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In the data science courses at the University of British Columbia, we define data science as the study, development and practice of reproducible and auditable processes to obtain insight from data. While reproducibility is core to our…
Should students be used as experimental subjects in software engineering? Given that students are in many cases readily available and cheap it is no surprise that the vast majority of controlled experiments in software engineering use them.…
The pursuit of creating artificial intelligence (AI) mirrors our longstanding fascination with understanding our own intelligence. From the myths of Talos to Aristotelian logic and Heron's inventions, we have sought to replicate the marvels…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
The aim of this review is to highlight the possibility to apply the mathematical formalism and methodology of quantum theory to model behaviour of complex biosystems, from genomes and proteins to animals, humans, ecological and social…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
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…
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…
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
We consider biological individuality in terms of information theoretic and graphical principles. Our purpose is to extract through an algorithmic decomposition system-environment boundaries supporting individuality. We infer or detect…
Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small datasets, and provide adaptive suggestions for sequential…
Reproducibility is a fundamental requirement of the scientific process since it enables outcomes to be replicated and verified. Computational scientific experiments can benefit from improved reproducibility for many reasons, including…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
The ubiquitous presence of computer simulations in all kinds of research areas evidence their role as the new driving force for the advancement of science and engineering research. Nothing seems to escape the image of success that computer…
Possible for science itself, conceptually, to have and will understand differently, let alone science also seen as technology, such as computer science. After all, science and technology are viewpoints diverse by either individual,…
A significant amount of high-impact contemporary scientific research occurs where biology, computer science, engineering and chemistry converge. Although programmes have been put in place to support such work, the complex dynamics of…
Simulation studies are computer experiments that involve creating data by pseudorandom sampling. The key strength of simulation studies is the ability to understand the behaviour of statistical methods because some 'truth' (usually some…
This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the…
The chapter supports educators and postgraduate students in understanding the role of simulation in software engineering research based on the authors' experience. This way, it includes a background positioning simulation-based studies in…
In a context where most published articles are devoted to the development of "new methods", comparison studies are generally appreciated by readers but surprisingly given poor consideration by many scientific journals. In connection with…