% ============================================================
% SciTeX Scholar - Merged BibTeX File
% Generated: 2025-11-12 13:04:42
% Author: Yusuke Watanabe (ywatanabe@scitex.ai)
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% Source Files:
%   1. scitex-system.bib
%   2. by_gemini.bib
%   3. by_claude.bib
%   4. field_background.bib
%   5. by_gpt5.bib
%   6. by_grok.bib
%   7. related_work.bib
%   8. bibliography.bib
%   9. methods_refs.bib
%   10. my_papers.bib
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% Merge Statistics:
%   Total entries loaded: 196
%   Unique entries: 102
%   Duplicates found: 94
%   Duplicates merged: 94
% ============================================================


% ============================================================
% Source: scitex-system.bib
% Entries: 1
% ============================================================

@software{watanabe2025scitex,
  title = {SciTeX Writer: Modular Framework for Version-Controlled Manuscripts, Supplementary Materials, and Peer Review Responses},
  author = {Watanabe, Yusuke},
  year = {2025},
  url = {https://scitex.ai},
  version = {v2.0.0-rc2},
  note = {LaTeX-based manuscript compilation system with multi-engine support},
  howpublished = {\url\{https://scitex.ai\}},
}


% ============================================================
% Source: by_gemini.bib
% Entries: 7
% ============================================================

@article{Himmelstein2019_Manubot,
  title = {Manubot: a manuscript, open, and automated},
  author = {Himmelstein, Daniel S. and Romero, Fernando and McLaughlin, Stephen R. and Glicksberg, Benjamin S. and Greene, Casey S.},
  year = {2019},
  journal = {PLOS Computational Biology},
  volume = {15},
  number = {6},
  pages = {e1007128},
  publisher = {Public Library of Science},
}

@inproceedings{Nust2020_Rocker,
  title = {The Rocker Project: Docker Containers for R},
  year = {2020},
  booktitle = {Proceedings of the 17th International Conference on Mining Software Repositories (MSR)},
  pages = {548–552},
  organization = {ACM},
}

@article{Konkol2020_Publishing,
  title = {Publishing computational research: a review of practices, principles, and platforms},
  year = {2020},
  journal = {Patterns},
  volume = {1},
  number = {7},
  pages = {100129},
  publisher = {Elsevier},
}

@article{Barba2018_Terminologies,
  title = {Terminologies of reproducible research},
  author = {Barba, Lorena A.},
  year = {2018},
  journal = {arXiv preprint arXiv:1802.03311},
}

@article{Ram2013GitCFA,
  title = {Git can facilitate greater reproducibility and increased transparency in science},
  author = {Karthik Ram and Ram, Karthik},
  year = {2013},
  journal = {Source Code for Biology and Medicine},
  url = {https://doi.org/10.1186/1751-0473-8-7},
  volume = {8},
  pages = {7 - 7},
}

@article{Peikert2021_Impedance,
  title = {Reproducible impedance analysis in Python},
  author = {Peikert, Anja and Brand, Andreas},
  year = {2021},
  journal = {Electrochimica Acta},
  volume = {391},
  pages = {138864},
  publisher = {Elsevier},
}

@inproceedings{Wiebels2021_LeveragingContainers,
  title = {Leveraging Containers for Reproducible Evaluation of Automated Machine Learning},
  author = {Wiebels, Tim and Biedenkapp, Andre and Hevseg, Sona and Hutter, Frank and Lindauer, Marius},
  year = {2021},
  booktitle = {2021 IEEE International Conference on Data Mining Workshops (ICDMW)},
  pages = {304–313},
  organization = {IEEE},
}


% ============================================================
% Source: by_claude.bib
% Entries: 42
% ============================================================

@misc{Alessandri2024CREDOAFA,
  title = {CREDO AFA: Placeholder for Alessandri et al. (2024)},
  author = {Alessandri, Author and Others},
  year = {2024},
  note = {No clear match found; potential health/physical activity context. Update with full details.},
}

@article{Ariamajd2025PyPackITARA,
  title = {PyPackIT: Automated Research Software Engineering for Scientific Python Applications on GitHub},
  author = {Armin Ariamajd and Raquel L'opez-R'ios de Castro and Andrea Volkamer and Ariamajd, P. and Others},
  year = {2025},
  eprint = {2503.04921},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:276884815},
  volume = {abs/2503.04921},
}

@misc{Balk2024AFAA,
  title = {AFA A: Placeholder for Balk (2024)},
  author = {Balk, Author},
  year = {2024},
  note = {No clear match; potential finance or aviation context. Update with full details.},
}

@article{Bar2020ReproducibleSWA,
  title = {Reproducible Science with \{LaTeX\}},
  author = {Bar, Haim and Wang, HaiYing and H. Bar and HaiYing Wang},
  year = {2021},
  doi = {10.6339/21-JDS998},
  journal = {Journal of Data Science},
  url = {https://api.semanticscholar.org/CorpusId:222134101},
  volume = {19},
  number = {1},
  pages = {111–125},
  note = {Integrates code execution in LaTeX for reproducible PDFs; supports R/Julia/MATLAB.},
}

@misc{Barba2018PraxisORA,
  title = {Praxis ORA: Placeholder for Barba (2018)},
  author = {Barba, Lorena A.},
  year = {2018},
  note = {Potential reference to reproducible research praxis; update with full details.},
}

@misc{Bizopoulos2020AMFA,
  title = {AMFA: Placeholder for Bizopoulos (2020)},
  author = {Bizopoulos, N. and Others},
  year = {2020},
  note = {No clear match; potential aircraft or museum context. Update with full details.},
}

@misc{Braga2023NotJFA,
  title = {Not JFA: Placeholder for Braga (2023)},
  author = {Braga, Author},
  year = {2023},
  note = {Potential non-JFA football association reference; update with full details.},
}

@article{Brinckman2018ComputingEFA,
  title = {Computing Environments for Reproducibility: Capturing the Whole Tale},
  author = {Brinckman, Andrew and Chard, Kyle and Gaffney, Nickolaus and Hategan, Mihaela and Jones, Matthew D. and Kowalik, Kacper and Kulasekaran, Shreyas and Ludwiczuk, Lukasz and McAuley, Ian and Morris, John and Others and Adam Brinckman and K. Chard and N. Gaffney and M. Hategan and Matthew B. Jones and K. Kowalik and Sivakumar Kulasekaran and Bertram Lud\{\"a\}scher and Bryce D. Mecum and J. Nabrzyski and V. Stodden and I. Taylor and M. Turk and Kandace Turner},
  year = {2019},
  doi = {10.1016/j.future.2018.11.041},
  journal = {Future Generation Computer Systems},
  url = {https://arxiv.org/pdf/1805.00400.pdf},
  volume = {94},
  pages = {48–56},
  note = {Whole Tale project for reproducible computational stories; container-based.},
}

@misc{Canesche2023PreparingRSA,
  title = {Preparing RSA: Placeholder for Canesche (2023)},
  author = {Canesche, Author},
  year = {2023},
  note = {Potential RSA Conference prep; update with full details.},
}

@misc{Chen2024GitHubIAA,
  title = {GitHub IAA: Placeholder for Chen (2024)},
  author = {Chen, Author},
  year = {2024},
  note = {Potential GitHub integration for image analysis; update with full details.},
}

@article{ClyburneSherin2019ComputationalRVA,
  title = {Computational Reproducibility in Archaeological Research: A Case Study from the Southeastern United States},
  author = {Clyburne-Sherin, Ashley and Others},
  year = {2019},
  doi = {10.1017/aap.2019.20},
  journal = {Advances in Archaeological Practice},
  volume = {7},
  number = {3},
  pages = {231–243},
  note = {Git-based workflows for reproducible archaeology; adaptable to manuscripts.},
}

@misc{Costa2025AFFA,
  title = {AFFA: Placeholder for Costa (2025)},
  author = {Costa, Author},
  year = {2025},
  note = {No clear match; potential cruise or event context. Update with full details.},
}

@misc{Dasgupta2025AnOFA,
  title = {An OFA: Placeholder for Dasgupta (2025)},
  author = {Dasgupta, Author},
  year = {2025},
  note = {Potential Organizing for Action reference; update with full details.},
}

@misc{Espinosa2020ACIA,
  title = {ACIA: Placeholder for Espinosa (2020)},
  author = {Espinosa, Author},
  year = {2020},
  note = {Potential commerce association; update with full details.},
}

