Merge pull request #934 from MooersLab/2024

Paper: Voice Computing with Python in Jupyter Notebooks fro publication

papers/blaine_mooers/mybib.bib

@@ -0,0 +1,332 @@
+# Feel free to delete these first few references, which are specific to the template:
+
+# Jupyter related
+
+@Article{Basu2017ReproducibleResearchWithJupyterNotebooks,
+  author    = {Basu, Arindam},
+  title     = {Reproducible research with jupyter notebooks},
+  doi       = {10.22541/au.151460905.57485984},
+  url       = {https://www.authorea.com/doi/full/10.22541/au.151460905.57485984},
+  journal   = {Authorea Preprints},
+  keywords  = {Jupyter, literate programming},
+  publisher = {Authorea},
+  year      = {2017},
+}
+
+@Article{Dedehayir2016TheHypeCycleModelAReviewAndFutureDirections,
+  author    = {Dedehayir, Ozgur and Steinert, Martin},
+  title     = {The hype cycle model: A review and future directions},
+  pages     = {28--41},
+  volume    = {108},
+  file      = {:Dedehayir2016TheHypeCycleModelAReviewAndFutureDirections.pdf:PDF},
+  journal   = {Technological Forecasting and Social Change},
+  keywords  = {Gartner hype cycle},
+  publisher = {Elsevier},
+  year      = {2016},
+  doi = {http://dx.doi.org/10.1016/j.techfore.2016.04.005},
+}
+
+
+@misc{Dictanote2024VoiceIn,
+  Author = {{Dictanote Inc.}},
+  title = {Voice In Plus},
+  url = {https://support.dictanote.co/},
+  note = {version 4.10},
+  year = {2024},
+  month ={Aug},
+}
+
+
+@Article{Mooers2021TemplatesForWritingPyMOLScripts,
+	author = {Mooers, Blaine HM and Brown, Marina E},
+	journal = {Protein Science},
+	title = {Templates for writing PyMOL scripts},
+	year = {2021},
+	number = {1},
+	pages = {262--269},
+	volume = {30},
+	annote = {I need to add some text.},
+	doi = {10.1002/pro.3997},
+	publisher = {Wiley Online Library},
+	related = {Mooers2016SimplifyingAndEnhancingTheUseOfPyMOLWithHorizontalScripts,Mooers2020ShortcutsForFasterImageCreationInPyMOL},
+	url = {https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3997}
+}
+
+
+@Article{Mooers2021APyMOLSnippetLibraryForJupyterToBoostResearcherProductivity,
+  author    = {Mooers, Blaine HM},
+  title     = {A PyMOL snippet library for Jupyter to boost researcher productivity},
+  doi       = {10.1109/MCSE.2021.3059536},
+  number    = {2},
+  pages     = {47-53},
+  volume    = {23},
+  annote    = {Introduces the jupyterlabpymolpysnips library. I gave a talk at JupyterCon 2020 about this topic. I was then invited by Hans Fanghor to submit a paper about it. The organizer of the meeting of Lorena Barba. She was also editor in chief of this journal.},
+  file      = {:Mooers2021APyMOLSnippetLibraryForJupyterToBoostResearcherProductivity.pdf:PDF},
+  journal   = {Computing in Science \& Engineering},
+  keywords  = {Jupyter, literate programming},
+  publisher = {IEEE},
+  related   = {Mooers2021},
+  year      = {2021},
+}
+
+@InProceedings{Mooers2023BiomolecularCrystallographicComputingWithJupyter,
+  author    = {{B}laine {H}. {M}. {M}ooers},
+  booktitle = {{P}roceedings of the 22nd {P}ython in {S}cience {C}onference},
+  title     = {{B}iomolecular {C}rystallographic {C}omputing with {J}upyter},
+  doi       = {10.25080/gerudo-f2bc6f59-004},
+  editor    = {{M}eghann {A}garwal and {C}hris {C}alloway and {D}illon {N}iederhut},
+  pages     = {32 - 39},
+  publisher = {Oxford University Press},
+  file      = {:Mooers2023BiomolecularCrystallographicComputingWithJupyter.pdf:PDF},
+  keywords  = {Jupyter, literate programming},
+  year      = {2023},
+}
+
+
+@Article{Perez2015ProjectJupyterComputationalNarrativesAsTheEngineOfCollaborativeDataScience,
+  author    = {Fernando Perez and Brian E. Granger and Perez, Fernando and Granger, Brian E},
+  title     = {Project Jupyter: Computational narratives as the engine of collaborative data science},
+  number    = {207},
+  pages     = {108},
+  volume    = {11},
+  annote    = {I need to read this.},
+  journal   = {Retrieved September},
+  keywords  = {Jupyter, literate programming},
+  publisher = {Oxford University Press},
