Related papers: A how-to guide for code-sharing in biology
Small to medium-scale data science experiments often rely on research software developed ad-hoc by individual scientists or small teams. Often there is no time to make the research software fast, reusable, and open access. The consequence…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
The scientific world is becoming more open to the public and fellow researchers. Open access publishing is becoming accepted, even if some publishers are resisting. The next step is the open code and data paradigm, which was briefly…
Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific…
This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing reproducibility and the avoidance of pitfalls. It details practical applications from website management using…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
This paper deals with the importance of developing codes of conduct for practitioners--be it journalists, doctors, attorneys, or other professions--that are encountering ethical issues when using computation, but do not have access to any…
In 2022, the Journal of Statistics and Data Science Education (JSDSE) instituted augmented requirements for authors to post deidentified data and code underlying their papers. These changes were prompted by an increased focus on…
The debate on data access and privacy is an ongoing one. It is kept alive by the never-ending changes/upgrades in (i) the shape of the data collected (in terms of size, diversity, sensitivity and quality), (ii) the laws governing data…
Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results,…
How should software engineering be adapted for Computational Science (CS)? If we understood that, then we could better support software sustainability, verifiability, reproducibility, comprehension, and usability for CS community. For…
Scientists spend an increasing amount of time building and using software. However, most scientists are never taught how to do this efficiently. As a result, many are unaware of tools and practices that would allow them to write more…
Computational scientists are facing a new era where the old ways of developing and reusing code have to be left behind and a few daring steps are to be made towards new horizons. The present work analyzes the needs that drive this change,…
Clinical coding is crucial for healthcare billing and data analysis. Manual clinical coding is labour-intensive and error-prone, which has motivated research towards full automation of the process. However, our analysis, based on US English…
In recent years, funding agencies and journals increasingly advocate for open science practices (e.g. data and method sharing) to improve the transparency, access, and reproducibility of science. However, quantifying these practices at…
The high incidence of irreproducible research has led to urgent appeals for transparency and equitable practices in open science. For the scientific disciplines that rely on computationally intensive analyses of large data sets, a granular…
Open-sourcing research publications is a key enabler for the reproducibility of studies and the collective scientific progress of a research community. As all fields of science develop more advanced algorithms, we become more dependent on…
Much of scientific progress now hinges on the reliability, falsifiability and reproducibility of computer source codes. Astrophysics in particular is a discipline that today leads other sciences in making useful scientific components freely…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…