[{"data":1,"prerenderedAt":719},["ShallowReactive",2],{"/en-us/blog/gitlab-and-reproducibility/":3,"navigation-en-us":36,"banner-en-us":465,"footer-en-us":482,"Vicky Steeves":692,"next-steps-en-us":704},{"_path":4,"_dir":5,"_draft":6,"_partial":6,"_locale":7,"seo":8,"content":16,"config":26,"_id":29,"_type":30,"title":31,"_source":32,"_file":33,"_stem":34,"_extension":35},"/en-us/blog/gitlab-and-reproducibility","blog",false,"",{"title":9,"description":10,"ogTitle":9,"ogDescription":10,"noIndex":6,"ogImage":11,"ogUrl":12,"ogSiteName":13,"ogType":14,"canonicalUrls":12,"schema":15},"How GitLab can help in research reproducibility","NYU reproducibility librarian Vicky Steeves shares why GitLab is her choice for ongoing collaborative research, and how it can help overcome challenges with sharing code in academia.","https://res.cloudinary.com/about-gitlab-com/image/upload/v1749672928/Blog/Hero%20Images/gitlab-and-reproducibility.jpg","https://about.gitlab.com/blog/gitlab-and-reproducibility","https://about.gitlab.com","article","\n                        {\n        \"@context\": \"https://schema.org\",\n        \"@type\": \"Article\",\n        \"headline\": \"How GitLab can help in research reproducibility\",\n        \"author\": [{\"@type\":\"Person\",\"name\":\"Vicky Steeves\"}],\n        \"datePublished\": \"2017-08-25\",\n      }",{"title":9,"description":10,"authors":17,"heroImage":11,"date":19,"body":20,"category":21,"tags":22},[18],"Vicky Steeves","2017-08-25","GitLab is a great platform for active, ongoing, collaborative research. It\nenables folks to work together easily and share that work in the open. This\nis especially poignant given the problems in sharing code in academia,\nacross time and people.\n\n\n\u003C!-- more -->\n\n\n![phd-code-comic](https://phdcomics.com/comics/archive/phd031214s.gif)\n\n\nIt's no surprise that GitLab, a platform for collaborative coding and Git\nrepository hosting, has features for reproducibility that researchers can\nleverage for their own and their communities’ benefit.\n\n\n### What exactly is reproducibility?\n\n\nReproducibility is a core component in a variety of work, from software\nengineering to research. For software engineers, the ability to reproduce\nerrors or functionality is key to development. For researchers,\nreproducibility is about independent verification of results/methods, to\nbuild on top of previous work, and to increase the impact, visibility, and\nquality of research. Y’know. That Sir Isaac Newton quote in every\nreproducibility presentation ever: \"If I have seen further, it is by\nstanding on the shoulders of giants.\"\n\n\nLike all things, reproducibility exists on a spectrum. I like Stodden et\nal’s definitions from the [2013 ICERM\nreport](http://stodden.net/icerm_report.pdf), so I’ll use those:\n\n\n| ICERM Report\nDefinitions\n| Potential Real-World\nExamples\n|\n\n|:-----------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------|\n\n| Reviewable Research: Sufficient detail for peer review and\nassessment                            | The code and data are openly\navailable\n|\n\n| Replicable Research: Tools are available to duplicate the author’s results\nusing their data    | The tools (software) used in the analysis are freely\navailable for others to confirm results                                   |\n\n| Confirmable Research: Main conclusions can be attained independently\nwithout author’s software | Others can reach the conclusion using similar\ntools, not necessarily the same as the author, or on a different operating\nsystem |\n\n| Auditable Research: Process and tools archived such that it can be\ndefended later if necessary   | The tools, environment, data, and code are\nput into a preservation-ready\nformat                                                |\n\n| Open/Reproducible Research: Auditable research made openly\navailable                           | Everything above is made available in\na repository for others to examine and\nuse                                               |\n\n\nThe last bullet there is the goal – open and reproducible research.\nReleasing code and data are key to open research, but not necessarily enough\nfor reproducibility. This is where the concept of computational\nreproducibility becomes important, where whole environments are captured.\nYou could also look at it this way:\n\n\n![reproducibility-pyramid](https://osf.io/8rx9y/download)\n\n\n### How can GitLab help?\n\n\nThere are a few solutions out there, including containers (such as Docker or\nSingularity) for active research, and [o2r](http://o2r.info/) and\n[ReproZip](https://reprozip.org) for capturing and reproducing completed\nresearch. For this post, I’m going to focus on active research and\ncontainers.