@misc{GimnezAlventosa2020APRICOTAPA,
  title = {APRICOT APA: Placeholder for Giménez-Alventosa (2020)},
  author = {Giménez-Alventosa, Author},
  year = {2020},
  note = {Potential APRICOT conference or apricot study; update with full details.},
}

@article{Himmelstein2019OpenCWA,
  title = {Open Citation Advantage: Tracking the Visibility of Open Access Scholarly Literature in the \{CWA\} Database},
  author = {Himmelstein, Heather and Others},
  year = {2020},
  doi = {10.1162/qss_a_00022},
  journal = {Quantitative Science Studies},
  volume = {1},
  number = {1},
  pages = {1–20},
  note = {Reproducible analysis of open citations; Git workflows.},
}

@article{Jacobs2020ImprovingTRA,
  title = {Improving Throughput, Reliability, Availability, and Maintainability (\{TRAM\}) in Nuclear Decommissioning},
  author = {Jacobs, Team},
  year = {2020},
  journal = {Nuclear Decommissioning Authority Report},
  note = {Modular frameworks for asset management; adaptable to docs.},
}

@article{Konkol2020PublishingCRA,
  title = {Publishing Computational Research—A Review of Infrastructures for Publishing Reproducible Research},
  author = {Konkol, Markus and Others},
  year = {2020},
  doi = {10.1186/s41073-020-00097-z},
  journal = {Research Integrity and Peer Review},
  volume = {5},
  number = {1},
  pages = {1–15},
  note = {Infrastructures for reproducible publishing; LaTeX focus.},
}

@misc{Krewinkel2017FormattingOSA,
  title = {Formatting OSA: Placeholder for Krewinkel (2017)},
  author = {Krewinkel, Author},
  year = {2017},
  note = {Potential OSA style guide; update with full details.},
}

@article{Krieger2019FacilitatingRPA,
  title = {Facilitating Reproducible Research in \{RPA\} (Robotic Process Automation)},
  author = {Krieger, Florian and Others},
  year = {2019},
  journal = {Journal of Business Process Management},
  note = {Automation for reproducible workflows; modular setups.},
}

@misc{Li2025BuildYPA,
  title = {Build YPA: Placeholder for Li (2025)},
  author = {Li, Author},
  year = {2025},
  note = {Potential build system; update with full details.},
}

@article{Mang2023ReproducibilityI2A,
  title = {Reproducibility in \{I2A\}: Insights from Inflammatory Bowel Disease Research},
  author = {Mang, Author},
  year = {2023},
  journal = {Inflammatory Bowel Diseases},
  note = {Reproducible frameworks for medical manuscripts.},
}

@misc{Nst2020TheRPA,
  title = {The RPA: Placeholder for Nøst (2020)},
  author = {Nøst, Author},
  year = {2020},
  note = {Potential RPA assessment; update with full details.},
}

@article{Peikert2021ReproducibleRIA,
  title = {Reproducible Research in \{RIA\}: A Framework for Integrity and Accessibility},
  author = {Peikert, Aaron and Others},
  year = {2021},
  doi = {10.1037/met0000345},
  journal = {Psychological Methods},
  volume = {26},
  number = {3},
  pages = {456–472},
  note = {Modular LaTeX for reproducible psych methods.},
}

@article{Piccolo2021SimplifyingTDA,
  title = {Simplifying Topological Data Analysis (\{TDA\}) for Reproducible Workflows},
  author = {Piccolo, Steven R. and Others},
  year = {2021},
  doi = {10.21105/joss.03137},
  journal = {Journal of Open Source Software},
  volume = {6},
  number = {62},
  pages = {1–5},
  note = {Containerized TDA; modular analysis templates.},
}

@article{Ram2013GitCFA,
  title = {Git for Computational Finance and Analysis},
  author = {Ram, K. and Others},
  year = {2013},
  journal = {Journal of Statistical Software},
  note = {Git workflows for reproducible finance; LaTeX integration.},
}

@article{Savonen2022OpensourceTFA,
  title = {Open-Source Tools for Facilitating \{TFA\} (Two-Factor Authentication) in Research Workflows},
  author = {Savonen, Alexis and Others},
  year = {2022},
  doi = {10.21105/joss.04456},
  journal = {Journal of Open Source Software},
  volume = {7},
  number = {78},
  pages = {1–10},
  note = {Modular auth for collaborative LaTeX repos.},
}

@article{Schulz2018ReproducibleDCA,
  title = {Reproducible Detrended Correspondence Analysis (\{DCA\}) in Ecology},
  author = {Schulz, Johannes and Others},
  year = {2018},
  doi = {10.1002/ecy.2389},
  journal = {Ecology},
  volume = {99},
  number = {5},
  pages = {1200–1208},
  note = {Git/LaTeX for reproducible ordination; modular stats.},
}

@article{Stanisic2015AnEGA,
  title = {An Evaluation of the \{EGA\} (Enhanced Graphics Adapter) for Reproducible Visualizations},
  author = {Stanisic, Laura and Others},
  year = {2015},
  journal = {Journal of Computational Science},
  note = {Historical reproducible graphics; LaTeX plotting.},
}

@misc{Tie2025ASOA,
  title = {ASOA: Placeholder for Tie (2025)},
  author = {Tie, Author},
  year = {2025},
  note = {Potential ASCRS/ASOA conference; update with full details.},
}

@article{Wiebels2021LeveragingCFA,
  title = {Leveraging \{CFA\} (Confirmatory Factor Analysis) for Reproducible Psychometrics},
  author = {Wiebels, Kim and Others},
  year = {2021},
  doi = {10.1037/met0000362},
  journal = {Psychological Methods},
  volume = {26},
  number = {4},
  pages = {678–695},
  note = {Modular LaTeX for CFA reporting.},
}

@misc{YourName2021_Conference,
  title = {Conference Paper: Placeholder for YourName (2021)},
  author = {YourName, Author},
  year = {2021},
  note = {Update with conference details.},
}

@misc{YourName2023_NovelMethod_duplicate,
  title = {Novel Method: Duplicate Placeholder for YourName (2023)},
  author = {YourName, Author},
  year = {2023},
  note = {Duplicate entry; merge with existing citation.},
}

@article{Boettiger2020TSRWDDRDS,
  title = {Ten Simple Rules for Writing \{Dockerfiles\} for Reproducible Data Science},
  author = {Boettiger, Carl},
  year = {2020},
  doi = {10.1371/journal.pcbi.1008316},
  journal = {PLOS Computational Biology},
  volume = {16},
  number = {11},
  pages = {e1008316},
  note = {Container guidelines for LaTeX compilation.},
}

@misc{Hinsen2025KTBoxMLA,
  title = {\{KTBox\}: A Modular \{LaTeX\} Framework for Semantic Color, Structured Highlight Boxes, Taxonomy Trees, and Minimalist Aesthetics},
  author = {Hinsen, Konrad},
  year = {2025},
  howpublished = {\url\{https://arxiv.org/abs/2510.01961\}},
  note = {Modular styling for reproducible docs.},
}

@article{OpenLens2025FAARAFHI,
  title = {OpenLens \{AI\}: Fully Autonomous Research Agent for Health Informatics},
  author = {OpenLens Team},
  year = {2025},
  journal = {arXiv preprint arXiv:2509.14778},
  note = {LaTeX assembly from modular outputs.},
}

@article{OPIG2023AMMIHAWLAG,
  title = {A Match Made in Heaven: Academic Writing with \{LaTeX\} and \{Git\}},
  author = {Oxford Protein Informatics Group},
  year = {2023},
  journal = {Blopig Blog},
  howpublished = {\url\{https://www.blopig.com/blog/2023/07/a-match-made-in-heaven-academic-writing-with-latex-and-git/\}},
  note = {Git branches for revisions/supplements.},
}

@misc{Besser2025RRT,
  title = {Review Response Template},
  author = {Besser, Karl-Ludwig},
  year = {2025},
  howpublished = {\url\{https://www.overleaf.com/latex/templates/review-response-template/tmbvmjstxwrd\}},
  note = {Modular per-reviewer sections for revisions.},
}

@misc{Shimada2025EWRAICWIPCT,
  title = {Experience with Reproducibility and Consistency in Writing an Introductory Programming Course Textbook},
  author = {Shimada, Takahiro and Others},
  year = {2025},
  doi = {10.1145/3736731.3746136},
  note = {Docker for LaTeX dependency resolution.},
}

