Related papers: A how-to guide for code-sharing in biology
Data management, which encompasses activities and strategies related to the storage, organization, and description of data and other research materials, helps ensure the usability of datasets -- both for the original research team and for…
Computational intelligence is broadly defined as biologically-inspired computing. Usually, inspiration is drawn from neural systems. This article shows how to analyze neural systems using information theory to obtain constraints that help…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other…
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…
Science advances not only through the accumulation of facts but also through the evolution of tools. Crucially, tools are rarely used in isolation. They form tool portfolios, combinations shaped by a discipline's workflows and analytical…
In recent decades the analysis of data has become increasingly computational. Correspondingly, this has changed how scientific and statistical work is shared. For example, it is now commonplace for underlying analysis code and data to be…
Context: Writing Clean Code understandable by other collaborators has become crucial to enhancing collaboration and productivity. However, very little is known regarding whether developers agree with Clean Code Principles and how they apply…
Scientific discovery is mediated by ideas that, after being formulated in hypotheses, can be tested, validated, and quantified before they eventually lead to accepted concepts. Computer-mediated discovery in astrophysics is no exception,…
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several…
Living labs have been established across different countries to evaluate how the interaction between humans and buildings can be optimized to improve comfort, health, and energy savings. However, existing living labs can be too…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present…
Writing complex computer programs to study scientific problems requires careful planning and an in-depth knowledge of programming languages and tools. In this chapter the importance of using the right tool for the right problem is…
Over the past few years, we have seen fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. At the same time, the amount of data collected in a wide array of scientific domains…
This study analyzes rates and ways of data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on human ancient DNA published between 1988 and 2013. For the most part, data are available in…
Life science and statistics have necessarily become essential partners. The need to plan complex, structured experiments, involving elaborated designs, and the need to analyse datasets in the era of systems biology and high throughput…
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users…