--- references: - id: BakerFive2021 accessed: - year: 2021 month: 9 day: 13 author: - family: Baker given: Monya citation-key: BakerFive2021 container-title: Nature DOI: 10.1038/d41586-021-02428-3 issue: '7875' issued: - year: 2021 month: 9 day: 6 language: en number: '7875' page: 293-294 publisher: Nature Publishing Group title: Five keys to writing a reproducible lab protocol type: article-journal volume: '597' - id: BoettigerIntroduction2015 author: - family: Boettiger given: Carl citation-key: BoettigerIntroduction2015 container-title: ACM SIGOPS Operating Systems Review DOI: 10.1145/2723872.2723882 ISSN: '01635980' issue: '1' issued: - year: 2015 month: 1 day: 20 page: 71-79 title: >- An introduction to Docker for reproducible research, with examples from the R environment type: article-journal URL: http://arxiv.org/abs/1410.0846 volume: '49' - id: ChattopadhyayWhat2020 author: - family: Chattopadhyay given: Souti - family: Prasad given: Ishita - family: Henley given: Austin Z - family: Sarma given: Anita - family: Barik given: Titus citation-key: ChattopadhyayWhat2020 issued: - year: 2020 language: en page: '12' title: >- What's Wrong with Computational Notebooks? Pain Points, Needs, and Design Opportunities type: article-journal - id: CommunityTuring2019 accessed: - year: 2020 month: 9 day: 16 author: - family: Community given: The Turing Way - family: Arnold given: Becky - family: Bowler given: Louise - family: Gibson given: Sarah - family: Herterich given: Patricia - family: Higman given: Rosie - family: Krystalli given: Anna - family: Morley given: Alexander - family: O'Reilly given: Martin - family: Whitaker given: Kirstie citation-key: CommunityTuring2019 DOI: 10.5281/ZENODO.3233853 issued: - year: 2019 month: 3 day: 25 publisher: Zenodo title: 'The Turing Way: A Handbook for Reproducible Data Science' type: software URL: https://zenodo.org/record/3233853 version: v0.0.4 - id: CormierGo2020 accessed: - year: 2020 month: 9 day: 17 author: - family: Cormier given: Michael J. - family: Belyeu given: Jonathan R. - family: Pedersen given: Brent S. - family: Brown given: Joseph - family: Koster given: Johannes - family: Quinlan given: Aaron R. citation-key: CormierGo2020 container-title: bioRxiv DOI: 10.1101/2020.09.10.291377 issued: - year: 2020 month: 9 day: 11 language: en page: 2020.09.10.291377 publisher: Cold Spring Harbor Laboratory section: New Results title: 'Go Get Data (GGD): simple, reproducible access to scientific data' type: article-journal URL: https://www.biorxiv.org/content/10.1101/2020.09.10.291377v2 - id: DonohoData2023 accessed: - year: 2023 month: 11 day: 19 author: - family: Donoho given: David citation-key: DonohoData2023 DOI: 10.48550/arXiv.2310.00865 issued: - year: 2023 month: 10 day: 1 number: arXiv:2310.00865 publisher: arXiv title: Data Science at the Singularity type: article URL: http://arxiv.org/abs/2310.00865 - id: FitschenCaosDB2019 accessed: - year: 2019 month: 6 day: 19 author: - family: Fitschen given: Timm - family: Schlemmer given: Alexander - family: Hornung given: Daniel - family: Wörden given: Henrik dropping-particle: tom - family: Parlitz given: Ulrich - family: Luther given: Stefan citation-key: FitschenCaosDB2019 container-title: Data container-title-short: Data DOI: 10.3390/data4020083 ISSN: 2306-5729 issue: '2' issued: - year: 2019 month: 6 day: 10 page: '83' title: >- CaosDB - Research Data Management for Complex, Changing, and Automated Research Workflows type: article-journal URL: http://arxiv.org/abs/1801.07653 volume: '4' - id: HimmelsteinOpen2019 accessed: - year: 2019 month: 9 day: 3 author: - family: Himmelstein given: Daniel S. - family: Rubinetti given: Vincent - family: Slochower given: David R. - family: Hu given: Dongbo - family: Malladi given: Venkat S. - family: Greene given: Casey S. - family: Gitter given: Anthony citation-key: HimmelsteinOpen2019 container-title: PLOS Computational Biology container-title-short: PLoS Comput Biol DOI: 10.1371/journal.pcbi.1007128 editor: - family: Schneidman-Duhovny given: Dina ISSN: 1553-7358 issue: '6' issued: - year: 2019 month: 6 day: 24 language: en page: e1007128 title: Open collaborative writing with Manubot type: article-journal URL: http://dx.plos.org/10.1371/journal.pcbi.1007128 volume: '15' - id: KurtzerHpcng2021 accessed: - year: 2022 month: 8 day: 22 author: - family: Kurtzer given: Gregory M. - family: Cclerget given: '' - family: Bauer given: Michael - family: Kaneshiro given: Ian - family: Trudgian given: David - family: Godlove given: David citation-key: KurtzerHpcng2021 DOI: 10.5281/ZENODO.1310023 issued: - year: 2021 month: 4 day: 6 publisher: Zenodo title: 'hpcng/singularity: Singularity 3.7.3' type: software URL: https://zenodo.org/record/1310023 version: v3.7.3 - id: MolderSustainable2021 accessed: - year: 2022 month: 8 day: 22 author: - family: Mölder given: Felix - family: Jablonski given: Kim Philipp - family: Letcher given: Brice - family: Hall given: Michael B. - family: Tomkins-Tinch given: Christopher H. - family: Sochat given: Vanessa - family: Forster given: Jan - family: Lee given: Soohyun - family: Twardziok given: Sven O. - family: Kanitz given: Alexander - family: Wilm given: Andreas - family: Holtgrewe given: Manuel - family: Rahmann given: Sven - family: Nahnsen given: Sven - family: Köster given: Johannes citation-key: MolderSustainable2021 container-title: F1000Research container-title-short: F1000Res DOI: 10.12688/f1000research.29032.1 ISSN: 2046-1402 issued: - year: 2021 month: 1 day: 18 language: en page: '33' title: Sustainable data analysis with Snakemake type: article-journal URL: https://f1000research.com/articles/10-33/v1 volume: '10' - id: SimonsohnSmall2015 accessed: - year: 2020 month: 10 day: 15 archive_location: 'Sage CA: Los Angeles, CA' author: - family: Simonsohn given: Uri citation-key: SimonsohnSmall2015 container-title: Psychological Science DOI: 10.1177/0956797614567341 issued: - year: 2015 month: 3 day: 23 language: en publisher: 'SAGE PublicationsSage CA: Los Angeles, CA' title: 'Small Telescopes: Detectability and the Evaluation of Replication Results' type: article-journal - id: TongStatistical2019 accessed: - year: 2019 month: 9 day: 22 author: - family: Tong given: Christopher citation-key: TongStatistical2019 container-title: The American Statistician DOI: 10.1080/00031305.2018.1518264 ISSN: 0003-1305 issue: sup1 issued: - year: 2019 month: 3 day: 29 page: 246-261 title: >- Statistical Inference Enables Bad Science; Statistical Thinking Enables Good Science type: article-journal volume: '73' ...