Dataset Information

Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions.

ABSTRACT: Scientific code is different from production software. Scientific code, by producing results that are then analyzed and interpreted, participates in the elaboration of scientific conclusions. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example, five characteristics that a scientific code in computational science should possess: re-runnable, repeatable, reproducible, reusable, and replicable. The code should be executable (re-runnable) and produce the same result more than once (repeatable); it should allow an investigator to reobtain the published results (reproducible) while being easy to use, understand and modify (reusable), and it should act as an available reference for any ambiguity in the algorithmic descriptions of the article (replicable).

SUBMITTER: Benureau FCY

PROVIDER: S-EPMC5758530 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Publications

Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions.

Benureau Fabien C Y FCY Rougier Nicolas P NP

Frontiers in neuroinformatics 20180104

Scientific code is different from production software. Scientific code, by producing results that are then analyzed and interpreted, participates in the elaboration of scientific conclusions. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example, five characteristics that a scientific code in computational science should possess: re-runnable, repeatable, reproducible, reusable, and replicable. The code should be executable (re-ru ...[more]

PMID: 29354046

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Project description:BACKGROUND:Falls are a common health problem, which in the worst cases can lead to death. To develop reliable fall detection algorithms as well as suitable prevention interventions, it is important to understand circumstances and characteristics of real-world fall events. Although falls are common, they are seldom observed, and reports are often biased. Wearable inertial sensors provide an objective approach to capture real-world fall signals. However, it is difficult to directly derive visualization and interpretation of body movements from the fall signals, and corresponding video data is rarely available. OBJECTIVE:The re-enactment method uses available information from inertial sensors to simulate fall events, replicate the data, validate the simulation, and thereby enable a more precise description of the fall event. The aim of this paper is to describe this method and demonstrate the validity of the re-enactment approach. METHODS:Real-world fall data, measured by inertial sensors attached to the lower back, were selected from the Fall Repository for the Design of Smart and Self-Adaptive Environments Prolonging Independent Living (FARSEEING) database. We focused on well-described fall events such as stumbling to be re-enacted under safe conditions in a laboratory setting. For the purposes of exemplification, we selected the acceleration signal of one fall event to establish a detailed simulation protocol based on identified postures and trunk movement sequences. The subsequent re-enactment experiments were recorded with comparable inertial sensor configurations as well as synchronized video cameras to analyze the movement behavior in detail. The re-enacted sensor signals were then compared with the real-world signals to adapt the protocol and repeat the re-enactment method if necessary. The similarity between the simulated and the real-world fall signals was analyzed with a dynamic time warping algorithm, which enables the comparison of two temporal sequences varying in speed and timing. RESULTS:A fall example from the FARSEEING database was used to show the feasibility of producing a similar sensor signal with the re-enactment method. Although fall events were heterogeneous concerning chronological sequence and curve progression, it was possible to reproduce a good approximation of the motion of a person's center of mass during fall events based on the available sensor information. CONCLUSIONS:Re-enactment is a promising method to understand and visualize the biomechanics of inertial sensor-recorded real-world falls when performed in a suitable setup, especially if video data is not available.

Dataset Information

Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions.

Publications

Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions.

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