Posts about reproducible paper (old posts, page 6)

Study on automatic citation screening in systematic reviews: reporting, reproducibility and complexity

Research into text mining based tool support for citation screening in systematic reviews is growing. The field has not experienced much independent validation. It is anticipated that more transparency in studies will increase reproducibility and in-depth understanding leading to the maturation of the field. The citation screen tool presented aims to support research transparency, reproducibility and timely evolution of sustainable tools.

The battle for reproducibility over storytelling

This issue of Cortex plays host to a lively debate about the reliability of cognitive neuroscience research. Across seven Discussion Forum pieces, scientists representing a range of backgrounds and career levels reflect on whether the "reproducibility crisis" – or "credibility revolution" (Vazire, 2018; Munafò et al., 2017) – that has achieved such prominence in psychology has extended into cognitive neuroscience. If so, they ask, what is the underlying cause and how can we solve it?

Successes and struggles with computational reproducibility: Lessons from the Fragile Families Challenge

Reproducibility is fundamental to science, and an important component of reproducibility is computational reproducibility: the ability of a researcher to recreate the results in a published paper using the original author's raw data and code. Although most people agree that computational reproducibility is important, it is still difficult to achieve in practice. In this paper, we describe our approach to enabling computational reproducibility for the 12 papers in this special issue of Socius about the Fragile Families Challenge. Our approach draws on two tools commonly used by professional software engineers but not widely used by academic researchers: software containers (e.g., Docker) and cloud computing (e.g., Amazon Web Services). These tools enabled us to standardize the computing environment around each submission, which will ease computational reproducibility both today and in the future. Drawing on our successes and struggles, we conclude with recommendations to authors and journals.

Designing for Reproducibility: A Qualitative Study of Challenges and Opportunities in High Energy Physics

Reproducibility should be a cornerstone of scientific research and is a growing concern among the scientific community and the public. Understanding how to design services and tools that support documentation, preservation and sharing is required to maximize the positive impact of scientific research. We conducted a study of user attitudes towards systems that support data preservation in High Energy Physics, one of science's most data-intensive branches. We report on our interview study with 12 experimental physicists, studying requirements and opportunities in designing for research preservation and reproducibility. Our findings suggest that we need to design for motivation and benefits in order to stimulate contributions and to address the observed scalability challenge. Therefore, researchers' attitudes towards communication, uncertainty, collaboration and automation need to be reflected in design. Based on our findings, we present a systematic view of user needs and constraints that define the design space of systems supporting reproducible practices.

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

Web technology has transformed our lives, and has led to a paradigm shift in the computational sciences. As the neuroimaging informatics research community amasses large datasets to answer complex neuroscience questions, we find that the web is the best medium to facilitate novel insights by way of improved collaboration and communication. Here, we review the landscape of web technologies used in neuroimaging research, and discuss future applications, areas for improvement, and the limitations of using web technology in research. Fully incorporating web technology in our research lifecycle requires not only technical skill, but a widespread culture change; a shift from the small, focused "wet lab" to a multidisciplinary and largely collaborative "web lab."

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows

Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing. While there are good examples if the use of scientific workflows in bioinformatics, medical informatics, biomedical imaging and data analysis, there are fewer examples in multi-scale computational modeling in general and cardiac electrophysiology in particular. Cardiac electrophysiology simulation is a mature area of multi-scale computational biology that serves as an excellent use case for developing and testing new scientific workflows. In this article, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale cardiac cell and tissue model that is expandable, modular and portable. The workflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing. During all stages of the workflow design, we rely on freely available open-source tools, to make our workflow freely usable by scientists.