Teaching computational reproducibility for neuroimaging

We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MRI scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science

Learning from open source software projects to improve scientific review

Peer-reviewed publications are the primary mechanism for sharing scientific results. The current peer-review process is, however, fraught with many problems that undermine the pace, validity, and credibility of science. We highlight five salient problems: (1) reviewers are expected to have comprehensive expertise; (2) reviewers do not have sufficient access to methods and materials to evaluate a study; (3) reviewers are neither identified nor acknowledged; (4) there is no measure of the quality of a review; and (5) reviews take a lot of time, and once submitted cannot evolve. We propose that these problems can be resolved by making the following changes to the review process. Distributing reviews to many reviewers would allow each reviewer to focus on portions of the article that reflect the reviewer's specialty or area of interest and place less of a burden on any one reviewer. Providing reviewers materials and methods to perform comprehensive evaluation would facilitate transparency, greater scrutiny, and replication of results. Acknowledging reviewers makes it possible to quantitatively assess reviewer contributions, which could be used to establish the impact of the reviewer in the scientific community. Quantifying review quality could help establish the importance of individual reviews and reviewers as well as the submitted article. Finally, we recommend expediting post-publication reviews and allowing for the dialog to continue and flourish in a dynamic and interactive manner. We argue that these solutions can be implemented by adapting existing features from open-source software management and social networking technologies. We propose a model of an open, interactive review system that quantifies the significance of articles, the quality of reviews, and the reputation of reviewers

Can Fear Be Effectively Assessed in Swine? A Study Measuring Fear Levels during a Human Approach Test

This study evaluated the effect of experience and social companionship on the degree of fearfulness in pigs during a human approach test. Experience had no significant effect on fearfulness of pigs while social companionship significantly decreased number of vocalizations (156 (unpaired) vs. 54 sec (paired) P \u3c 0.05), latency to enter within 1 meter (97 (unpaired) vs. 50 sec (paired) P \u3c0.05), and 0.5 meter (133 (unpaired) vs. 70 sec (paired) P \u3c 0.05), as well as significantly increased number of contact bouts (5.7 (unpaired) vs. 7.75 (paired) P \u3c 0.05). These results suggest that experience with a novel environment and novel human will not necessarily decrease fear, but the social environment does play a large role in decreasing fearfulness in pigs. Producers can use the human approach test to evaluate levels of fear and implement positive management strategies to decrease fearfulness in the herd

Association of Vocalizations and Swine Behavior during a Human Approach Test

The objective of this study was to determine if the duration and total number of pig vocalizations when divided into low and high call categories was related to pig behaviors during a fear test. Twenty barrows and 20 gilts were tested over two consecutive weeks between 1300 and 1900 hours using a human approach test (HAT). Throughout the test, vocalizations and behavior were recorded. These results suggest that while high calls are typically the primary measure of stress vocalizations, low calls are also meaningful measures during the stressor of HAT