+  year      = {2015},
+}
+
+
+@Article{Perkel2021TenComputerCodesThatTransformedScience,
+  author    = {Perkel, Jeffrey M},
+  title     = {Ten computer codes that transformed science.},
+  doi       = {10.1038/d41586-021-00075-2},
+  number    = {7842},
+  pages     = {344--349},
+  volume    = {589},
+  annote    = {A survery of sceintists, the nature editors found that Jupyter ranked number three of 10 computer codes that had the biggest impact on their work. I learned about this article in a talk by Fernando Perez at JupyterCon 2023.},
+  file      = {:Perkel2021TenComputerCodesThatTransformedScience.pdf:PDF},
+  journal   = {Nature},
+  keywords  = {Jupyter notebook, IPython notebook, transformative computer codes, Jupyter, literate programming},
+  publisher = {Nature Publishing Group},
+  year      = {2021},
+}
+
+
+@Article{Perez2018SimulationsMeetMachineLearningInStructuralBiology,
+	author = {P{\'e}rez, Adri{\`a} and Mart{\'\i}nez-Rosell, Gerard and De Fabritiis, Gianni},
+	title = {Simulations meet machine learning in structural biology},
+	journal = {Current opinion in structural biology},
+	year = {2018},
+	volume = {49},
+	pages = {139--144},
+	publisher = {Elsevier}
+}
+
+
+@Article{Randles2017UsingTheJupyterNotebookAsAToolForOpenScienceAnEmpiricalStudy,
+  author    = {Bernadette M. Randles and Irene V. Pasquetto and Milena S. Golshan and C. Borgman},
+  title     = {Using the Jupyter Notebook as a Tool for Open Science: An Empirical Study},
+  doi       = {10.1109/jcdl.2017.7991618},
+  pages     = {1-2},
+  file      = {:Randles2017UsingTheJupyterNotebookAsAToolForOpenScienceAnEmpiricalStudy.pdf:PDF},
+  journal   = {2017 ACM/IEEE Joint Conference on Digital Libraries (JCDL)},
+  keywords  = {Jupyter, literate programming},
+  publisher = {Oxford University Press},
+  year      = {2017},
+}
+
+
+
+@Book{Reitz2016TheHitchhikersGuideToPythonBestPracticesForDevelopment,
+  author    = {Reitz, Kenneth and Schlusser, Tanya},
+  title     = {The Hitchhiker's guide to Python: best practices for development},
+  publisher = {" O'Reilly Media, Inc."},
+  annote    = {This is the nuts-and-bolts of software engineering a Python project. It even has a chapter on Jupyter Notebooks.},
+  keywords  = {Jupyter, literate programming},
+  year      = {2016},
+}
+
+
+@Article{Smith2016TeachingComputerScienceToBiologistsAndChemistsUsingJupyterNotebooksTutorialPresentation,
+  author     = {Smith, Adam A.},
+  title      = {Teaching Computer Science to Biologists and Chemists, Using Jupyter Notebooks: Tutorial Presentation},
+  doi        = {10.5555/3007225.3007252},
+  issn       = {1937-4771},
+  number     = {1},
+  pages      = {126–128},
+  volume     = {32},
+  abstract   = {In this tutorial we will discuss teaching basic computer science skills to natural science majors (primarily biologists and chemists). I have spent the last year developing such a course at the University of Puget Sound. CSCI 141: Programming for Natural Scientists is a reformulation of a more typical Introduction to Computer Science class, but aimed at natural scientists rather than computer science and math majors. Offering a class such as this has many benefits for a computer science department:},
+  address    = {Evansville, IN, USA},
+  issue_date = {October 2016},
+  journal    = {J. Comput. Sci. Coll.},
+  keywords   = {Jupyter, literate programming},
+  month      = oct,
+  numpages   = {3},
+  publisher  = {Consortium for Computing Sciences in Colleges},
+  year       = {2016},
+}
+
+
+@Book{Sweigart2015AutomateTheBoringStuffWithPythonPracticalProgrammingForTotalBeginners,
+	title = {Automate the boring stuff with Python: practical programming for total beginners},
+	publisher = {No Starch Press},
+	year = {2015},
+	author = {Sweigart, Al},
+	annote = {Chapters of this book are available on-line in html. The book is available in the Metro Library.}
+}
+
+
+@InProceedings{Thomas2017TowardInteractiveSupercomputingAtNERSCWithJupyter,