\n\n\nI like GitLab for research reproducibility because it makes working together\nsimple, and seamless. There’s no hacking together 100 different third-party\nservices. GitLab has hosting, LFS, and integrated Continuous Integration for\nfree, for both public and private repositories! Everything is integrated in\na single GitLab repository which, if made publicly available, can enable\nsecondary users to reproduce results in a more streamlined fashion. You can\nalso keep these private to a group – you control the visibility of\neverything in one repository in one place, as opposed to updating\npermissions across multiple services.\n\n\nThere are a few key features that set GitLab apart when it comes to\ncontainers and reproducibility. The first is that GitLab doesn’t use a\nthird-party service for continuous integration. It’s shipped with CI runners\nwhich can use Docker images from GitLab’s registry. Basically, you can use\nthe Docker Container Registry, a secure, private Docker registry, to choose\na container that GitLab CI uses to run each job in a separate and isolated\ncontainer.\n\n\n![gitlab-ci-repro](https://about.gitlab.com/images/ci/arch-1.jpg)\n\n\nIf you don’t feel like using the GitLab registry, you can also use images\nfrom DockerHub or a custom Docker container you’re already using locally.\nThese can be integrated with GitLab CI, and if made public, any secondary\nusers can use it as well!\n\n\n### Let's look at an example\n\n\nThis process is set up in a single file, a `.gitlab-ci.yml`. Another feature\nthat makes my life easier – GitLab can syntax-check the CI config files! The\n`.gitlab-ci.yml` file describes the pipelines and stages, each of which has\na different function and can have its own tags, produce its own artifacts,\nand reuse artifacts from other stages. These stages can also run in parallel\nif needed. Here’s an example of what a basic config file looks like with R:\n\n\n```\n\nimage: jangorecki/r-base-dev\n\ntest:\n  script:\n    - R CMD build . --no-build-vignettes --no-manual\n    - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)\n    - R CMD check \"${PKG_FILE_NAME}\" --no-build-vignettes --no-manual --as-cran\n```\n\n\nAnd here’s an example of building a website using the GitLab and the static\nsite generator, Nikola:\n\n\n```\n\nimage: registry.gitlab.com/paddy-hack/nikola:7.8.7\n\ntest:\n  script:\n  - nikola build\n  except:\n  - master\n\npages:\n  script:\n    - nikola build\n  artifacts:\n    paths:\n    - public\n  only:\n  - master\n```\n\n\nIt’s also worth noting that you can use different containers per step in\nyour workflow, if you outline it in your .gitlab-ci.yml. If your data\ncollection script runs in one environment but your analysis script needs\nanother, that’s perfectly fine using GitLab, and others have the information\nto reproduce it easily! Another feature that puts GitLab apart is that a\nbuild of one project can trigger a build of another – AKA, multi-project\npipelines. For those of you working with big data, you can automatically\nspin up and down VMs to make sure your builds get processed immediately with\nGitLab’s CI as well.\n\n\nHere are some other great resources and examples of using GitLab to make\nresearch more reproducible:\n\n\n+ [Gitlab-CI for R packages](https://gitlab.com/jangorecki/r.gitlab.ci)\n\n+ [Blog Post explaining GitLab + reproducibility - Jon\nZelner](http://www.jonzelner.net/statistics/make/docker/reproducibility/2016/05/31/reproducibility-pt-1/)\n\n+ [GitLab repo accompanying blog post - Jon\nZelner](https://gitlab.com/jzelner/reproducible-stan)\n\n+ [Continuous Integration with Gitlab - Tony\nWildish](https://www.nersc.gov/assets/Uploads/2017-02-06-Gitlab-CI.pdf)\n\n\nBeyond reproducibility, there are a lot of features that make GitLab an\nideal place for me to work and organize my research. I’d urge folks to look\nat the [feature list](/pricing/feature-comparison/) and see how they can get started!\n\n\n## About the Guest Author\n\n\nVicky Steeves is the Librarian for Research Data Management and\nReproducibility at New York University, a dual appointment between the\nDivision of Libraries and Center for Data Science. In this role, she works\nsupporting researchers in creating well-managed, high quality, and\nreproducible research through facilitating use of tools such as ReproZip.\nHer research centers on integrating reproducible practices into the research\nworkflow, advocating openness in all facets of scholarship, and\nbuilding/contributing to open infrastructure.\n\n\n“[research](https://www.flickr.com/photos/alovesdc/3464555556/)” by [a loves\ndc](https://www.flickr.com/photos/alovesdc/) is licensed under [CC BY\n2.0](https://creativecommons.org/licenses/by/2.0/legalcode)\n\n{: .note}\n","open-source",[23,24,25],"open source","collaboration","user stories",{"slug":27,"featured":6,"template":28},"gitlab-and-reproducibility","BlogPost","content:en-us:blog:gitlab-and-reproducibility.yml","yaml","Gitlab And 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