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Computational Workflows are widely used in data analysis, enabling innovation and decision-making. In many domains (bioinformatics, image analysis, & radio astronomy) the analysis components are numerous and written in multiple different…
Computational reproducibility refers to obtaining consistent results when rerunning an experiment. Jupyter Notebook, a web-based computational notebook application, facilitates running, publishing, and sharing computational experiments…
This paper introduces reproducible research, and explains its importance, benefits and challenges. Some important tools for conducting reproducible research in Transportation Research are also introduced. Moreover, the source code for…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
Software developers often submit questions to technical Q&A sites like Stack Overflow (SO) to resolve code-level problems. In practice, they include example code snippets with questions to explain the programming issues. Existing research…
This article is intended as a guide for new graduate students in the field of computational science. With the increasing influx of students from diverse backgrounds joining the ever-popular field, this short guide aims to help students…
With the advent of Open Science, researchers have started to publish their research artefacts (i. e., data, software, and other products of the investigations) in order to allow others to reproduce their investigations. While this…
Effective use of parallel and distributed computing in science depends upon multiple interdependent entities and activities that form an ecosystem. Active engagement between application users and technology catalysts is a crucial activity…
Objective: Reproducibility is a core tenet of scientific research. A reproducible study is one where the results can be recreated by different investigators in different circumstances using the same methodology and materials. Unfortunately,…
Software is now a vital scientific instrument, providing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the humanities. The software used in research is often home-grown and…
Even though computational reproducibility is widely accepted as necessary for research validation and reuse, it is often not considered during the research process. This is because reproducibility tools are typically stand-alone and require…
While extensive guidance exists for ensuring the reproducibility of one's own study, there is little discussion regarding the reproduction and replication of external studies within one's own research. To initiate this discussion, drawing…
The design of algorithms that generate personalized ranked item lists is a central topic of research in the field of recommender systems. In the past few years, in particular, approaches based on deep learning (neural) techniques have…
Containers are an emerging technology that hold promise for improving productivity and code portability in scientific computing. We examine Linux container technology for the distribution of a non-trivial scientific computing software stack…
This paper proposes a procedure to execute external source codes from a LaTeX document and include the calculation outputs in the resulting Portable Document Format (pdf) file automatically. It integrates programming tools into the LaTeX…
Many existing scientific workflows require High Performance Computing environments to produce results in a timely manner. These workflows have several software library components and use different environments, making the deployment and…
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…
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…
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.…