+  author       = {Thomas, Rollin and Canon, Shane and Cholia, Shreyas and Gerhardt, Lisa and Racah, Evan},
+  booktitle    = {Cray User Group (CUG) Conference Proceedings},
+  title        = {Toward interactive supercomputing at NERSC with Jupyter},
+  organization = {Cray User Group (CUG)},
+  publisher    = {Oxford University Press},
+  annote       = {I need to read this.},
+  keywords     = {Jupyter, literate programming},
+  year         = {2017},
+}
+
+@Book{Toomey2017JupyterForDataScienceExploratoryAnalysisStatisticalModelingMachineLearningAndDataVisualizationWithJupyter,
+  author    = {Toomey, Dan},
+  title     = {Jupyter for data science: Exploratory analysis, statistical modeling, machine learning, and data visualization with Jupyter},
+  publisher = {Packt Publishing Ltd},
+  keywords  = {Jupyter, literate programming},
+  year      = {2017},
+}
+
+
+# These references may be helpful:
+
+@inproceedings{jupyter,
+  abstract  = {It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.},
+  author    = {Kluyver, Thomas and Ragan-Kelley, Benjamin and Pérez, 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, Damián and Abdalla, Safia and Willing, Carol and {Jupyter development team}},
+  editor    = {Loizides, Fernando and Scmidt, Birgit},
+  location  = {Netherlands},
+  publisher = {IOS Press},
+  url       = {https://eprints.soton.ac.uk/403913/},
+  booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
+  year      = {2016},
+  pages     = {87--90},
+  title     = {Jupyter Notebooks - a publishing format for reproducible computational workflows},
+}
+
+@article{matplotlib,
+  abstract     = {Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.},
+  author       = {Hunter, J. D.},
+  publisher    = {IEEE COMPUTER SOC},
+  year         = {2007},
+	doi          = {https://doi.org/10.1109/MCSE.2007.55},
+  journal      = {Computing in Science \& Engineering},
+  number       = {3},
+  pages        = {90--95},
+  title        = {Matplotlib: A 2D graphics environment},
+  volume       = {9},
+}
+
+@article{numpy,
+  author       = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, Stéfan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and van Kerkwijk, Marten H. and Brett, Matthew and Haldane, Allan and del Río, Jaime Fernández and Wiebe, Mark and Peterson, Pearu and Gérard-Marchant, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
+  publisher    = {Springer Science and Business Media {LLC}},
+  doi          = {https://doi.org/10.1038/s41586-020-2649-2},
+  date         = {2020-09},
+  year         = {2020},
+  journal      = {Nature},
+  number       = {7825},
+  pages        = {357--362},
+  title        = {Array programming with {NumPy}},
+  volume       = {585},
+}
+
+@misc{pandas1,
+  author    = {{The Pandas Development Team}},
+  title     = {pandas-dev/pandas: Pandas},
+  month     = feb,
+  year      = {2020},
+  publisher = {Zenodo},
+  version   = {latest},
+  url       = {https://doi.org/10.5281/zenodo.3509134},
+}
+
+@inproceedings{pandas2,
+  author    = {Wes McKinney},
+  title     = {{D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython},
+  booktitle = {{P}roceedings of the 9th {P}ython in {S}cience {C}onference},
+  pages     = {56 - 61},
+  year      = {2010},
+  editor    = {{S}t\'efan van der {W}alt and {J}arrod {M}illman},
+	doi       = {https://doi.org/10.25080/Majora-92bf1922-00a},
+}
+
+@article{scipy,
+  author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
+            Haberland, Matt and Reddy, Tyler and Cournapeau, David and
+            Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
+            Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
+            Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
+            Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
+            Kern, Robert and Larson, Eric and Carey, C J and
+            Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
+            {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
+            Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
