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bioRxiv · 10.1101/239947

Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines

Kulkarni, N.·Alessandri, L.·Panero, R.·Arigoni, M.·Olivero, M.·Cordero, F.·Beccuti, M.·Calogero, R. A.
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Abstract

BackgroundReproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and the operator. Therefore, a study can be considered reproducible only if all used data are available and the exploited computational analysis workflow is clearly described. However, today for reproducing a complex bioinformatics analysis, the raw data and a list of tools used in the workflow could be not enough to guarantee the reproducibility of the results obtained. Indeed, different releases of the same tools and/or of the system libraries (exploited by such tools) might lead to sneaky reproducibility issues.\n\nResultsTo address this challenge, we established the Reproducible Bioinformatics Project (RBP), which is a non-profit and open-source project, whose aim is to provide a schema and an infrastructure, based on docker images and R package, to provide reproducible results in Bioinformatics. One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository. Thus, a bioinformatician participating to the project has firstly to integrate her/his workflow modules into Docker image(s) exploiting an Ubuntu docker image developed ad hoc by RPB to make easier this task. Secondly, the workflow implementation must be realized in R according to an R-skeleton function made available by RPB to guarantee homogeneity and reusability among different RPB functions. Moreover she/he has to provide the R vignette explaining the package functionality together with an example dataset which can be used to improve the user confidence in the workflow utilization.\n\nConclusionsReproducible Bioinformatics Project provides a general schema and an infrastructure to distribute robust and reproducible workflows. Thus, it guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture.

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Kulkarni, N., Alessandri, L., Panero, R., Arigoni, M., Olivero, M., Cordero, F., Beccuti, M., Calogero, R. A.. 2017-12-26. Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines. https://doi.org/10.1101/239947

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