Related papers: A how-to guide for code-sharing in biology
At the frontier of most areas in science, computer simulations play a central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and…
Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…
Progress is being made in code discoverability and preservation, but as discussed at ADASS XXI, many codes still remain hidden from public view. With the Astrophysics Source Code Library (ASCL) now indexed by the SAO/NASA Astrophysics Data…
Learning to code, and more broadly, learning about computer science is a growing field of activity and research. Under the label of computational thinking, computational concepts are increasingly used as cognitive tools in many subject…
Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a…
An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to…
Scientific software registries and repositories serve various roles in their respective disciplines. These resources improve software discoverability and research transparency, provide information for software citations, and foster…
Computer vision can accelerate ecology research by automating the analysis of raw imagery from sensors like camera traps, drones, and satellites. However, computer vision is an emerging discipline that is rarely taught to ecologists. This…
Probabilistic biological network growth models have been utilized for many tasks including but not limited to capturing mechanism and dynamics of biological growth activities, null model representation, capturing anomalies, etc. Well-known…
Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years sustainable software development practices have made progress in being considered as an integral component of research.…
In the last few decades or so, we witness a paradigm shift in our nature studies - from a data-processing based computational approach to an information-processing based cognitive approach. The process is restricted and often misguided by…
Sharing artifacts -- such as trained models, pre-built indexes, and the code to use them -- aids in reproducibility efforts by allowing researchers to validate intermediate steps and improves the sustainability of research by allowing…
The application of new artificial intelligence (AI) discoveries is transforming healthcare research. However, the standards of reporting are variable in this still evolving field, leading to potential research waste. The aim of this work is…
Neuroscience is undergoing a period of rapid experimental progress and expansion. New mathematical tools, previously unknown in the neuroscience community, are now being used to tackle fundamental questions and analyze emerging data sets.…
We introduce seven foundational principles for creating a culture of constructive criticism in computational legal studies. Beginning by challenging the current perception of papers as the primary scholarly output, we call for a more…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Ensuring the reproducibility of scientific work is crucial as it allows the consistent verification of scientific claims and facilitates the advancement of knowledge by providing a reliable foundation for future research. However,…
Research methods are essential parts in conducting any research project. Although they have been theorized and summarized based on best practices, every field of science requires an adaptation of the overall approaches to perform research…
Science and technology journalists today face challenges in finding newsworthy leads due to increased workloads, reduced resources, and expanding scientific publishing ecosystems. Given this context, we explore computational methods to aid…
Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and…