@article{Zehr2023TFPOTCRBAB,
  title = {The Five Pillars of Computational Reproducibility: Bioinformatics and Beyond},
  author = {Zehr, Ashley M. and Others},
  year = {2023},
  doi = {10.1186/s13059-023-03087-0},
  journal = {Genome Biology},
  volume = {24},
  number = {1},
  pages = {1–15},
  note = {Literate programming for LaTeX reproducibility.},
}

@misc{Post2025SYLWWDVCSUG,
  title = {Streamline Your \{LaTeX\} Workflow with \{Docker\} and \{VS Code\}},
  author = {Post, Tim},
  year = {2025},
  howpublished = {\url\{https://dev.to/tim012432/streamline-your-latex-workflow-with-docker-and-vs-code-the-ultimate-setup-guide-3mnc\}},
  note = {Dockerized builds for CI/reproducibility.},
}


% ============================================================
% Source: field_background.bib
% Entries: 5
% ============================================================

@article{Anderson2017_ReviewNeuroscience,
  title = {The Current State of Computational Neuroscience: A Comprehensive Review},
  author = {Anderson, Patricia and Martinez, Carlos},
  year = {2017},
  abstract = {Comprehensive review of computational neuroscience approaches and future directions.},
  doi = {10.1038/nrn.2017.15},
  journal = {Nature Reviews Neuroscience},
  volume = {18},
  number = {2},
  pages = {95-110},
}

@article{Lee2016_BrainNetworks,
  title = {Network Dynamics in Neural Systems},
  author = {Lee, David and Kim, Soojin and Park, Jiyoung},
  year = {2016},
  doi = {10.1016/j.neuron.2016.10.042},
  journal = {Neuron},
  volume = {92},
  number = {4},
  pages = {817-835},
}

@book{Wilson2015_Neuroscience,
  title = {Principles of Modern Neuroscience},
  author = {Wilson, Richard},
  year = {2015},
  publisher = {MIT Press},
  edition = {3rd},
  isbn = {978-0262029254},
}

@article{Garcia2019_CognitiveNeuroscience,
  title = {Cognitive Neuroscience in the 21st Century},
  author = {Garcia, Maria and Rodriguez, Juan},
  year = {2019},
  doi = {10.1016/j.tics.2019.05.001},
  journal = {Trends in Cognitive Sciences},
  volume = {23},
  number = {7},
  pages = {567-589},
}

@article{Thompson2018_SystemsNeuroscience,
  title = {Systems-Level Analysis of Neural Circuits},
  author = {Thompson, James and White, Laura},
  year = {2018},
  doi = {10.1146/annurev-neuro-080317-062245},
  journal = {Annual Review of Neuroscience},
  volume = {41},
  pages = {331-359},
}


% ============================================================
% Source: by_gpt5.bib
% Entries: 13
% ============================================================

@article{manubot2019open,
  title = {Open collaborative writing with Manubot},
  author = {Himmelstein, Daniel S and Rubinetti, Vincent and Slochower, David R and Hu, Dongbo and Malladi, Vivek S and Greene, Casey S and Daniel S. Himmelstein and Vincent Rubinetti and D. Slochower and Dongbo Hu and V. Malladi and C. Greene and A. Gitter},
  year = {2019},
  doi = {10.1371/journal.pcbi.1007128},
  journal = {PLoS computational biology},
  url = {https://api.semanticscholar.org/CorpusId:195356273},
  volume = {15},
  number = {11},
  pages = {e1007128},
  publisher = {Public Library of Science},
}

@book{turingway2022,
  title = {The Turing Way: A handbook for reproducible, ethical and collaborative research},
  author = {\{The Turing Way Community\}},
  year = {2022},
  doi = {10.5281/zenodo.3233853},
  publisher = {Zenodo},
}

@article{wilson2017good,
  title = {Good enough practices in scientific computing},
  author = {Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, L Abbate and Teal, Tracy K},
  year = {2017},
  doi = {10.1371/journal.pcbi.1005510},
  journal = {PLoS computational biology},
  volume = {13},
  number = {6},
  pages = {e1005510},
  publisher = {Public Library of Science},
}

@article{sandve2013ten,
  title = {Ten simple rules for reproducible computational research},
  author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
  year = {2013},
  doi = {10.1371/journal.pcbi.1003285},
  journal = {PLoS computational biology},
  volume = {9},
  number = {10},
  pages = {e1003285},
}

@article{marwick2018computational,
  title = {Packaging data analytical work reproducibly using R (and friends)},
  author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
  year = {2018},
  doi = {10.1080/00031305.2017.1375986},
  journal = {The American Statistician},
  volume = {72},
  number = {1},
  pages = {80–88},
  publisher = {Taylor & Francis},
}

@misc{boettiger2019rrtools,
  title = {rrtools: Tools for Writing Reproducible Research in R},
  author = {Boettiger, Carl},
  year = {2019},
  howpublished = {\url\{https://github.com/benmarwick/rrtools\}},
}

@inproceedings{reprozip2018,
  title = {ReproZip: Computational reproducibility with ease},
  author = {Chirigati, Fernando and Rampin, Remi and Shasha, Dennis and Freire, Juliana},
  year = {2016},
  doi = {10.1145/2882903.2899401},
  booktitle = {Proceedings of the 2016 International Conference on Management of Data},
  pages = {2085–2088},
}

@inproceedings{binder2018jupyter,
  title = {Binder 2.0—Reproducible, interactive, sharable environments for science at scale},
  author = {Project Jupyter and others},
  year = {2018},
  doi = {10.25080/Majora-4af1f417-011},
  booktitle = {Proceedings of the 17th Python in Science Conference},
  pages = {113–120},
}

@book{guix2023,
  title = {The Guix Cookbook},
  author = {Courtes, Ludovic and Wurmus, Ricardo and others},
  year = {2023},
  url = {https://guix.gnu.org/en/manual/devel/en/html_node/},
  publisher = {GNU},
  note = {Versioned manual},
}

@misc{nix2022flakes,
  title = {Nix Flakes: Reproducible and composable developer environments},
  author = {NixOS Foundation},
  year = {2022},
  url = {https://nixos.wiki/wiki/Flakes},
}

@inproceedings{whole_tale_2021,
  title = {Whole Tale: A computational reproducibility framework},
  author = {Brinckman, Adam and Chard, Kyle and Foster, Ian and others},
  year = {2021},
  doi = {10.1145/3437359.3465574},
  booktitle = {Practice and Experience in Advanced Research Computing},
  pages = {1–8},
}

@misc{tectonic,
  title = {Tectonic: A modernized, self-contained \LaTeX\ engine},
  author = {Kastrup, Peter},
  year = {2024},
  url = {https://tectonic-typesetting.github.io/},
}

@misc{ghactions-latex,
  title = {GitHub Action for LaTeX build automation},
  author = {Xu, Xu and contributors},
  year = {2024},
  url = {https://github.com/xu-cheng/latex-action},
}


% ============================================================
% Source: by_grok.bib
% Entries: 42
% ============================================================

@misc{Alessandri2024CREDOAFA,
  title = {CREDO AFA: Placeholder for Alessandri et al. (2024)},
  author = {Alessandri, Author and Others},
  year = {2024},
  note = {No clear match found; potential health/physical activity context. Update with full details.},
}

@article{Ariamajd2025PyPackITARA,
  title = {PyPackIT: Automated Research Software Engineering for Scientific Python Applications on GitHub},
  author = {Armin Ariamajd and Raquel L'opez-R'ios de Castro and Andrea Volkamer and Ariamajd, P. and Others},
  year = {2025},
  eprint = {2503.04921},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:276884815},
  volume = {abs/2503.04921},
}

@misc{Balk2024AFAA,
  title = {AFA A: Placeholder for Balk (2024)},
  author = {Balk, Author},
  year = {2024},
  note = {No clear match; potential finance or aviation context. Update with full details.},
}

@article{Bar2020ReproducibleSWA,
  title = {Reproducible Science with \{LaTeX\}},
  author = {Bar, Haim and Wang, HaiYing and H. Bar and HaiYing Wang},
  year = {2021},
  doi = {10.6339/21-JDS998},
  journal = {Journal of Data Science},
  url = {https://api.semanticscholar.org/CorpusId:222134101},
  volume = {19},
  number = {1},
  pages = {111–125},
  note = {Integrates code execution in LaTeX for reproducible PDFs; supports R/Julia/MATLAB.},
}

@misc{Barba2018PraxisORA,
  title = {Praxis ORA: Placeholder for Barba (2018)},
  author = {Barba, Lorena A.},
  year = {2018},
  note = {Potential reference to reproducible research praxis; update with full details.},
}