+            Harris, Charles R. and Archibald, Anne M. and
+            Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
+            {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
+  title   = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
+            Computing in Python}},
+  journal = {Nature Methods},
+  year    = {2020},
+  volume  = {17},
+  pages   = {261--272},
+  adsurl  = {https://rdcu.be/b08Wh},
+	doi     = {https://doi.org/10.1038/s41592-019-0686-2},
+}
+
+@article{seaborn,
+    doi = {10.21105/joss.03021},
+    url = {https://doi.org/10.21105/joss.03021},
+    year = {2021},
+    publisher = {The Open Journal},
+    volume = {6},
+    number = {60},
+    pages = {3021},
+    author = {Michael L. Waskom},
+    title = {seaborn: statistical data visualization},
+    journal = {Journal of Open Source Software}
+ }
+
+
+@article{sklearn1,
+  author       = {Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
+  year         = {2011},
+  journal      = {Journal of Machine Learning Research},
+  pages        = {2825--2830},
+  title        = {Scikit-learn: Machine Learning in {P}ython},
+  volume       = {12},
+}
+
+@inproceedings{sklearn2,
+  author    = {Buitinck, Lars and Louppe, Gilles and Blondel, Mathieu and Pedregosa, Fabian and Mueller, Andreas and Grisel, Olivier and Niculae, Vlad and Prettenhofer, Peter and Gramfort, Alexandre and Grobler, Jaques and Layton, Robert and VanderPlas, Jake and Joly, Arnaud and Holt, Brian and Varoquaux, Gaël},
+  booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
+  year      = {2013},
+  pages     = {108--122},
+  title     = {{API} design for machine learning software: experiences from the scikit-learn project},
+}
+
+
+@article{tabibian2019enhancinghumanlearningviaspacedrepetitionoptimization,
+  author =       {Behzad Tabibian and Utkarsh Upadhyay and Abir De and
+                  Ali Zarezade and Bernhard Sch{\"o}lkopf and Manuel
+                  Gomez-Rodriguez},
+  title =        {Enhancing human learning via spaced repetition
+                  optimization},
+  journal =      {Proceedings of the National Academy of Sciences},
+  volume =       116,
+  number =       10,
+  pages =        {3988-3993},
+  year =         2019,
+  doi =          {10.1073/pnas.1815156116},
+  url =          {http://dx.doi.org/10.1073/pnas.1815156116},
+  DATE_ADDED =   {Mon Aug 19 18:40:55 2024},
+}
+

papers/blaine_mooers/myst.yml

@@ -0,0 +1,49 @@
+# See docs at: https://mystmd.org/guide/frontmatter
+version: 1
+project:
+  id: scipy-2024-blaine_mooers
+  # id: 748163c7-a7d5-41f6-b9a0-337ab3b5f6d6
+  title: Voice Computing with Python in Jupyter Notebooks
+  # description:
+  keywords:     
+    - accessibility
+    - productivity
+    - human-computer interface
+  authors: 
+      - name: Blaine H. M. Mooers
+        roles: 
+            - Conceptualization
+            - Code development and testing
+            - Writing and editing
+            - Funding
+        email: [email protected]
+        orcid: 0000-0001-8181-8987
+        affiliations:
+            - Department of Biochemistry and Physiology, College of Medicine, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, USA
+            - Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, USA
+            - Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, USA
+        corresponding: true
+  github: https://github.com/mooerslab/scipy_proceedings
+  # bibliography: []
+  # title:
+  # options:
+  #   favicon: favicon.ico
+  #   logo: site_logo.png
+  error_rules:
+    - rule: doi-exists
+      severity: ignore
+      keys:
+        - markdown
+        - voice-triggered snippets
+        - human-computer interface
+        - speech-to-text
+        - software engineering
+  # A banner will be generated for you on publication, this is a placeholder
+  banner: banner.png
+  subject: Research Article
+  open_access: true
+  license: CC-BY-4.0
+  venue: Scipy 2024
+  date: 2024-07-10
+site:
+  template: article-theme