Related papers: A how-to guide for code-sharing in biology
Fashion recommendation is a key research field in computational fashion research and has attracted considerable interest in the computer vision, multimedia, and information retrieval communities in recent years. Due to the great demand for…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research…
Co-authorship in publications within a discipline uncovers interesting properties of the analysed field. We represent collaboration in academic papers of computer science in terms of differently grained networks, including those…
Should one teach coding in a required introductory statistics and data science class for non-major students? Many professors advise against it, considering it a distraction from the important and challenging statistical topics that need to…
``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…
Computational reproducibility, the possibility for independent researchers to exactly reproduce published empirical results, is fundamental to science. Despite its importance, the proportion of research articles aiming for reproducibility…
In contrast to many other scientific disciplines, computer science considers conference publications. Conferences have the advantage of providing fast publication of papers and of bringing researchers together to present and discuss the…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
In the emerging era of big data, larger available clinical datasets and computational advances have sparked a massive interest in machine learning-based approaches. The number of manuscripts related to machine learning or artificial…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
Neurophysiology research has demonstrated that it is possible and valuable to investigate sensory processing in scenarios involving continuous sensory streams, such as speech and music. Over the past 10 years or so, novel analytic…
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
Computational physics increasingly depends on large simulation datasets generated by software that remains under active development for many years. In such settings, reproducibility requires not only well documented data but also explicit…
Insufficient performance of optimization approaches for fitting of mathematical models is still a major bottleneck in systems biology. In this manuscript, the reasons and methodological challenges are summarized as well as their impact in…
As the bioinformatics field grows, it must keep pace not only with new data but with new algorithms. Here we contribute a thorough analysis of 13 state-of-the-art, commonly used machine learning algorithms on a set of 165 publicly available…
This document captures the discussion and deliberation of the FAIR for Research Software (FAIR4RS) subgroup that took a fresh look at the applicability of the FAIR Guiding Principles for scientific data management and stewardship for…
Contemporary debates on "open science" mostly focus on the pub- lic accessibility of the products of scientific and academic work. In contrast, this paper presents arguments for "opening" the ongoing work of science. That is, this paper is…
Emerging data-driven scientific workflows are seeking to leverage distributed data sources to understand end-to-end phenomena, drive experimentation, and facilitate important decision-making. Despite the exponential growth of available…