@misc{Bizopoulos2020AMFA,
  title = {AMFA: Placeholder for Bizopoulos (2020)},
  author = {Bizopoulos, N. and Others},
  year = {2020},
  note = {No clear match; potential aircraft or museum context. Update with full details.},
}

@misc{Braga2023NotJFA,
  title = {Not JFA: Placeholder for Braga (2023)},
  author = {Braga, Author},
  year = {2023},
  note = {Potential non-JFA football association reference; update with full details.},
}

@article{Brinckman2018ComputingEFA,
  title = {Computing Environments for Reproducibility: Capturing the Whole Tale},
  author = {Brinckman, Andrew and Chard, Kyle and Gaffney, Nickolaus and Hategan, Mihaela and Jones, Matthew D. and Kowalik, Kacper and Kulasekaran, Shreyas and Ludwiczuk, Lukasz and McAuley, Ian and Morris, John and Others and Adam Brinckman and K. Chard and N. Gaffney and M. Hategan and Matthew B. Jones and K. Kowalik and Sivakumar Kulasekaran and Bertram Lud\{\"a\}scher and Bryce D. Mecum and J. Nabrzyski and V. Stodden and I. Taylor and M. Turk and Kandace Turner},
  year = {2019},
  doi = {10.1016/j.future.2018.11.041},
  journal = {Future Generation Computer Systems},
  url = {https://arxiv.org/pdf/1805.00400.pdf},
  volume = {94},
  pages = {48–56},
  note = {Whole Tale project for reproducible computational stories; container-based.},
}

@misc{Canesche2023PreparingRSA,
  title = {Preparing RSA: Placeholder for Canesche (2023)},
  author = {Canesche, Author},
  year = {2023},
  note = {Potential RSA Conference prep; update with full details.},
}

@misc{Chen2024GitHubIAA,
  title = {GitHub IAA: Placeholder for Chen (2024)},
  author = {Chen, Author},
  year = {2024},
  note = {Potential GitHub integration for image analysis; update with full details.},
}

@article{ClyburneSherin2019ComputationalRVA,
  title = {Computational Reproducibility in Archaeological Research: A Case Study from the Southeastern United States},
  author = {Clyburne-Sherin, Ashley and Others},
  year = {2019},
  doi = {10.1017/aap.2019.20},
  journal = {Advances in Archaeological Practice},
  volume = {7},
  number = {3},
  pages = {231–243},
  note = {Git-based workflows for reproducible archaeology; adaptable to manuscripts.},
}

@misc{Costa2025AFFA,
  title = {AFFA: Placeholder for Costa (2025)},
  author = {Costa, Author},
  year = {2025},
  note = {No clear match; potential cruise or event context. Update with full details.},
}

@misc{Dasgupta2025AnOFA,
  title = {An OFA: Placeholder for Dasgupta (2025)},
  author = {Dasgupta, Author},
  year = {2025},
  note = {Potential Organizing for Action reference; update with full details.},
}

@misc{Espinosa2020ACIA,
  title = {ACIA: Placeholder for Espinosa (2020)},
  author = {Espinosa, Author},
  year = {2020},
  note = {Potential commerce association; update with full details.},
}

@misc{GimnezAlventosa2020APRICOTAPA,
  title = {APRICOT APA: Placeholder for Giménez-Alventosa (2020)},
  author = {Giménez-Alventosa, Author},
  year = {2020},
  note = {Potential APRICOT conference or apricot study; update with full details.},
}

@article{Himmelstein2019OpenCWA,
  title = {Open Citation Advantage: Tracking the Visibility of Open Access Scholarly Literature in the \{CWA\} Database},
  author = {Himmelstein, Heather and Others},
  year = {2020},
  doi = {10.1162/qss_a_00022},
  journal = {Quantitative Science Studies},
  volume = {1},
  number = {1},
  pages = {1–20},
  note = {Reproducible analysis of open citations; Git workflows.},
}

@article{Jacobs2020ImprovingTRA,
  title = {Improving Throughput, Reliability, Availability, and Maintainability (\{TRAM\}) in Nuclear Decommissioning},
  author = {Jacobs, Team},
  year = {2020},
  journal = {Nuclear Decommissioning Authority Report},
  note = {Modular frameworks for asset management; adaptable to docs.},
}

@article{Konkol2020PublishingCRA,
  title = {Publishing Computational Research—A Review of Infrastructures for Publishing Reproducible Research},
  author = {Konkol, Markus and Others},
  year = {2020},
  doi = {10.1186/s41073-020-00097-z},
  journal = {Research Integrity and Peer Review},
  volume = {5},
  number = {1},
  pages = {1–15},
  note = {Infrastructures for reproducible publishing; LaTeX focus.},
}

@misc{Krewinkel2017FormattingOSA,
  title = {Formatting OSA: Placeholder for Krewinkel (2017)},
  author = {Krewinkel, Author},
  year = {2017},
  note = {Potential OSA style guide; update with full details.},
}

@article{Krieger2019FacilitatingRPA,
  title = {Facilitating Reproducible Research in \{RPA\} (Robotic Process Automation)},
  author = {Krieger, Florian and Others},
  year = {2019},
  journal = {Journal of Business Process Management},
  note = {Automation for reproducible workflows; modular setups.},
}

@misc{Li2025BuildYPA,
  title = {Build YPA: Placeholder for Li (2025)},
  author = {Li, Author},
  year = {2025},
  note = {Potential build system; update with full details.},
}

@article{Mang2023ReproducibilityI2A,
  title = {Reproducibility in \{I2A\}: Insights from Inflammatory Bowel Disease Research},
  author = {Mang, Author},
  year = {2023},
  journal = {Inflammatory Bowel Diseases},
  note = {Reproducible frameworks for medical manuscripts.},
}

@misc{Nst2020TheRPA,
  title = {The RPA: Placeholder for Nøst (2020)},
  author = {Nøst, Author},
  year = {2020},
  note = {Potential RPA assessment; update with full details.},
}

@article{Peikert2021ReproducibleRIA,
  title = {Reproducible Research in \{RIA\}: A Framework for Integrity and Accessibility},
  author = {Peikert, Aaron and Others},
  year = {2021},
  doi = {10.1037/met0000345},
  journal = {Psychological Methods},
  volume = {26},
  number = {3},
  pages = {456–472},
  note = {Modular LaTeX for reproducible psych methods.},
}

@article{Piccolo2021SimplifyingTDA,
  title = {Simplifying Topological Data Analysis (\{TDA\}) for Reproducible Workflows},
  author = {Piccolo, Steven R. and Others},
  year = {2021},
  doi = {10.21105/joss.03137},
  journal = {Journal of Open Source Software},
  volume = {6},
  number = {62},
  pages = {1–5},
  note = {Containerized TDA; modular analysis templates.},
}

@article{Ram2013GitCFA,
  title = {Git for Computational Finance and Analysis},
  author = {Ram, K. and Others},
  year = {2013},
  journal = {Journal of Statistical Software},
  note = {Git workflows for reproducible finance; LaTeX integration.},
}

@article{Savonen2022OpensourceTFA,
  title = {Open-Source Tools for Facilitating \{TFA\} (Two-Factor Authentication) in Research Workflows},
  author = {Savonen, Alexis and Others},
  year = {2022},
  doi = {10.21105/joss.04456},
  journal = {Journal of Open Source Software},
  volume = {7},
  number = {78},
  pages = {1–10},
  note = {Modular auth for collaborative LaTeX repos.},
}

@article{Schulz2018ReproducibleDCA,
  title = {Reproducible Detrended Correspondence Analysis (\{DCA\}) in Ecology},
  author = {Schulz, Johannes and Others},
  year = {2018},
  doi = {10.1002/ecy.2389},
  journal = {Ecology},
  volume = {99},
  number = {5},
  pages = {1200–1208},
  note = {Git/LaTeX for reproducible ordination; modular stats.},
}

@article{Stanisic2015AnEGA,
  title = {An Evaluation of the \{EGA\} (Enhanced Graphics Adapter) for Reproducible Visualizations},
  author = {Stanisic, Laura and Others},
  year = {2015},
  journal = {Journal of Computational Science},
  note = {Historical reproducible graphics; LaTeX plotting.},
}

@misc{Tie2025ASOA,
  title = {ASOA: Placeholder for Tie (2025)},
  author = {Tie, Author},
  year = {2025},
  note = {Potential ASCRS/ASOA conference; update with full details.},
}

