more interested in analyzing its potential in the field of computational biology. A…
In the last few years it has been seen that many software vendors have started delivering projects incrementally with very short release cycles. Best examples of success of this approach has been Ubuntu Operating system that has a 6 months…
Despite the importance of scientific software for research, it is often not formally recognized and rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden,…
Scientific communities naturally tend to organize around data ecosystems created by the combination of their observational devices, their data repositories, and the workflows essential to carry their research from observation to discovery.…
The establishment of bioRxiv facilitated the rapid adoption of preprints in the life sciences, accelerating the dissemination of new research findings. However, the sheer volume of preprints published daily can be overwhelming, making it…
Process mining, i.e., a sub-field of data science focusing on the analysis of event data generated during the execution of (business) processes, has seen a tremendous change over the past two decades. Starting off in the early 2000's, with…
We present an open-source accessory for the NAO robot, which enables to test computationally demanding algorithms in an external platform while preserving robot's autonomy and mobility. The platform has the form of a backpack, which can be…
Scientific Workflow Systems such as Galaxy and Nextflow are essential for scalable, reproducible, and automated bioinformatics analyses. However, developing and understanding scientific workflows remains challenging for many domain…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
Increasing emphasis on data and quantitative methods in the biomedical sciences is making biological research more computational. Collecting, curating, processing, and analysing large genomic and imaging data sets poses major computational…
Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a…
In this paper, we discuss the need for an integrated software stack that unites artificial intelligence (AI) and modeling and simulation (ModSim) tools to advance scientific discovery. The authors advocate for a unified AI/ModSim software…
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…