Reproducible Research Platform RStudio Player Bundle

RRP RStudio Reproducible Research Platform (RRP) project including the RStudio IDE for lab record keeping including analysis and report generation with R. Overview This RRP project repository demonstrates how to work with R-Studio and R Markdown on RRP for keeping lab records in a computational notebook and analyse data (subset taken from [1]) stored in a research data management system (RDMS) to finally generate reports. The report and figures are stored in the results folder of RRP. This special folder can be used to register relevant outputs to the RDMS and demonstrates the round trip to make important results FAIR. The main outcome of this example is: Example a lab notebook with R. Usage of RStudio and R Markdwon for analysis and report generation Features Integration with RRP and openBIS ELN-LIMS: Mounts data from the RDMS openBIS in RRP for direct use in RStudio. RStudio: Keeping user habits allowing to work with a familiar IDE. Installation Prerequisites Local Docker installation. Steps Download and extract the .zip file Run the play script for your operating system Linux / macOS: play Windows: play.bat or play.ps1 Usage Workflow Overview Lab record keeping: Double click on the file lab_notebook.ipynb to open a Jupyter Notebook with R as the Kernel allowing to use R directly in the notebook or Markdwon otherwise to document the process. Analysis and report writing: In the Launcher RStudio can be opened in a new tab and the file report.Rmd be opened. Here we document an experiment and perform analysis of the data mounted in openbis/data. Results generation: Using Knit (in RStudio) the whole report can be compiled in a single pdf which is saved under results among other outputs such as figures. Directory Structure ├── .binder/ # Environment specifications, R version, packages etc. ├── .rrp/ # Specification of openBIS server and required data from RDMS openBIS ELN-LIMS (e.g. data) ├── LICENSE # License ├── README.md # This file ├── lab_notebook.ipynb # Example lab notebook ├── NOTICE # License details ├── references.bib # Reference file for bibtext └── report.Rmd # Analysis and report Contributing We welcome contributions to improve this repository! Please follow these steps: Fork the repository. Create a new branch for your feature or bug fix. Submit a pull request with a clear description of your changes. Authors and acknowledgment Andreas P. Cuny, ETH Zurich initial implementation License This project is licensed under the Apache 2.0 License. See LICENSE file for details. Copyright © 2020-2025 ETH Zurich, Andreas P. Cuny, D-BSSE, CSB Group References Schmidt, G. W., Cuny, A. P. & Rudolf, F. Preventing photomorbidity in long-term multi-color fluorescence imaging of saccharomyces cerevisiae and S. Pombe. G3 Genes, Genomes, Genet. 10, 4373–4385 (2020).