Update JOSS Paper (#705)

* chore: Add missing DOIs * chore: Remove abstract * Add Acknowledgements section * chore: Update jscatter ref * Add Funding * Add additional related work * Update statement of need * Update manuscript * Use hrefs
manzt · Oct 22, 2024 · 059084b · 059084b
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diff --git a/paper/export-pdf.ts b/paper/export-pdf.ts
@@ -31,6 +31,16 @@ data["margin"] = [
 		content: "Correspondence: [author-email]",
 	},
 ];
+data["abstract"] = `\
+The anywidget project provides a specification and toolset for creating
+portable web-based widgets for computational notebooks. It defines a standard
+for front-end widget code using ECMAScript modules and offers tools for
+authoring, distributing, and executing these modules across Jupyter-compatible
+platforms (e.g., JupyterLab, Google Colab, VS Code). The project has spurred
+the creation of many interactive visualization libraries and has been
+integrated into existing ones. The standard has been embraced by other
+notebook platforms and web frameworks, extending the reach of interactive
+widgets beyond the Jupyter ecosystem.`.trim();
 
 let markdown = raw
 	// Replace markdown images with myst images

diff --git a/paper/paper.bib b/paper/paper.bib
@@ -10,8 +10,7 @@ @software{JupyterBook
 }
 
 @misc{JupyterBookMyst,
-  author       = {Holdgraf, Chris and
-                  The Executable Books Community},
+  author       = {Holdgraf, Chris and others},
   title        = {{Jupyter Book and MyST: A community-led, 
                    extensible, modular ecosystem for creating
                    computational narratives}},
@@ -56,7 +55,8 @@ @ARTICLE{EDAssistant
   year      =  2023,
   address   = "New York, NY, USA",
   keywords  = "computational notebooks, code search, software visualization,
-               Exploratory data analysis"
+               Exploratory data analysis",
+  doi={10.1145/3545995}
 }
 
 % The entry below contains non-ASCII chars that could not be converted
@@ -108,7 +108,8 @@ @ARTICLE{Zhao2022
   month     =  sep,
   year      =  2022,
   copyright = "http://creativecommons.org/licenses/by-nc/4.0/",
-  language  = "en"
+  language  = "en",
+  doi={10.1002/spe.3098}
 }
 
 @INPROCEEDINGS{Wang2023,
@@ -146,8 +147,7 @@ @INPROCEEDINGS{Wang2023
   address   = "New York, NY, USA",
   keywords  = "computational notebooks, data science., human-AI collaboration,
                natural language processing, slides generation",
-  location  = "<conf-loc>, <city>Hamburg</city>, <country>Germany</country>,
-               </conf-loc>"
+  doi={10.1145/3544548.3580753}
 }
 
 @INPROCEEDINGS{Drosos2020,
@@ -182,8 +182,7 @@ @INPROCEEDINGS{Drosos2020
   year      =  2020,
   address   = "New York, NY, USA",
   keywords  = "computational notebooks, data science, program synthesis",
-  location  = "<conf-loc>, <city>Honolulu</city>, <state>HI</state>,
-               <country>USA</country>, </conf-loc>"
+  doi={10.1145/3313831.3376442}
 }
 
 @INPROCEEDINGS{Li2023,
@@ -218,8 +217,7 @@ @INPROCEEDINGS{Li2023
   year      =  2023,
   address   = "New York, NY, USA",
   keywords  = "computational notebooks, data storytelling, data visualization",
-  location  = "<conf-loc>, <city>Hamburg</city>, <country>Germany</country>,
-               </conf-loc>"
+  doi={10.1145/3544548.3580965}
 }
 
 @INPROCEEDINGS{Jain2022,
@@ -256,7 +254,8 @@ @INPROCEEDINGS{Jain2022
   month     =  jul,
   year      =  2022,
   address   = "New York, NY, USA",
-  location  = "Pittsburgh, Pennsylvania"
+  location  = "Pittsburgh, Pennsylvania",
+  doi={10.1145/3510003.3510203}
 }
 
 @ARTICLE{Wang2022,
@@ -287,7 +286,8 @@ @ARTICLE{Wang2022
   year          =  2022,
   archivePrefix = "arXiv",
   primaryClass  = "cs.HC",
-  eprint        = "2205.03963"
+  eprint        = "2205.03963",
+  doi={10.48550/arXiv.2205.03963}
 }
 
 @INPROCEEDINGS{Wang2024,
@@ -325,8 +325,7 @@ @INPROCEEDINGS{Wang2024
   address   = "New York, NY, USA",
   keywords  = "Computational Notebook, Cross-Platform Visualization, Data
                Science, Design, Interactive Visualization, Systematic Review",
-  location  = "<conf-loc> <city>Honolulu</city> <state>HI</state>
-               <country>USA</country> </conf-loc>"
+  doi={10.1145/3613905.3650848}
 }
 
