{"id":19492007,"url":"https://github.com/neelsoumya/dsmiscellaneous","last_synced_at":"2026-07-23T09:30:20.684Z","repository":{"id":118678602,"uuid":"435962360","full_name":"neelsoumya/dsMiscellaneous","owner":"neelsoumya","description":"Miscellaneous tools for use in 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dsMiscellaneous\n\n[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)\n\n## Introduction\n\n`dsMiscellaneous` is a set of miscellaneous development tools and beginner's resources for use in DataSHIELD. \n\nDataSHIELD is a platform for privacy preserving federated analysis.\n\nhttps://github.com/datashield\n\n\n## Files\n\n`installer_unix.sh`  Installer in UNIX (shell script)\n\n`installation_steps_workflow.md` Installation steps for DataSHIELD\n\n`datashield_installer_basic.R` R installation script to install R packages for DataSHIELD\n\n`baby_steps.R` First coding project in DataSHIELD\n\n`ds.retStr.R` First client side script to learn coding in DataSHIELD\n\t     \n\t     https://github.com/neelsoumya/dsBaseClient/blob/test_functions_branch/R/ds.retStr.R\n\n`retStrDS.R` First server side script to learn coding in DataSHIELD\n\t     \n\t     https://github.com/neelsoumya/dsBase/blob/test_functions_branch/R/retStrDS.R\n\n`testthat.R` Simple R script for using testthat for unit testing\n\n`teaching_resources.md` Teaching resources using DataSHIELD\n\n`opal_instructions.txt` Instructions for setting up and using Opal server (data warehouse)\n\n\n## Installation\n\nDownload and install VirtualBox\n\n   * https://www.virtualbox.org/wiki/Downloads \n\nInstall Ubuntu (in Virtual Box if necessary)\n\n   * https://ubuntu.com/download/desktop\n\n\n\nClone the repository\n\n```r\ngit clone https://github.com/neelsoumya/dsMiscellaneous\n\ncd dsMiscellaneous\n\n```\n\nRun `installer_unix.sh`\n\n```r\nchmod 7555 installer_unix.sh\n\n./installer_unix.sh\n\n```\n\nRun the following from the terminal\n\n```r\n\nR --no-save \u003c datashield_installer_basic.R\n\n```\n\nor type R at the terminal and at the R command prompt type the following\n\n```r\n\ninstall.packages('devtools')\nlibrary(devtools)\n\ndevtools::install_github('neelsoumya/dsMiscellaneous')\n\n```\n\nStart RStudio Server by typing the following command at the Terminal\n\n```r\nrstudio-server start\n```\n\n\nGo to Firefox, and type localhost:8787 to go to R Studio server\n\n\n\nDownload and install the development Virtual Machine in Virtual Box\n\n   * https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1658093595/RStudio+Server+based+Development+VM\n    \nDocker for DataSHIELD\n\n* https://wilmarigl.de/?p=424\n\n\n## Usage\n\n\nFrom the Terminal run the following command\n\n```r\n\nR --no-save \u003c baby_steps.R\n\n```\n\nor in R Studio open and run the file `baby_steps.R`\n\n\n\n## Instructions for using DataSHIELD as a developer\n\n\n* opal_instructions.txt\n\n\t* instructions for uploading data dictionary, data and creating tables in Opal server\n\n\t* Opal javascript code\n\t\n\t\t https://opaldoc.obiba.org/en/latest/magma-user-guide/value/value.html\n\t\n\n* Other resources about DataSHIELD and Opal\n\n     * Opal\n\n                 https://opaldoc.obiba.org/en/latest/cookbook/index.html\n\n\t* Installation of virtual machines and DataSHIELD\n\t\n\t         https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/931069953/Installation+Training+Hub-+DataSHIELD+v6\n\n\n    * Virtual Box VM download\n\n              https://www.virtualbox.org/wiki/Downloads \n\n    * Ubuntu ISO image\n\n              https://ubuntu.com/download/desktop\n\n    * Installation of development VM\n\n              https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1658093595/RStudio+Server+based+Development+VM\n\n\t* Installation for development environment\n\t\n\t\t https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/12943461/Getting+started\n\t\t\n\t* Testing and development\n\t\n\t\t https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/735314034/Writing+some+tests\n\t\t\n\t* Git tips and tricks\n\t\n\t\t https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/1006633032/GitHub+Bring+edits+from+another+repository+to+your+own\n\t\t\n\t* Developer tips and tricks\n\t\n\t\t https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/702218241/Developer+Tricks+and+Tips\n\t\t\n        \t https://isglobal-brge.github.io/resource_bookdown/package-info.html#example-of-datashield-package-development\n\t\t\n\t* Setting up Opal server and loading data\n\t\n\t\t https://gitlab.inesctec.pt/wp4-recap/wp4_workshop/-/wikis/opal\n\t\n\t* Creating your own VM (Virtual Machine)\n\n                 https://data2knowledge.atlassian.net/wiki/spaces/DSDEV/pages/367656962/Vagrant \n\t\n\t* DataSHIELD repository\n\t\n\t\t https://github.com/datashield\t\n\n                 https://opaldoc.obiba.org/en/latest/cookbook/index.html\n\t\n\n\t* Demo servers\n\t\n\t\t https://opal-demo.obiba.org/\n\n\t\t username: administrator    password: password\t\n\n\t\t https://datashield-demo.obiba.org/\n\n\n## Acknowledgements\n\nWe acknowledge the help and support of the DataSHIELD technical team. We are especially grateful to Tom RP Bishop, Elaine Smith, Eleanor Hyde, Stuart Wheater, Yannick Marcon, Paul Burton, Demetris Avraam, Patricia Ryser-Welch, Kevin Rue-Albrecht and Wolfgang Viechtbauer for fruitful discussions and feedback.\n\n## Contact\n\nSoumya Banerjee\n\nsb2333@cam.ac.uk\n\n\n## Citation\n\nIf you find this helpful, please cite the following DOI\n\n10.5281/zenodo.5772830\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5772831.svg)](https://doi.org/10.5281/zenodo.5772831)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneelsoumya%2Fdsmiscellaneous","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneelsoumya%2Fdsmiscellaneous","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneelsoumya%2Fdsmiscellaneous/lists"}