Add markdown paper version

Author: agoscinski

paper/paper.bib

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+@incollection{notebooks-in-chemistry,
+    author = {Grace Yin Stokes},
+    title = {How Faculty with Minimal Programming Experience Implemented Jupyter Notebooks in Physical and General Chemistry Courses},
+    booktitle = {Teaching Programming across the Chemistry Curriculum},
+    publisher = {American Chemical Society},
+    year = {2021},
+    chapter = {2},
+    pages = {13--27},
+    doi = {10.1021/bk-2021-1387.ch002}
+}
+
+
+
+@incollection{notebooks-in-physics,
+	author = {Hu, Danfei and Ahn, Janet N. and Lakatos, Alyssa and Bello, Jose and McTague, Jonathan and Foley, Jonathan J. IV},
+	chapter = {7},
+	month = {2025/07/02},
+	number = {0},
+	pages = {89-105},
+	publisher = {American Chemical Society},
+	series = {ACS Symposium Series},
+	title = {Integrating Programming to Reinforce Quantum Mechanical Principles in Physical Chemistry},
+	doi = {10.1021/bk-2021-1387.ch007},
+	volume = {1387},
+	year = {2021}}
+
+
+@article{notebooks-in-mathematics,
+    author = {Sümmermann, M. L. and Sommerhoff, D. and Rott, B.},
+    title = {Mathematics in the digital age: The case of simulation-based proofs},
+    journal = {International Journal of Research in Undergraduate Mathematics Education},
+    volume = {7},
+    number = {3},
+    year = {2021},
+    pages = {438--465},
+    doi = {10.1007/s40753-020-00125-6}
+}
+
+@article{vrl-survey,
+    author = {Ruben Heradio and Luis de la Torre and Sebastian Dormido},
+    title = {Virtual and Remote Labs in Control Education: A Survey},
+    journal = {Computers \& Education},
+    volume = {98},
+    year = {2016},
+    pages = {14--38},
+    doi = {10.1016/j.arcontrol.2016.08.001}
+}
+
+@incollection{jupyter,
+  title = {Jupyter Notebooks -- a publishing format for reproducible computational workflows},
+  url = {http://dx.doi.org/10.3233/978-1-61499-649-1-87},
+  DOI = {10.3233/978-1-61499-649-1-87},
+  booktitle = {Positioning and Power in Academic Publishing: Players,  Agents and Agendas},
+  publisher = {IOS Press},
+  pages = {87--90},
+  author = {Kluyver Thomas and Ragan-Kelley Benjamin and P\'erez Fernando and Granger Brian and Bussonnier Matthias and Frederic Jonathan and Kelley Kyle and Hamrick Jessica and Grout Jason and Corlay Sylvain and Ivanov Paul and Avila Dami\'an and Abdalla Safia and Willing Carol and Jupyter Development Team},
+  year = {2016}
+}
+
+@article{jupyter-narrative,
+  title = {Jupyter: Thinking and Storytelling With Code and Data},
+  volume = {23},
+  ISSN = {1558-366X},
+  url = {http://dx.doi.org/10.1109/MCSE.2021.3059263},
+  DOI = {10.1109/mcse.2021.3059263},
+  number = {2},
+  journal = {Computing in Science \& Engineering},
+  publisher = {Institute of Electrical and Electronics Engineers (IEEE)},
+  author = {Granger,  Brian E. and Perez,  Fernando},
+  year = {2021},
+  month = mar,
+  pages = {7–14}
+}
+
+@article{sutchenkov2020active,
+  title = {Active investigation and publishing of calculation web based applications for studying process},
+  volume = {1691},
+  ISSN = {1742-6596},
+  url = {http://dx.doi.org/10.1088/1742-6596/1691/1/012096},
+  DOI = {10.1088/1742-6596/1691/1/012096},
+  number = {1},
+  journal = {Journal of Physics: Conference Series},
+  publisher = {IOP Publishing},
+  author = {Sutchenkov,  A A and Tikhonov,  A I},
+  year = {2020},
+  month = nov,
+  pages = {012096}
+}
+
+
+@article{du2023osscar,
+	author = {Dou Du and Taylor J. Baird and Sara Bonella and Giovanni Pizzi},
+	journal = {Computer Physics Communications},
+	pages = {108546},
+	title = {{OSSCAR}, an open platform for collaborative development of computational tools for education in science},
+	volume = {282},
+	year = {2023}}
+
+
+@article{du2024widget,
+	author = {Dou Du and Taylor J. Baird and Kristjan Eimre and Sara Bonella and Giovanni Pizzi},
+	journal = {Computer Physics Communications},
+	pages = {109353},
+	title = {Jupyter widgets and extensions for education and research in computational physics and chemistry},
+	volume = {305},
+	year = {2024}}
+
+
+
