Posts about reproducible paper (old posts, page 14)

The Reproducibility Crisis and Academic Libraries

In recent years, evidence has emerged from disciplines ranging from biology to economics that many scientific studies are not reproducible. This evidence has led to declarations in both the scientific and lay press that science is experiencing a “reproducibility crisis” and that this crisis has significant impacts on both science and society, including misdirected effort, funding, and policy implemented on the basis of irreproducible research. In many cases, academic libraries are the natural organizations to lead efforts to implement recommendations from journals, funders, and societies to improve research reproducibility. In this editorial, we introduce the reproducibility crisis, define reproducibility and replicability, and then discusses how academic libraries can lead institutional support for reproducible research.

Scientific replication in the study of social animals

This chapter is written to help undergraduate students better understand the role of replication in psychology and how it applies to the study of social behavior. We briefly review various replication initiatives in psychology and the events that preceded our renewed focus on replication. We then discuss challenges in interpreting the low rate of replication in psychology, especially social psychology. Finally, we stress the need for better methods and theories to learn the right lessons when replications fail.

Utilising Semantic Web Ontologies To publish Experimental Workflows

Reproducibility in experiments is necessary to verify claims and to reuse prior work in experiments that advance research. However, the traditional model of publication validates research claims through peer-review without taking reproducibility into account. Workflows encapsulate experiment descriptions and components and are suitable for representing reproducibility. Additionally, they can be published alongside traditional patterns as a form of documentation for the experiment which can be combined with linked open data. For reproducibility utilising published datasets, it is necessary to declare the conditions or restrictions for permissible reuse. In this paper, we take a look at the state of workflow reproducibility through a browser based tool and a corresponding study to identify how workflows might be combined with traditional forms of documentation and publication. We also discuss the licensing aspects for data in workflows and how it can be annotated using linked open data ontologies.


This document reviews the stability of the main LHC operational parameters, namely orbit, tune, coupling and chromaticity. The analysis will be based on the LSA settings, measured parameters and real-time trims. The focus will be set on ramp and high energy reproducibility as they are more diflicult to assess and correct on a daily basis for certain parameters like chromaticity and coupling. The reproducibility of the machine in collision will be analysed in detail, in particular the beam offsets at the IPS since the ever decreasing beam sizes at the IPs make beam steering at the IP more and mode delicate.

A survey on provenance: What for? What form? What from?

Provenance refers to any information describing the production process of an end product, which can be anything from a piece of digital data to a physical object. While this survey focuses on the former type of end product, this definition still leaves room for many different interpretations of and approaches to provenance. These are typically motivated by different application domains for provenance (e.g., accountability, reproducibility, process debugging) and varying technical requirements such as runtime, scalability, or privacy. As a result, we observe a wide variety of provenance types and provenance-generating methods. This survey provides an overview of the research field of provenance, focusing on what provenance is used for (what for?), what types of provenance have been defined and captured for the different applications (what form?), and which resources and system requirements impact the choice of deploying a particular provenance solution (what from?). For each of these three key questions, we provide a classification and review the state of the art for each class. We conclude with a summary and possible future research challenges.

Jug: Software for parallel reproducible computation in Python

As computational pipelines become a bigger part of science, it is important to ensure that the results are reproducible, a concern which has come to the fore in recent years. All developed software should be able to be run automatically without any user intervention. In addition to being valuable to the wider community, which may wish to reproduce or extend a published analysis, reproducible research practices allow for better control over the project by the original authors themselves. For example, keeping a non-executable record of parameters and command line arguments leads to error-prone analysis and opens up the possibility that, when the results are to be written up for publication, the researcher will no longer be able to even completely describe the process that led to them. For large projects, the use of multiple computational cores (either in a multi-core machine or distributed across a compute cluster) is necessary to obtain results in a useful time frame. Furthermore, it is often the case that, as the project evolves, it becomes necessary to save intermediate results while down-stream analyses are designed (or redesigned) and implemented. Under many frameworks, this causes having a single point of entry for the computation becomes increasingly difficult. Jug is a software framework which addresses these issues by caching intermediate results and distributing the computational work as tasks across a network. Jug is written in Python without the use of compiled modules, is completely crossplatform, and available as free software under the liberal MIT license.