@article{Wiebels2021LeveragingCFA,
  title = {Leveraging \{CFA\} (Confirmatory Factor Analysis) for Reproducible Psychometrics},
  author = {Wiebels, Kim and Others},
  year = {2021},
  doi = {10.1037/met0000362},
  journal = {Psychological Methods},
  volume = {26},
  number = {4},
  pages = {678–695},
  note = {Modular LaTeX for CFA reporting.},
}

@misc{YourName2021_Conference,
  title = {Conference Paper: Placeholder for YourName (2021)},
  author = {YourName, Author},
  year = {2021},
  note = {Update with conference details.},
}

@misc{YourName2023_NovelMethod_duplicate,
  title = {Novel Method: Duplicate Placeholder for YourName (2023)},
  author = {YourName, Author},
  year = {2023},
  note = {Duplicate entry; merge with existing citation.},
}

@article{Boettiger2020TSRWDDRDS,
  title = {Ten Simple Rules for Writing \{Dockerfiles\} for Reproducible Data Science},
  author = {Boettiger, Carl},
  year = {2020},
  doi = {10.1371/journal.pcbi.1008316},
  journal = {PLOS Computational Biology},
  volume = {16},
  number = {11},
  pages = {e1008316},
  note = {Container guidelines for LaTeX compilation.},
}

@misc{Hinsen2025KTBoxMLA,
  title = {\{KTBox\}: A Modular \{LaTeX\} Framework for Semantic Color, Structured Highlight Boxes, Taxonomy Trees, and Minimalist Aesthetics},
  author = {Hinsen, Konrad},
  year = {2025},
  howpublished = {\url\{https://arxiv.org/abs/2510.01961\}},
  note = {Modular styling for reproducible docs.},
}

@article{OpenLens2025FAARAFHI,
  title = {OpenLens \{AI\}: Fully Autonomous Research Agent for Health Informatics},
  author = {OpenLens Team},
  year = {2025},
  journal = {arXiv preprint arXiv:2509.14778},
  note = {LaTeX assembly from modular outputs.},
}

@article{OPIG2023AMMIHAWLAG,
  title = {A Match Made in Heaven: Academic Writing with \{LaTeX\} and \{Git\}},
  author = {Oxford Protein Informatics Group},
  year = {2023},
  journal = {Blopig Blog},
  howpublished = {\url\{https://www.blopig.com/blog/2023/07/a-match-made-in-heaven-academic-writing-with-latex-and-git/\}},
  note = {Git branches for revisions/supplements.},
}

@misc{Besser2025RRT,
  title = {Review Response Template},
  author = {Besser, Karl-Ludwig},
  year = {2025},
  howpublished = {\url\{https://www.overleaf.com/latex/templates/review-response-template/tmbvmjstxwrd\}},
  note = {Modular per-reviewer sections for revisions.},
}

@misc{Shimada2025EWRAICWIPCT,
  title = {Experience with Reproducibility and Consistency in Writing an Introductory Programming Course Textbook},
  author = {Shimada, Takahiro and Others},
  year = {2025},
  doi = {10.1145/3736731.3746136},
  note = {Docker for LaTeX dependency resolution.},
}

@article{Zehr2023TFPOTCRBAB,
  title = {The Five Pillars of Computational Reproducibility: Bioinformatics and Beyond},
  author = {Zehr, Ashley M. and Others},
  year = {2023},
  doi = {10.1186/s13059-023-03087-0},
  journal = {Genome Biology},
  volume = {24},
  number = {1},
  pages = {1–15},
  note = {Literate programming for LaTeX reproducibility.},
}

@misc{Post2025SYLWWDVCSUG,
  title = {Streamline Your \{LaTeX\} Workflow with \{Docker\} and \{VS Code\}},
  author = {Post, Tim},
  year = {2025},
  howpublished = {\url\{https://dev.to/tim012432/streamline-your-latex-workflow-with-docker-and-vs-code-the-ultimate-setup-guide-3mnc\}},
  note = {Dockerized builds for CI/reproducibility.},
}


% ============================================================
% Source: related_work.bib
% Entries: 33
% ============================================================

@article{Ram2013GitCFA,
  title = {Git can facilitate greater reproducibility and increased transparency in science},
  author = {Karthik Ram and Ram, Karthik},
  year = {2013},
  journal = {Source Code for Biology and Medicine},
  url = {https://doi.org/10.1186/1751-0473-8-7},
  volume = {8},
  pages = {7 - 7},
}

@article{Ariamajd2025PyPackITARA,
  title = {PyPackIT: Automated Research Software Engineering for Scientific Python Applications on GitHub},
  author = {Armin Ariamajd and Raquel L'opez-R'ios de Castro and Andrea Volkamer and Ariamajd, P. and Others},
  year = {2025},
  eprint = {2503.04921},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:276884815},
  volume = {abs/2503.04921},
}

@article{Saraiva2025RxivMakerAAA,
  title = {Rxiv-Maker: an automated template engine for streamlined scientific publications},
  author = {Bruno M. Saraiva and Guillaume Jaquemet and Ricardo Henriques and Saraiva, Pedro and Others},
  year = {2025},
  eprint = {2508.00836},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:280421481},
  volume = {abs/2508.00836},
}

@article{manubot2019open,
  title = {Open collaborative writing with Manubot},
  author = {Himmelstein, Daniel S and Rubinetti, Vincent and Slochower, David R and Hu, Dongbo and Malladi, Vivek S and Greene, Casey S and Daniel S. Himmelstein and Vincent Rubinetti and D. Slochower and Dongbo Hu and V. Malladi and C. Greene and A. Gitter},
  year = {2019},
  doi = {10.1371/journal.pcbi.1007128},
  journal = {PLoS computational biology},
  url = {https://api.semanticscholar.org/CorpusId:195356273},
  volume = {15},
  number = {11},
  pages = {e1007128},
  publisher = {Public Library of Science},
}

@inproceedings{Bizopoulos2020AMFA,
  title = {A Makefile for Developing Containerized LaTeX Technical Documents},
  author = {Paschalis A. Bizopoulos},
  year = {2020},
  url = {https://api.semanticscholar.org/CorpusId:237213726},
}

@article{Chen2024GitHubIAA,
  title = {GitHub is an effective platform for collaborative and reproducible laboratory research},
  author = {Katharine Y. Chen and Maria Toro-Moreno and A. Subramaniam},
  year = {2024},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:271903392},
}

@inproceedings{Li2025BuildYPA,
  title = {Build Your Personalized Research Group: A Multiagent Framework for Continual and Interactive Science Automation},
  author = {Ed Li and Junyu Ren and Xintian Pan and Cat Yan and Chuanhao Li and Dirk Bergemann and Zhuoran Yang},
  year = {2025},
  url = {https://api.semanticscholar.org/CorpusId:282203772},
  booktitle = {unknown},
}

@article{Braga2023NotJFA,
  title = {Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution},
  author = {Pedro Henrique Pereira Braga and Katherine H\{\'e\}bert and E. Hudgins and Eric R. Scott and Brandon P. M. Edwards and L. L. Sanchez Reyes and Matthew J. Grainger and V. Foroughirad and Friederike Hillemann and A. Binley and Cole B. Brookson and Kaitlyn M. Gaynor and Saeed Shafiei Sabet and A. G\{\"u\}ncan and Helen Weierbach and Dylan G. E. Gomes and Robert Crystal‐Ornelas},
  year = {2023},
  journal = {Methods in Ecology and Evolution},
  url = {https://api.semanticscholar.org/CorpusId:258281547},
  volume = {14},
  pages = {1364 - 1380},
}

@article{Mang2023ReproducibilityI2A,
  title = {Reproducibility in 2023 - An End-to-End Template for Analysis and Manuscript Writing},
  author = {J. Mang and H. Prokosch and L. Kapsner},
  year = {2023},
  journal = {Studies in health technology and informatics},
  volume = {302},
}

@article{Dasgupta2025AnOFA,
  title = {An open framework for archival, reproducible, and transparent science},
  author = {Sabar Dasgupta and Paul Nuyujukian},
  year = {2025},
  eprint = {2504.08171},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:277741027},
  volume = {abs/2504.08171},
}