+@misc{appmode,
+    author = {{Ole Schuett}},
+    title = {Appmode: A Jupyter extension that turns notebooks into web applications},
+    howpublished = {{G}itHub repository: \url{https://github.com/oschuett/appmode}},
+    note = {Accessed 1 July 2025}
+}
+
+@misc{traitlets,
+    author = {{IPython Development Team}},
+    title = {Traitlets: Lightweight eventful properties for Python},
+    howpublished = {{G}itHub repository: \url{https://github.com/ipython/traitlets}},
+    note = {Accessed 1 July 2025}
+}
+
+@article{aiidalab,
+  title = {AiiDAlab – an ecosystem for developing,  executing,  and sharing scientific workflows},
+  volume = {188},
+  ISSN = {0927-0256},
+  url = {http://dx.doi.org/10.1016/j.commatsci.2020.110165},
+  DOI = {10.1016/j.commatsci.2020.110165},
+  journal = {Computational Materials Science},
+  publisher = {Elsevier BV},
+  author = {Yakutovich,  Aliaksandr V. and Eimre,  Kristjan and Sch\"{u}tt,  Ole and Talirz,  Leopold and Adorf,  Carl S. and Andersen,  Casper W. and Ditler,  Edward and Du,  Dou and Passerone,  Daniele and Smit,  Berend and Marzari,  Nicola and Pizzi,  Giovanni and Pignedoli,  Carlo A.},
+  year = {2021},
+  month = feb,
+  pages = {110165}
+}
+
+@misc{supplementary-code,
+    author = {Goscinski, Alexander and
+Baird, Taylor James and
+Du, Dou and
+Prado, João and
+Suman, Divya and
+Sodjargal, Tulga-Erdene and
+Bonella, Sara and
+Pizzi, Giovanni and
+Ceriotti, Michele},
+    title = {scicode-widgets: Supplementary code for figures},
+    journal = {Zenodo},
+    howpublished = {\url{https://doi.org/10.5281/zenodo.15783260}}
+}
+
+@misc{iam-notebooks,
+title={Introduction to Atomistic Modeling, Course Notebooks},
+howpublished = {{G}itHub repository: 
+{\url{https://github.com/ceriottm/iam-notebooks}}},
+note = {Accessed 4 July 2025}
+}
+
+
+@inproceedings{urcelay-olabarria_jupyter_2017,
+	location = {Porto, Portugal},
+	title = {Jupyter Notebook as the Physics Experimental Laboratory's Logbook - First Approach:},
+	isbn = {978-989-758-239-4 978-989-758-240-0},
+	url = {http://www.scitepress.org/DigitalLibrary/Link.aspx?doi=10.5220/0006352104580463},
+	doi = {10.5220/0006352104580463},
+	shorttitle = {Jupyter Notebook as the Physics Experimental Laboratory's Logbook - First Approach},
+	eventtitle = {9th International Conference on Computer Supported Education},
+	pages = {458--463},
+	booktitle = {Proceedings of the 9th International Conference on Computer Supported Education},
+	publisher = {{SCITEPRESS} - Science and Technology Publications},
+	author = {Urcelay-Olabarria, Irene and Lazkoz, Ruth and Urrestilla, Jon and Leonardo, Aritz and Igartua, Josu M.},
+	urldate = {2025-07-04},
+	date = {2017},
+}
+
+@article{tufino_using_2025,
+	title = {Using Jupyter Notebooks to foster computational skills and professional practice in an introductory physics lab course},
+	volume = {2950},
+	issn = {1742-6588, 1742-6596},
+	url = {https://iopscience.iop.org/article/10.1088/1742-6596/2950/1/012022},
+	doi = {10.1088/1742-6596/2950/1/012022},
+	pages = {012022},
+	number = {1},
+	journaltitle = {Journal of Physics: Conference Series},
+	journal = {Journal of Physics: Conference Series},
+	shortjournal = {J. Phys.: Conf. Ser.},
+	author = {Tufino, Eugenio and Oss, Stefano and Alemani, Micol},
+	urldate = {2025-07-04},
+	date = {2025-02-01},
+}
+@book{bishop,
+    author = {Bishop, Christopher M.},
+    title = {Pattern Recognition and Machine Learning (Information Science and Statistics)},
+    pages = {144-146},
+    year = {2006},
+    isbn = {0387310738},
+    publisher = {Springer-Verlag},
+    address = {Berlin, Heidelberg},
+    DOI = {10.5555/1162264}
+}
+
+@misc{selenium,
+  author       = {{Selenium Development Team}},
+  title        = {Selenium Browser Automation Project},
+  howpublished = {\url{https://www.selenium.dev}},
+  note = {Accessed 4 July 2025}
+}
+
+@misc{jupyterlab,
+  author       = {{Jupyter Development Team}},
+  title        = {JupyterLab computational environment},
+  howpublished = {{G}itHub repository: \url{https://github.com/jupyterlab/jupyterlab}},
+  note         = {Accessed 4 July 2025},
+}