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In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the…
This paper presents an open-source, lightweight, yet comprehensive software framework, named RPC, which integrates physics-based simulators, planning and control libraries, debugging tools, and a user-friendly operator interface. RPC…
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…
The file system provides the mechanism for online storage and access to file contents, including data and programs. This paper covers the high-level details of file systems, as well as related topics such as the disk cache, the file system…
Black box systems for automated decision making, often based on machine learning over (big) data, map a user's features into a class or a score without exposing the reasons why. This is problematic not only for lack of transparency, but…
Our society is digital: industry, science, governance, and individuals depend, often transparently, on the inter-operation of large numbers of distributed computer systems. Although the society takes them almost for granted, these computer…
Scientific inference is often undermined by the vast but rarely explored "multiverse" of defensible modelling choices, which can generate results as variable as the phenomena under study. We introduce RobustiPy, an open-source Python…
Computational micromagnetics has become an essential tool in academia and industry to support fundamental research and the design and development of devices. Consequently, computational micromagnetics is widely used in the community, and…
Nature is often used to inspire solutions for complex engineering problems, but achieving its full potential is challenging due to difficulties in discovering relevant analogies and synthesizing from them. Here, we present an end-to-end…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
Human routines structure daily life, yet remain challenging for computational systems to understand. This paper presents the first systematic review of routine computing, a previously implicit but increasingly recognized field that focuses…
The cutting edge of applying AI to science is the closed-loop automation of scientific research: robot scientists. We have previously developed two robot scientists: `Adam' (for yeast functional biology), and `Eve' (for early-stage drug…
Interactivity, experimenting and performing laboratory practicals contribute much to the efficiency of natural science and engineering education. Computers represent a natural element for today's students, thus the use of computers in…
In the last decades, great achievements have been made in the development of computing machines. However, due to exponential growth of transistor density and in particular due to tremendously increasing power consumption, researchers expect…
The scientific process is a means to turn the results of experiments into knowledge about the world in which we live. Much research effort has been directed toward automating this process. To do this, one needs to formulate the scientific…
High Performance Computing (HPC) is a highly demanded discipline in companies and institutions. However, as students and also afterwards as professors, we observed a lack of HPC related content in the engineering degrees at our university,…
Artificial intelligence (AI) has recently seen transformative breakthroughs in the life sciences, expanding possibilities for researchers to interpret biological information at an unprecedented capacity, with novel applications and advances…
In recent years, the research community, but also the general public, has raised serious questions about the reproducibility and replicability of scientific work. Since many studies include some kind of computational work, these issues are…
The reproducibility crisis in scientific computing constrains robotics research. Existing studies reveal that up to 70% of robotics algorithms cannot be reproduced by independent teams, while many others fail to reach deployment because…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…