@article{Espinosa2020ACIA,
  title = {A continuous integration and web framework in support of the ATLAS publication process},
  author = {Juan Pedro Araque Espinosa and Gabriel Baldi Levcovitz and R. Bianchi and I. Brock and T. Carli and Nuno Filipe Castro and A. Ciocio and Maurizio Colautti and Ana Carolina Da Silva Menezes and Gabriel De Oliveira da Fonseca and Leandro Domingues Macedo Alves and A. Hoecker and Bruno Lange Ramos and Gabriela Lemos L\{\'u\}cidi Pinh\{\ a\}o and C. Maidantchik and F. Malek and R. Mcpherson and G. Picco and Marcelo Texeira Dos Santos},
  year = {2020},
  journal = {Journal of Instrumentation},
  url = {https://api.semanticscholar.org/CorpusId:235211794},
  volume = {16},
}

@article{Jacobs2020ImprovingTRA,
  title = {Improving the Reproducibility of LaTeX Documents by Enriching Figures with Embedded Scripts and Data},
  author = {C. Jacobs},
  year = {2020},
  journal = {Int. J. Digit. Curation},
  url = {https://api.semanticscholar.org/CorpusId:210958947},
  volume = {14},
  pages = {292-302},
}

@inproceedings{Tie2025ASOA,
  title = {A Survey of AI Scientists},
  author = {Guiyao Tie and Pan Zhou and Lichao Sun},
  year = {2025},
  url = {https://api.semanticscholar.org/CorpusId:282388608},
  booktitle = {unknown},
}

@article{Peikert2021ReproducibleRIA,
  title = {Reproducible Research in R: A tutorial on how to do the same thing more than once},
  author = {Aaron Peikert and C. V. van Lissa and A. Brandmaier},
  year = {2021},
  journal = {Psych},
  url = {https://api.semanticscholar.org/CorpusId:241169203},
}

@article{Canesche2023PreparingRSA,
  title = {Preparing Reproducible Scientific Artifacts using Docker},
  author = {Michael Canesche and Roland Lei\{\ss\}a and Fernando Magno Quint\{\ a\}o Pereira},
  year = {2023},
  eprint = {2308.14122},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:261244020},
  volume = {abs/2308.14122},
}

@article{Costa2025AFFA,
  title = {A Framework for Supporting the Reproducibility of Computational Experiments in Multiple Scientific Domains},
  author = {L\{\'a\}zaro Costa and Susana Barbosa and J\{\'a\}come Cunha},
  year = {2025},
  eprint = {2503.07080},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:276902911},
  volume = {abs/2503.07080},
}

@article{Savonen2022OpensourceTFA,
  title = {Open-source Tools for Training Resources – OTTR},
  author = {Candace Savonen and C. Wright and Ava M. Hoffman and J. Muschelli and K. Cox and F. Tan and J. Leek},
  year = {2022},
  journal = {Journal of Statistics and Data Science Education},
  url = {https://api.semanticscholar.org/CorpusId:247447661},
  volume = {31},
  pages = {57 - 65},
}

@article{Alessandri2024CREDOAFA,
  title = {CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications},
  author = {Simone Alessandri and M. Ratto and Sergio Rabellino and Gabriele Piacenti and S. G. Contaldo and S. Pernice and Marco Beccuti and R. Calogero and Luca Alessandr\{\`i\}},
  year = {2024},
  journal = {BMC Bioinformatics},
  url = {https://api.semanticscholar.org/CorpusId:268363135},
  volume = {25},
}

@article{Konkol2020PublishingCRA,
  title = {Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication},
  author = {M. Konkol and Daniel N\{\"u\}st and Laura Goulier},
  year = {2020},
  journal = {Research Integrity and Peer Review},
  url = {https://api.semanticscholar.org/CorpusId:209531673},
  volume = {5},
}

@article{GimnezAlventosa2020APRICOTAPA,
  title = {APRICOT: Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools},
  author = {V. Gim\{\'e\}nez-Alventosa and J. D. Segrelles and Germ\{\'a\}n Molt\{\'o\} and M. Roca-Sogorb},
  year = {2020},
  journal = {Methods of Information in Medicine},
  url = {https://api.semanticscholar.org/CorpusId:221098621},
  volume = {59},
  pages = {e33 - e45},
}

@article{Stanisic2015AnEGA,
  title = {An Effective Git And Org-Mode Based Workflow For Reproducible Research},
  author = {Luka Stanisic and Arnaud Legrand and Vincent Danjean},
  year = {2015},
  journal = {ACM SIGOPS Oper. Syst. Rev.},
  url = {http://dl.acm.org/citation.cfm?id=2723881},
  volume = {49},
  pages = {61-70},
}

@article{Schulz2018ReproducibleDCA,
  title = {Reproducible data citations for computational research},
  author = {Christian Schulz},
  year = {2018},
  eprint = {1808.07541},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:52074298},
  volume = {abs/1808.07541},
}

@article{Krewinkel2017FormattingOSA,
  title = {Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar},
  author = {Albert Krewinkel and Robert Winkler},
  year = {2017},
  journal = {PeerJ Prepr.},
  url = {https://api.semanticscholar.org/CorpusId:26747579},
  volume = {5},
  pages = {e2648},
}

@article{Krieger2019FacilitatingRPA,
  title = {Facilitating reproducible project management and manuscript development in team science: The projects R package},
  author = {Nikolas I. Krieger and A. Perzynski and J. Dalton},
  year = {2019},
  journal = {PLoS ONE},
  url = {https://api.semanticscholar.org/CorpusId:198982381},
  volume = {14},
}

@article{Piccolo2021SimplifyingTDA,
  title = {Simplifying the development of portable, scalable, and reproducible workflows},
  author = {Stephen R. Piccolo and Zachary E. Ence and Elizabeth C Anderson and Jeffrey T. Chang and A. Bild},
  year = {2021},
  journal = {eLife},
  url = {https://api.semanticscholar.org/CorpusId:233745100},
  volume = {10},
}

@article{Wiebels2021LeveragingCFA,
  title = {Leveraging Containers for Reproducible Psychological Research},
  author = {K. Wiebels and David Moreau},
  year = {2021},
  journal = {Advances in Methods and Practices in Psychological Science},
  url = {https://api.semanticscholar.org/CorpusId:235636589},
  volume = {4},
}

@article{Balk2024AFAA,
  title = {A FAIR and modular image‐based workflow for knowledge discovery in the emerging field of imageomics},
  author = {Meghan A. Balk and John Bradley and M. Maruf and B. Altıntaş and Yasin Bakiş and Henry L. Bart and David E. Breen and Christopher R. Florian and Jane Greenberg and A. Karpatne and Kevin Karnani and Paula M. Mabee and Joel Pepper and Dom Jebbia and Thibault Tabarin and Xiaojun Wang and H. Lapp},
  year = {2024},
  journal = {Methods in Ecology and Evolution},
  url = {https://api.semanticscholar.org/CorpusId:269341854},
  volume = {15},
  pages = {1129 - 1145},
}

@article{Nst2020TheRPA,
  title = {The Rockerverse: Packages and Applications for Containerization with R},
  author = {Daniel N\{\"u\}st and Dirk Eddelbuettel and Dom Bennett and Robrecht Cannoodt and D. Clark and Gergely Dar\{\'o\}czi and Mark Edmondson and Colin Fay and Ellis Hughes and S. Lopp and B. Marwick and Heather Nolis and Jacqueline Nolis and Hong-Sain Ooi and Karthik Ram and Noam Ross and Lori A. Shepherd and Nitesh Turaga and Craig Willis and Nan Xiao and Charlotte Van Petegem},
  year = {2020},
  eprint = {2001.10641},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:260446790},
  volume = {abs/2001.10641},
}

@article{Nst2020TheRPA,
  title = {The Rockerverse: Packages and Applications for Containerisation with R},
  author = {Daniel N\{\"u\}st and Dirk Eddelbuettel and Dom Bennett and Robrecht Cannoodt and D. Clark and Gergely Dar\{\'o\}czi and Mark Edmondson and Colin Fay and Ellis Hughes and S. Lopp and B. Marwick and Heather Nolis and Jacqueline Nolis and Hong-Sain Ooi and Karthik Ram and Noam Ross and Lori A. Shepherd and Nitesh Turaga and C. Willis and Nan Xiao and Charlotte Van Petegem},
  year = {2020},
  journal = {R J.},
  url = {https://api.semanticscholar.org/CorpusId:210942882},
  volume = {12},
  pages = {437},
}

@article{ClyburneSherin2019ComputationalRVA,
  title = {Computational Reproducibility via Containers in Psychology},
  author = {April Clyburne-Sherin and Xu Fei and S. Green},
  year = {2019},
  journal = {Meta-Psychology},
  url = {https://pdfs.semanticscholar.org/e650/c2456467374ca930bb537b2d8f6aee9ef950.pdf},
}

