Related papers: Facilitating Bioinformatics Reproducibility
With the proliferation of simple and complex bioinformatics tools, there is the need to teach researchers how to use these tools effectively. To evaluate the potential of cognitive tutoring in the wide-scale adoption of several…
Over the recent years the importance of numerical experiments has gradually been more recognized. Nonetheless, sufficient documentation of how computational results have been obtained is often not available. Especially in the scientific…
In this work we introduce repro_eval - a tool for reactive reproducibility studies of system-oriented information retrieval (IR) experiments. The corresponding Python package provides IR researchers with measures for different levels of…
Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing. This is despite the fact that the Windows is the most popular operating system used among life…
Reproducibility is inseparable from transparency, as sharing data, code and computational environment is a pre-requisite for being able to retrace the steps of producing the research results. Others have made the case that this artifact…
The reproducibility of scientific experiment is vital for the advancement of disciplines based on previous work. To achieve this goal, many researchers focus on complex methodology and self-invented tools which have difficulty in practical…
Reproducibility, the ability to recompute results, and replicability, the chances other experimenters will achieve a consistent result, are two foundational characteristics of successful scientific research. Consistent findings from…
Computational notebooks have gained widespread adoption among researchers from academia and industry as they support reproducible science. These notebooks allow users to combine code, text, and visualizations for easy sharing of experiments…
Online artificial intelligence (AI) algorithms are an important component of digital health interventions. These online algorithms are designed to continually learn and improve their performance as streaming data is collected on…
In this paper, we reproduce the experimental results presented in our previous work titled "Making Users Indistinguishable: Attribute-wise Unlearning in Recommender Systems," which was published in the proceedings of the 31st ACM…
Replication of scientific experiments is critical to the advance of science. Unfortunately, the discipline of Computer Science has never treated replication seriously, even though computers are very good at doing the same thing over and…
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…
Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of…
Crowdsourcing is a multidisciplinary research area including disciplines like artificial intelligence, human-computer interaction, database, and social science. To facilitate cooperation across disciplines, reproducibility is a crucial…
Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the "uncertainty" of a solution; that is, the probability of the solution…
In year 2006 Bio-Linux with the work of Tim Booth and team gives its rising and provide an operating system that was and still specialized in providing a bioinformatic specific software environment for the working needs in this corner of…
Provenance templates are now a recognised methodology for the construction of data provenance records. Each template defines the provenance of a domain-specific action in abstract form, which may then be instantiated as required by a single…
Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However,…
Increased reproducibility of machine learning research has been a driving force for dramatic improvements in learning performances. The scientific community further fosters this effort by including reproducibility ratings in reviewer forms…
The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…