Related papers: $\texttt{Davos}$: a Python "smuggler" for construc…
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…
Using computational notebooks (e.g., Jupyter Notebook), data scientists rationalize their exploratory data analysis (EDA) based on their prior experience and external knowledge such as online examples. For novices or data scientists who…
Large language models (LLMs) have become a dominant and important tool for NLP researchers in a wide range of tasks. Today, many researchers use LLMs in synthetic data generation, task evaluation, fine-tuning, distillation, and other…
Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a…
In this paper, we describe DiOS, a lightweight model operating system which can be used to execute programs that make use of POSIX APIs. Such executions are fully reproducible: running the same program with the same inputs twice will result…
The traditional foundation of science lies on the cornerstones of theory and experiment. Theory is used to explain experiment, which in turn guides the development of theory. Since the advent of computers and the development of…
Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…
The Collaborative Analysis Versioning Environment System (CAVES) project concentrates on the interactions between users performing data and/or computing intensive analyses on large data sets, as encountered in many contemporary scientific…
Leadership computing facilities around the world support cutting-edge scientific research across a broad spectrum of disciplines including understanding climate change, combating opioid addiction, or simulating the decay of a neutron. While…
We present an algorithm and package, Redistributor, which forces a collection of scalar samples to follow a desired distribution. When given independent and identically distributed samples of some random variable $S$ and the continuous…
Scientists rely on simulations to study natural phenomena. Trusting the simulation results is vital to develop sciences in any field. One approach to build trust is to ensure the reproducibility and traceability of the simulations through…
Reproducibility is an ideal that no researcher would dispute "in the abstract", but when aspirations meet the cold hard reality of the academic grind, reproducibility often "loses out". In this essay, I share some personal experiences…
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software…
Science has a data management problem, as well as a project management problem. While industrial-grade data science teams have embraced the agile mindset, and adopted or created all kind of tools to create reproducible workflows,…
In this paper, we detail the integration of Python data analysis into a first-year physics laboratory course, a task accomplished without significant alterations to the existing course structure. We introduced tailored laboratory…
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…
Although it is possible to increase confidence in Free and Open Source Software (FOSS) by reviewing its source code, trusting code is not the same as trusting its executable counterparts. These are typically built and distributed by…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
With the recognized crisis of credibility in scientific research, there is a growth of reproducibility studies in computer science, and although existing surveys have reviewed reproducibility from various perspectives, especially very…
The work presented in this thesis seeks to improve programmer productivity in the following ways: - by reducing the amount of code that has to be written to construct an application; - by increasing the reliability of the code written; and…