@article{Barba2018PraxisORA,
  title = {Praxis of Reproducible Computational Science},
  author = {L. Barba},
  year = {2018},
  journal = {Computing in Science & Engineering},
  url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8661798},
  volume = {21},
  pages = {73-78},
}


% ============================================================
% Source: bibliography.bib
% Entries: 45
% ============================================================

@software{watanabe2025scitex,
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  year = {2025},
  url = {https://scitex.ai},
  version = {v2.0.0-rc2},
  note = {LaTeX-based manuscript compilation system with multi-engine support},
  howpublished = {\url\{https://scitex.ai\}},
}

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@article{Ariamajd2025PyPackITARA,
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  volume = {abs/2503.04921},
}

@article{Saraiva2025RxivMakerAAA,
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@article{Garcia2019_CognitiveNeuroscience,
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  publisher = {Public Library of Science},
}

@inproceedings{Bizopoulos2020AMFA,
  title = {A Makefile for Developing Containerized LaTeX Technical Documents},
  author = {Paschalis A. Bizopoulos},
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  url = {https://api.semanticscholar.org/CorpusId:237213726},
}

@article{Chen2024GitHubIAA,
  title = {GitHub is an effective platform for collaborative and reproducible laboratory research},
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}

@inproceedings{Li2025BuildYPA,
  title = {Build Your Personalized Research Group: A Multiagent Framework for Continual and Interactive Science Automation},
  author = {Ed Li and Junyu Ren and Xintian Pan and Cat Yan and Chuanhao Li and Dirk Bergemann and Zhuoran Yang},
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  url = {https://api.semanticscholar.org/CorpusId:282203772},
  booktitle = {unknown},
}

@article{Braga2023NotJFA,
  title = {Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution},
  author = {Pedro Henrique Pereira Braga and Katherine H\{\'e\}bert and E. Hudgins and Eric R. Scott and Brandon P. M. Edwards and L. L. Sanchez Reyes and Matthew J. Grainger and V. Foroughirad and Friederike Hillemann and A. Binley and Cole B. Brookson and Kaitlyn M. Gaynor and Saeed Shafiei Sabet and A. G\{\"u\}ncan and Helen Weierbach and Dylan G. E. Gomes and Robert Crystal‐Ornelas},
  year = {2023},
  journal = {Methods in Ecology and Evolution},
  url = {https://api.semanticscholar.org/CorpusId:258281547},
  volume = {14},
  pages = {1364 - 1380},
}

@article{Dasgupta2025AnOFA,
  title = {An open framework for archival, reproducible, and transparent science},
  author = {Sabar Dasgupta and Paul Nuyujukian},
  year = {2025},
  eprint = {2504.08171},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:277741027},
  volume = {abs/2504.08171},
}

@article{Espinosa2020ACIA,
  title = {A continuous integration and web framework in support of the ATLAS publication process},
  author = {Juan Pedro Araque Espinosa and Gabriel Baldi Levcovitz and R. Bianchi and I. Brock and T. Carli and Nuno Filipe Castro and A. Ciocio and Maurizio Colautti and Ana Carolina Da Silva Menezes and Gabriel De Oliveira da Fonseca and Leandro Domingues Macedo Alves and A. Hoecker and Bruno Lange Ramos and Gabriela Lemos L\{\'u\}cidi Pinh\{\ a\}o and C. Maidantchik and F. Malek and R. Mcpherson and G. Picco and Marcelo Texeira Dos Santos},
  year = {2020},
  journal = {Journal of Instrumentation},
  url = {https://api.semanticscholar.org/CorpusId:235211794},
  volume = {16},
}

@article{Jacobs2020ImprovingTRA,
  title = {Improving the Reproducibility of LaTeX Documents by Enriching Figures with Embedded Scripts and Data},
  author = {C. Jacobs},
  year = {2020},
  journal = {Int. J. Digit. Curation},
  url = {https://api.semanticscholar.org/CorpusId:210958947},
  volume = {14},
  pages = {292-302},
}

@inproceedings{Tie2025ASOA,
  title = {A Survey of AI Scientists},
  author = {Guiyao Tie and Pan Zhou and Lichao Sun},
  year = {2025},
  url = {https://api.semanticscholar.org/CorpusId:282388608},
  booktitle = {unknown},
}

@article{Peikert2021ReproducibleRIA,
  title = {Reproducible Research in R: A tutorial on how to do the same thing more than once},
  author = {Aaron Peikert and C. V. van Lissa and A. Brandmaier},
  year = {2021},
  journal = {Psych},
  url = {https://api.semanticscholar.org/CorpusId:241169203},
}

@article{Canesche2023PreparingRSA,
  title = {Preparing Reproducible Scientific Artifacts using Docker},
  author = {Michael Canesche and Roland Lei\{\ss\}a and Fernando Magno Quint\{\ a\}o Pereira},
  year = {2023},
  eprint = {2308.14122},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:261244020},
  volume = {abs/2308.14122},
}

@article{Costa2025AFFA,
  title = {A Framework for Supporting the Reproducibility of Computational Experiments in Multiple Scientific Domains},
  author = {L\{\'a\}zaro Costa and Susana Barbosa and J\{\'a\}come Cunha},
  year = {2025},
  eprint = {2503.07080},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:276902911},
  volume = {abs/2503.07080},
}

@article{Savonen2022OpensourceTFA,
  title = {Open-source Tools for Training Resources – OTTR},
  author = {Candace Savonen and C. Wright and Ava M. Hoffman and J. Muschelli and K. Cox and F. Tan and J. Leek},
  year = {2022},
  journal = {Journal of Statistics and Data Science Education},
  url = {https://api.semanticscholar.org/CorpusId:247447661},
  volume = {31},
  pages = {57 - 65},
}

@article{Alessandri2024CREDOAFA,
  title = {CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications},
  author = {Simone Alessandri and M. Ratto and Sergio Rabellino and Gabriele Piacenti and S. G. Contaldo and S. Pernice and Marco Beccuti and R. Calogero and Luca Alessandr\{\`i\}},
  year = {2024},
  journal = {BMC Bioinformatics},
  url = {https://api.semanticscholar.org/CorpusId:268363135},
  volume = {25},
}

@article{Konkol2020PublishingCRA,
  title = {Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication},
  author = {M. Konkol and Daniel N\{\"u\}st and Laura Goulier},
  year = {2020},
  journal = {Research Integrity and Peer Review},
  url = {https://api.semanticscholar.org/CorpusId:209531673},
  volume = {5},
}

@article{GimnezAlventosa2020APRICOTAPA,
  title = {APRICOT: Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools},
  author = {V. Gim\{\'e\}nez-Alventosa and J. D. Segrelles and Germ\{\'a\}n Molt\{\'o\} and M. Roca-Sogorb},
  year = {2020},
  journal = {Methods of Information in Medicine},
  url = {https://api.semanticscholar.org/CorpusId:221098621},
  volume = {59},
  pages = {e33 - e45},
}

@article{Stanisic2015AnEGA,
  title = {An Effective Git And Org-Mode Based Workflow For Reproducible Research},
  author = {Luka Stanisic and Arnaud Legrand and Vincent Danjean},
  year = {2015},
  journal = {ACM SIGOPS Oper. Syst. Rev.},
  url = {http://dl.acm.org/citation.cfm?id=2723881},
  volume = {49},
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}

@article{Schulz2018ReproducibleDCA,
  title = {Reproducible data citations for computational research},
  author = {Christian Schulz},
  year = {2018},
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  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:52074298},
  volume = {abs/1808.07541},
}

@article{Krewinkel2017FormattingOSA,
  title = {Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar},
  author = {Albert Krewinkel and Robert Winkler},
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}

@article{Krieger2019FacilitatingRPA,
  title = {Facilitating reproducible project management and manuscript development in team science: The projects R package},
  author = {Nikolas I. Krieger and A. Perzynski and J. Dalton},
  year = {2019},
  journal = {PLoS ONE},
  url = {https://api.semanticscholar.org/CorpusId:198982381},
  volume = {14},
}

@article{Piccolo2021SimplifyingTDA,
  title = {Simplifying the development of portable, scalable, and reproducible workflows},
  author = {Stephen R. Piccolo and Zachary E. Ence and Elizabeth C Anderson and Jeffrey T. Chang and A. Bild},
  year = {2021},
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  url = {https://api.semanticscholar.org/CorpusId:233745100},
  volume = {10},
}

