Posts about reproducible paper (old posts, page 9)

Issues in Reproducible Simulation Research

In recent years, serious concerns have arisen about reproducibility in science. Estimates of the cost of irreproducible preclinical studies range from 28 billion USD per year in the USA alone (Freedman et al. in PLoS Biol 13(6):e1002165, 2015) to over 200 billion USD per year worldwide (Chalmers and Glasziou in Lancet 374:86–89, 2009). The situation in the social sciences is not very different: Reproducibility in psychological research, for example, has been estimated to be below 50% as well (Open Science Collaboration in Science 349:6251, 2015). Less well studied is the issue of reproducibility of simulation research. A few replication studies of agent-based models, however, suggest the problem for computational modeling may be more severe than for laboratory experiments (Willensky and Rand in JASSS 10(4):2, 2007; Donkin et al. in Environ Model Softw 92:142–151, 2017; Bajracharya and Duboz in: Proceedings of the symposium on theory of modeling and simulation—DEVS integrative M&S symposium, pp 6–11, 2013). In this perspective, we discuss problems of reproducibility in agent-based simulations of life and social science problems, drawing on best practices research in computer science and in wet-lab experiment design and execution to suggest some ways to improve simulation research practice.

Reproducibility study of a PDEVS model application to fire spreading

The results of a scientific experiment have to be reproduced to be valid. The scientific method is well known in experimental sciences but it is not always the case for computer scientists. Recent publications and studies has shown that there is a significant reproducibility crisis in Biology and Medicine. This problem has also been demonstrated for hundreds of publications in computer science where only a limited set of publication results could be reproduced. In this paper we present the reproducibility challenge and we examine the reproducibility of a Parallel Discrete Event System Specification (PDEVS) model with two different execution frameworks.

Simple changes of individual studies can improve the reproducibility of the biomedical scientific process as a whole

We developed a new probabilistic model to assess the impact of recommendations rectifying the reproducibility crisis (by publishing both positive and 'negative' results and increasing statistical power) on competing objectives, such as discovering causal relationships, avoiding publishing false positive results, and reducing resource consumption. In contrast to recent publications our model quantifies the impact of each single suggestion not only for an individual study but especially their relation and consequences for the overall scientific process. We can prove that higher-powered experiments can save resources in the overall research process without generating excess false positives. The better the quality of the pre-study information and its exploitation, the more likely this beneficial effect is to occur. Additionally, we quantify the adverse effects of both neglecting good practices in the design and conduct of hypotheses-based research, and the omission of the publication of 'negative' findings. Our contribution is a plea for adherence to or reinforcement of the good scientific practice and publication of 'negative' findings.

Editorial: Data repositories, registries, and standards in the search for valid and reproducible biomarkers

The paucity of major scientific breakthroughs leading to new or improved treatments, and the inability to identify valid and reproducible biomarkers that improve clinical management, has produced a crisis in confidence in the validity of our pathogenic theories and the reproducibility of our research findings. This crisis in turn has driven changes in standards for research methodologies and prompted calls for the creation of open‐access data repositories and the preregistration of research hypotheses. Although we should embrace the creation of repositories and registries, and the promise for greater statistical power, reproducibility, and generalizability of research findings they afford, we should also recognize that they alone are no substitute for sound design in minimizing study confounds, and they are no guarantor of faith in the validity of our pathogenic theories, findings, and biomarkers. One way, and maybe the only sure way, of knowing that we have a valid understanding of brain processes and disease mechanisms in human studies is by experimentally manipulating variables and predicting its effects on outcome measures and biomarkers.

Practical guidelines for rigor and reproducibility in preclinical and clinical studies on cardioprotection

We refer to the recent guidelines for experimental models of myocardial ischemia and infarction [279], and aim to provide now practical guidelines to ensure rigor and reproducibility in preclinical and clinical studies on cardioprotection. In line with the above guidelines [279], we define rigor as standardized state-of-the-art design, conduct and reporting of a study, which is then a prerequisite for reproducibility, i.e. replication of results by another laboratory when performing exactly the same experiment.

ReproServer: Making Reproducibility Easier and Less Intensive

Reproducibility in the computational sciences has been stymied because of the complex and rapidly changing computational environments in which modern research takes place. While many will espouse reproducibility as a value, the challenge of making it happen (both for themselves and testing the reproducibility of others' work) often outweigh the benefits. There have been a few reproducibility solutions designed and implemented by the community. In particular, the authors are contributors to ReproZip, a tool to enable computational reproducibility by tracing and bundling together research in the environment in which it takes place (e.g. one's computer or server). In this white paper, we introduce a tool for unpacking ReproZip bundles in the cloud, ReproServer. ReproServer takes an uploaded ReproZip bundle (.rpz file) or a link to a ReproZip bundle, and users can then unpack them in the cloud via their browser, allowing them to reproduce colleagues' work without having to install anything locally. This will help lower the barrier to reproducing others' work, which will aid reviewers in verifying the claims made in papers and reusing previously published research.