Related papers: Reproducible Science with LaTeX
We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…
Retrieval systems for scholarly literature offer the ability for the scientific community to search, explore and download scholarly articles across various scientific disciplines. Mostly used by the experts in the particular field, these…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Across the social and medical sciences, researchers recognize that specifying planned research activities (i.e., 'registration') prior to the commencement of research has benefits for both the transparency and rigour of science. Despite…
This paper presents CodeRefine, a novel framework for automatically transforming research paper methodologies into functional code using Large Language Models (LLMs). Our multi-step approach first extracts and summarizes key text chunks…
The quality of scientific code is a critical concern for the research community. Poorly written code can result in irreproducible results, incorrect findings, and slower scientific progress. In this study, we evaluate scientific code…
The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of…
Large language models (LLMs) have been touted to enable increased productivity in many areas of today's work life. Scientific research as an area of work is no exception: the potential of LLM-based tools to assist in the daily work of…
With the emergence and rapid evolution of large language models (LLM), automating coding tasks has become an important research topic. Many efforts are underway and literature abounds about the efficacy of models and their ability to…
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how…
Scientific knowledge graphs have been proposed as a solution to structure the content of research publications in a machine-actionable way and enable more efficient, computer-assisted workflows for many research activities. Crowd-sourcing…
Large language models (LLMs) are being used in many applications and prompts for these models are integrated into software applications as code-like artifacts. These prompts behave much like traditional software in that they take inputs,…
LaTeX's precision and flexibility in typesetting have made it the gold standard for the preparation of scientific documentation. Large Language Models (LLMs) present a promising opportunity for researchers to produce publication-ready…
Expository documents are vital resources for conveying complex information to readers. Despite their usefulness, writing expository text by hand is a challenging process that requires careful content planning, obtaining facts from multiple…
Academic trade requires juggling multiple variants of the same content published in different formats: manuscripts, presentations, posters and computational notebooks. The need to track versions to accommodate for the…
This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda…
Reproducibility is widely acknowledged as a fundamental principle in scientific research. Currently, the scientific community grapples with numerous challenges associated with reproducibility, often referred to as the ''reproducibility…
Reconstructing numerical simulations from control systems research papers is often hindered by underspecified parameters and ambiguous implementation details. We define the task of Paper to Simulation Recoverability, the ability of an…
Adding citations while drafting in LaTeX often requires leaving the editor, searching for a paper in mind, copying its BibTeX entry into the project bibliography, renaming the cite key, and then returning to the sentence. \texttt{OverCite}…
As computer systems grow ever larger and more complex, a crucial task in software development is for one person (the system expert) to communicate to another (the system novice) how a certain program works. This paper reports on the…