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Bashing irreproducibility with shournal.

ABSTRACT: Arguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the shell or suffer from a large overhead. Here, we present shournal, which integrates tightly into the shell and automatically records all shell commands along with their associated file events. Thus, for all files, it can later be told how they were generated and processed. Additionally, it allows the creation of detailed reports for whole project folders. shournal retrieves its data directly from the Linux kernel and allows the monitoring of whole process trees with low overhead.

SUBMITTER: Kirchner T

PROVIDER: S-EPMC10901821 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Bashing irreproducibility with shournal.

Kirchner Tycho T Riege Konstantin K Hoffmann Steve S

Scientific reports 20240228 1

Arguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the shell or suffer from a large overhead. Here, we present shournal, which integrates tightly into the shell and automatically records all shell commands along with their associated file events. Thus, for all fi ...[more]

PMID: 38418837

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Project description:BackgroundThe Centers for Disease Control and Prevention (CDC) bottle bioassay is a commonly used susceptibility test for measuring insect response to insecticide exposure. However, inconsistencies and high variability in insect response when conducting CDC bottle bioassays have been reported in previous publications. We hypothesized that the CDC bottle bioassay results may be compromised when expected and actual insecticide concentrations in the bottles are not equivalent and that inadequate bottle cleaning and/or loss during insecticide introduction and bottle storage steps could be responsible. We explored this hypothesis by quantifying insecticides using gas chromatography tandem mass spectrometry (GC-MS/MS) in bottles that had been cleaned, prepared, and stored according to the CDC guidelines.MethodsWe investigated the bottle cleaning, preparation, and storage methods outlined in the CDC bottle bioassay procedure to identify sources of irreproducibility. We also investigated the effectiveness of cleaning bottles by autoclaving because this method is commonly used in insecticide assessment laboratories. The two insecticides used in this study were chlorpyrifos and lambda-cyhalothrin (λ-cyhalothrin). Insecticides were removed from glass bioassay bottles by rinsing with ethyl-acetate and n-hexane and then quantified using GC-MS/MS.ResultsThe CDC bottle bioassay cleaning methods did not sufficiently remove both insecticides from the glass bottles. The cleaning methods removed chlorpyrifos, which has higher water solubility, more effectively than λ-cyhalothrin. Chlorpyrifos experienced significant loss during the bottle-coating process whereas λ-cyhalothrin did not. As for bottle storage, no significant decreases in insecticide concentrations were observed for 6 h following the initial drying period for either insecticide.ConclusionsThe CDC bottle bioassay protocol is susceptible to producing inaccurate results since its recommended bottle cleaning method is not sufficient and semi-volatile insecticides can volatilize from the bottle during the coating process. This can lead to the CDC bottle bioassay producing erroneous LC50 values. High levels of random variation were also observed in our experiments, as others have previously reported. We have outlined several steps that CDC bottle bioassay users could consider that would lead to improved accuracy and reproducibility when acquiring toxicity data.

Dataset Information

Bashing irreproducibility with shournal.

Publications

Bashing irreproducibility with shournal.

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