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IEEE Trans Biomed Eng. 2016 Oct;63(10):2021-35. doi: 10.1109/TBME.2016.2539602. Epub 2016 Mar 8.

Reproducibility in Computational Neuroscience Models and Simulations.

Abstract

OBJECTIVE:

Like all scientific research, computational neuroscience research must be reproducible. Big data science, including simulation research, cannot depend exclusively on journal articles as the method to provide the sharing and transparency required for reproducibility.

METHODS:

Ensuring model reproducibility requires the use of multiple standard software practices and tools, including version control, strong commenting and documentation, and code modularity.

RESULTS:

Building on these standard practices, model-sharing sites and tools have been developed that fit into several categories: 1) standardized neural simulators; 2) shared computational resources; 3) declarative model descriptors, ontologies, and standardized annotations; and 4) model-sharing repositories and sharing standards.

CONCLUSION:

A number of complementary innovations have been proposed to enhance sharing, transparency, and reproducibility. The individual user can be encouraged to make use of version control, commenting, documentation, and modularity in development of models. The community can help by requiring model sharing as a condition of publication and funding.

SIGNIFICANCE:

Model management will become increasingly important as multiscale models become larger, more detailed, and correspondingly more difficult to manage by any single investigator or single laboratory. Additional big data management complexity will come as the models become more useful in interpreting experiments, thus increasing the need to ensure clear alignment between modeling data, both parameters and results, and experiment.

PMID:
27046845
PMCID:
PMC5016202
DOI:
10.1109/TBME.2016.2539602
[Indexed for MEDLINE]
Free PMC Article

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