 @INPROCEEDINGS{Kluyver2016,
@@ -352,7 +351,8 @@ @INPROCEEDINGS{Kluyver2016
   year       =  2016,
   language   = "en",
   conference = "20th International Conference on Electronic Publishing
-                (01/01/16)"
+                (01/01/16)",
+  doi={10.3233/978-1-61499-649-1-87}
 }
 
 @ARTICLE{Perez2007,
@@ -369,7 +369,8 @@ @ARTICLE{Perez2007
   volume    =  9,
   number    =  3,
   pages     = "21--29",
-  year      =  2007
+  year      =  2007,
+  doi={10.1109/MCSE.2007.53}
 }
 
 @ARTICLE{Granger2021,
@@ -391,7 +392,8 @@ @ARTICLE{Granger2021
   volume    =  23,
   number    =  2,
   pages     = "7--14",
-  year      =  2021
+  year      =  2021,
+  doi={10.22541/au.161298309.98344404/v3}
 }
 
 @ARTICLE{Heer2024,
@@ -423,7 +425,8 @@ @ARTICLE{Heer2024
   pages    = "436--446",
   month    =  jan,
   year     =  2024,
-  language = "en"
+  language = "en",
+  doi={10.1109/TVCG.2023.3327189}
 }
 
 @ARTICLE{Ouyang2019,
@@ -437,7 +440,8 @@ @ARTICLE{Ouyang2019
   pages    = "1199--1200",
   month    =  dec,
   year     =  2019,
-  language = "en"
+  language = "en",
+  doi={10.1038/s41592-019-0627-0}
 }
 
 @misc{voila,
@@ -456,12 +460,17 @@ @misc{nbconvert
   note = {Accessed: 2024-06-05}
 }
 
-@misc{jscatter,
-  author = {Fritz Lekschas},
-  title = {Jupyter Scatter},
+@article{jscatter,
+  title = {{Jupyter Scatter}: Interactive Exploration of Large-Scale Datasets},
+  author = {Fritz Lekschas and Trevor Manz},
+  journal = {Journal of Open Source Software},
+  publisher = {The Open Journal},
   year = {2024},
-  url = {https://github.com/flekschas/jupyter-scatter},
-  note = {Accessed: 2024-06-05}
+  volume = {9},
+  number = {101},
+  pages = {7059},
+  doi = {10.21105/joss.07059},
+  url = {https://doi.org/10.21105/joss.07059},
 }
 
 @ARTICLE{gos,
@@ -485,7 +494,8 @@ @ARTICLE{gos
   number   =  1,
   month    =  jan,
   year     =  2023,
-  language = "en"
+  language = "en",
+  doi={10.1093/bioinformatics/btad050}
 }
 
 
@@ -508,7 +518,8 @@ @UNPUBLISHED{vitessce
   month    =  oct,
   year     =  2021,
   keywords = "bioimaging; bioinformatics; data visualization; single-cell;
-              spatial omics; visualization"
+              spatial omics; visualization",
+  doi={10.31219/osf.io/y8thv}
 }
 
 @ARTICLE{viv,
@@ -523,7 +534,8 @@ @ARTICLE{viv
   pages    = "515--516",
   month    =  may,
   year     =  2022,
-  language = "en"
+  language = "en",
+  doi={10.1038/s41592-022-01482-7}
 }
 
 @misc{lonboard,
@@ -574,7 +586,8 @@ @ARTICLE{altair
   pages     = "1057",
   month     =  dec,
   year      =  2018,
-  copyright = "http://creativecommons.org/licenses/by/4.0/"
+  copyright = "http://creativecommons.org/licenses/by/4.0/",
+  doi={10.21105/joss.01057}
 }
 
 @misc{scipy,
@@ -661,3 +674,20 @@ @misc{ecma
   section={16.2},
   notes="Accessed 2024-06-07"
 }
+
+@misc{bokeh,
+  title = {Bokeh: Python library for interactive visualization},
+  author = {{Bokeh Development Team}},
+  year = {2018},
+  url = {https://bokeh.pydata.org/en/latest/},
+  note = {Accessed: 2024-09-23}
+}
+
+@misc{streamlit,
+  title = {Create a Component},
+  author = {{Streamlit}},
+  year = {2024},
+  url = {https://docs.streamlit.io/develop/concepts/custom-components/create},
+  note = {Accessed: 2024-09-23},
+  organization = {Snowflake Inc.}
+}