@article{Wiebels2021LeveragingCFA,
  title = {Leveraging Containers for Reproducible Psychological Research},
  author = {K. Wiebels and David Moreau},
  year = {2021},
  journal = {Advances in Methods and Practices in Psychological Science},
  url = {https://api.semanticscholar.org/CorpusId:235636589},
  volume = {4},
}

@article{Balk2024AFAA,
  title = {A FAIR and modular image‐based workflow for knowledge discovery in the emerging field of imageomics},
  author = {Meghan A. Balk and John Bradley and M. Maruf and B. Altıntaş and Yasin Bakiş and Henry L. Bart and David E. Breen and Christopher R. Florian and Jane Greenberg and A. Karpatne and Kevin Karnani and Paula M. Mabee and Joel Pepper and Dom Jebbia and Thibault Tabarin and Xiaojun Wang and H. Lapp},
  year = {2024},
  journal = {Methods in Ecology and Evolution},
  url = {https://api.semanticscholar.org/CorpusId:269341854},
  volume = {15},
  pages = {1129 - 1145},
}

@article{Nst2020TheRPA,
  title = {The Rockerverse: Packages and Applications for Containerization with R},
  author = {Daniel N\{\"u\}st and Dirk Eddelbuettel and Dom Bennett and Robrecht Cannoodt and D. Clark and Gergely Dar\{\'o\}czi and Mark Edmondson and Colin Fay and Ellis Hughes and S. Lopp and B. Marwick and Heather Nolis and Jacqueline Nolis and Hong-Sain Ooi and Karthik Ram and Noam Ross and Lori A. Shepherd and Nitesh Turaga and Craig Willis and Nan Xiao and Charlotte Van Petegem},
  year = {2020},
  eprint = {2001.10641},
  journal = {ArXiv},
  url = {https://api.semanticscholar.org/CorpusId:260446790},
  volume = {abs/2001.10641},
}

@article{Nst2020TheRPA,
  title = {The Rockerverse: Packages and Applications for Containerisation with R},
  author = {Daniel N\{\"u\}st and Dirk Eddelbuettel and Dom Bennett and Robrecht Cannoodt and D. Clark and Gergely Dar\{\'o\}czi and Mark Edmondson and Colin Fay and Ellis Hughes and S. Lopp and B. Marwick and Heather Nolis and Jacqueline Nolis and Hong-Sain Ooi and Karthik Ram and Noam Ross and Lori A. Shepherd and Nitesh Turaga and C. Willis and Nan Xiao and Charlotte Van Petegem},
  year = {2020},
  journal = {R J.},
  url = {https://api.semanticscholar.org/CorpusId:210942882},
  volume = {12},
  pages = {437},
}

@article{ClyburneSherin2019ComputationalRVA,
  title = {Computational Reproducibility via Containers in Psychology},
  author = {April Clyburne-Sherin and Xu Fei and S. Green},
  year = {2019},
  journal = {Meta-Psychology},
  url = {https://pdfs.semanticscholar.org/e650/c2456467374ca930bb537b2d8f6aee9ef950.pdf},
}

@article{Barba2018PraxisORA,
  title = {Praxis of Reproducible Computational Science},
  author = {L. Barba},
  year = {2018},
  journal = {Computing in Science & Engineering},
  url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8661798},
  volume = {21},
  pages = {73-78},
}

@article{Smith2020_NeuralAnalysis,
  title = {Advanced Neural Signal Processing Techniques for Electrophysiology},
  author = {Smith, John and Doe, Jane},
  year = {2020},
  abstract = {A comprehensive review of modern signal processing methods for neural data analysis.},
  doi = {10.1016/j.jneumeth.2020.108123},
  journal = {Journal of Neuroscience Methods},
  pages = {108-123},
  volume = {345},
}

@article{Johnson2019_SpectralAnalysis,
  title = {Spectral Analysis Methods for Time-Series Neural Data},
  author = {Johnson, Michael and Williams, Sarah},
  year = {2019},
  doi = {10.1007/s10827-019-00712-4},
  journal = {Computational Neuroscience},
  number = {3},
  pages = {234-256},
  volume = {42},
}

@article{Chen2021_MachineLearning,
  title = {Machine Learning Approaches for Neural Data Classification},
  author = {Chen, Wei and Zhang, Li and Wang, Ming},
  year = {2021},
  doi = {10.1162/neco_a_01378},
  journal = {Neural Computation},
  number = {5},
  pages = {1234-1267},
  volume = {33},
}

@inproceedings{Brown2018_DeepLearning,
  title = {Deep Learning for Neural Signal Decoding},
  author = {Brown, Robert and Taylor, Emily},
  year = {2018},
  booktitle = {Advances in Neural Information Processing Systems},
  pages = {5678-5689},
  publisher = {NeurIPS},
}

@article{YourName2023_NovelMethod_duplicate,
  title = {A Novel Method for Neural Data Analysis},
  author = {Your-Name, First and Collaborator, Second and Your-Name, F. and Collaborator, S.},
  year = {2023},
  abstract = {We present a novel computational method for analyzing neural time-series data.},
  doi = {10.1038/s41598-023-12345-6},
  journal = {Scientific Reports},
  note = {This is a duplicate entry to demonstrate deduplication by DOI},
  pages = {12345},
  volume = {13},
}

@article{YourName2022_PreviousWork,
  title = {Foundations of Neural Signal Processing},
  author = {Your-Name, First and Advisor, Principal},
  year = {2022},
  doi = {10.1152/jn.00123.2022},
  journal = {Journal of Neurophysiology},
  number = {4},
  pages = {1567-1589},
  volume = {128},
}

@inproceedings{YourName2021_Conference,
  title = {Machine Learning Approaches for Brain Signal Classification},
  author = {Your-Name, First and Team, Member},
  year = {2021},
  booktitle = {International Conference on Machine Learning},
  organization = {ICML},
  pages = {7890-7901},
}


% ============================================================
% Source: methods_refs.bib
% Entries: 4
% ============================================================

@article{Smith2020_NeuralAnalysis,
  title = {Advanced Neural Signal Processing Techniques for Electrophysiology},
  author = {Smith, John and Doe, Jane},
  year = {2020},
  abstract = {A comprehensive review of modern signal processing methods for neural data analysis.},
  doi = {10.1016/j.jneumeth.2020.108123},
  journal = {Journal of Neuroscience Methods},
  pages = {108-123},
  volume = {345},
}

@article{Johnson2019_SpectralAnalysis,
  title = {Spectral Analysis Methods for Time-Series Neural Data},
  author = {Johnson, Michael and Williams, Sarah},
  year = {2019},
  doi = {10.1007/s10827-019-00712-4},
  journal = {Computational Neuroscience},
  number = {3},
  pages = {234-256},
  volume = {42},
}

@article{Chen2021_MachineLearning,
  title = {Machine Learning Approaches for Neural Data Classification},
  author = {Chen, Wei and Zhang, Li and Wang, Ming},
  year = {2021},
  doi = {10.1162/neco_a_01378},
  journal = {Neural Computation},
  number = {5},
  pages = {1234-1267},
  volume = {33},
}

@inproceedings{Brown2018_DeepLearning,
  title = {Deep Learning for Neural Signal Decoding},
  author = {Brown, Robert and Taylor, Emily},
  year = {2018},
  booktitle = {Advances in Neural Information Processing Systems},
  pages = {5678-5689},
  publisher = {NeurIPS},
}


% ============================================================
% Source: my_papers.bib
% Entries: 4
% ============================================================

@article{YourName2023_NovelMethod_duplicate,
  title = {A Novel Method for Neural Data Analysis},
  author = {Your-Name, First and Collaborator, Second and Your-Name, F. and Collaborator, S.},
  year = {2023},
  abstract = {We present a novel computational method for analyzing neural time-series data.},
  doi = {10.1038/s41598-023-12345-6},
  journal = {Scientific Reports},
  note = {This is a duplicate entry to demonstrate deduplication by DOI},
  pages = {12345},
  volume = {13},
}

@article{YourName2022_PreviousWork,
  title = {Foundations of Neural Signal Processing},
  author = {Your-Name, First and Advisor, Principal},
  year = {2022},
  doi = {10.1152/jn.00123.2022},
  journal = {Journal of Neurophysiology},
  number = {4},
  pages = {1567-1589},
  volume = {128},
}

@inproceedings{YourName2021_Conference,
  title = {Machine Learning Approaches for Brain Signal Classification},
  author = {Your-Name, First and Team, Member},
  year = {2021},
  booktitle = {International Conference on Machine Learning},
  organization = {ICML},
  pages = {7890-7901},
}
